Uses Of Primary Data_typeset Gibf Data Training Manual En V1

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Arthur D. Chapman1
Abstract:
This paper examines uses for primary species-
occurrence data in research, education and in
other areas of human endeavour, and provides
examples from the literature of many of these
uses. The paper examines not only data from
labels, or from observational notes, but the data
inherent in museum and herbarium collections
themselves, which are long-term storage
receptacles of information and data that are still
largely untouched. Projects include the study of
the species and their distributions through both
time and space, their use for education, both
formal and public, for conservation and scientific
research, use in medicine and forensic studies, in
natural resource management and climate change,
in art, history and recreation, and for social and
political use. Uses are many and varied and may
well form the basis of much of what we do as
people every day.
1 Australian Biodiversity Information Services
PO Box 7491, Toowoomba South, Qld, Australia
email: papers.digit@gbif.org
USES OF PRIMARY
SPECIES-
OCCURRENCE
DATA
© 2005, Global Biodiversity Information Facility
Material in this publication is free to use, with proper attribution. Recommended citation format:
Chapman, A. D. 2005. Uses of Primary Species-Occurrence Data, version 1.0. Report for the
Global Biodiversity Information Facility, Copenhagen.
This paper was commissioned from Arthur Chapman in 2004 by the GBIF DIGIT programme to
highlight the importance of data quality as it relates to primary species occurrence data. Our
understanding of these issues and the tools available for facilitating error checking and cleaning is
rapidly evolving. As a result we see this paper as an interim discussion of the topics as they stood in
2004. Therefore, we expect there will be future versions of this document and would appreciate the
data provider and user communities’ input.
Comments and suggestions can be submitted to:
Larry Speers
Senior Programme Officer
Digitization of Natural History Collections
Global Biodiversity Information Facility
Universitetsparken 15
2100 Copenhagen Ø
Denmark
E-mail: lspeers@gbif.org
and
Arthur Chapman
Australian Biodiversity Information Services
PO Box 7491, Toowoomba South
Queensland 4352
Australia
E-mail: papers.gbif@achapman.org
July 2005
Cover image © Else Østergaard Andersen 2005
Dactylorhiza maculata (L.) Soo ssp. fuchsii (Druce) Hyl.
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Contents
Introduction................................................................................................................. 1
Data interchange and distributed data ...................................................................... 3
Multiple uses ............................................................................................................ 4
GBIF Demonstration Project 2003........................................................................... 4
Benefits of making species-occurrence data available............................................. 4
Taxonomy..................................................................................................................... 7
Taxonomic Research ................................................................................................ 7
Name and Taxonomic Indices.................................................................................. 7
Floras and Faunas..................................................................................................... 8
Taxonomy and Ecological Biogeography ................................................................ 9
Field Guides............................................................................................................ 10
Integrated electronic resources............................................................................... 11
Check lists and inventories..................................................................................... 12
Image Databases..................................................................................................... 12
Phylogenies............................................................................................................. 12
Parataxonomy......................................................................................................... 13
Automated Identification Tools.............................................................................. 13
Biogeographic Studies............................................................................................... 14
Distribution Atlases................................................................................................ 14
Species Distribution Modelling.............................................................................. 16
Predicting new species distributions ...................................................................... 18
Studying species decline......................................................................................... 18
Species Diversity and Populations ........................................................................... 19
Species Diversity, Richness and Density ............................................................... 19
Population Modelling — Population Viability Analysis........................................ 21
Species Inter-relations ............................................................................................ 22
Protecting Communities......................................................................................... 22
Life Histories and Phenologies................................................................................. 23
Life History Studies................................................................................................ 23
Phenology............................................................................................................... 23
Endangered, Migratory and Invasive Species........................................................ 24
Endangered Species................................................................................................ 24
Invasive species and translocation studies ............................................................. 25
Migratory Species................................................................................................... 28
Impact of Climate Change........................................................................................ 31
On Native Species .................................................................................................. 31
On Primary Production........................................................................................... 31
Desertification ........................................................................................................ 32
Ecology, Evolution and Genetics.............................................................................. 33
Vegetation Classification........................................................................................ 33
Mapping Vegetation............................................................................................... 33
Habitat loss............................................................................................................. 34
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Ecosystem function ................................................................................................ 34
Survey Design - Finding the Gaps.......................................................................... 35
Evolution, Extinction and Genetics........................................................................ 36
Microbial diversity and speciation ......................................................................... 37
Archaeological studies............................................................................................ 38
Environmental Regionalisation................................................................................ 39
National Planning studies....................................................................................... 39
Regional Planning Studies...................................................................................... 39
Marine Regionalisations......................................................................................... 40
Aquatic Regionalisations........................................................................................ 40
Conservation Planning.............................................................................................. 41
Rapid Biodiversity Assessment.............................................................................. 41
Identifying Biodiversity Priority Areas.................................................................. 41
Reserve Selection ................................................................................................... 42
Complementarity.................................................................................................... 42
Ex-situ Conservation .............................................................................................. 43
Sustainable Use ...................................................................................................... 44
Seed Banks and Germplasm Banks........................................................................ 44
Natural Resource Management ............................................................................... 45
Land Resources ...................................................................................................... 45
Water Resources..................................................................................................... 45
Environment Protection.......................................................................................... 45
Environmental Monitoring..................................................................................... 46
Agriculture, Forestry, Fisheries and Mining.......................................................... 47
Agriculture.............................................................................................................. 47
Forestry................................................................................................................... 50
Fishing.................................................................................................................... 51
Nursery and Pet Industry........................................................................................ 53
Mining .................................................................................................................... 54
Health and Public Safety .......................................................................................... 56
Diseases and disease vectors .................................................................................. 56
Bioterrorism............................................................................................................ 57
Biosafety................................................................................................................. 57
Environmental Contaminants ................................................................................. 57
Antivenoms............................................................................................................. 58
Parasitology............................................................................................................ 58
Safer Herbal Products............................................................................................. 59
Bioprospecting........................................................................................................... 60
Pharmaceuticals...................................................................................................... 60
Forensics..................................................................................................................... 61
Border Control and Wildlife Trade......................................................................... 64
Border Controls and Customs ................................................................................ 64
Quarantine .............................................................................................................. 65
Wildlife Trade ........................................................................................................ 65
Education and Public Outreach............................................................................... 66
School level education............................................................................................ 66
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University level education...................................................................................... 66
Training of Parataxonomists................................................................................... 67
Public awareness .................................................................................................... 67
Museum displays.................................................................................................... 68
Image Databases..................................................................................................... 68
Public Participation Programs................................................................................ 68
Tree of Life............................................................................................................. 69
Ecotourism................................................................................................................. 70
Valuing Ecotourism................................................................................................ 70
Training Guides and Operators .............................................................................. 70
Guide Books........................................................................................................... 70
Gardens, Zoos, Aquariums, Museums and Wildlife Parks .................................... 71
Art and History.......................................................................................................... 72
History of Science—Tracking Explorers and Collectors....................................... 72
Art and Science....................................................................................................... 72
Indigenous Art........................................................................................................ 73
Stamps .................................................................................................................... 73
Society and Politics.................................................................................................... 74
Social Uses of Biodiversity .................................................................................... 74
Anthropology and Language.................................................................................. 74
Ethnobiology .......................................................................................................... 75
Data Repatriation.................................................................................................... 75
Biodiversity collecting............................................................................................ 76
Recreational Activities.............................................................................................. 77
Recreational fishing................................................................................................ 77
Hunting................................................................................................................... 77
Photography and Film-making............................................................................... 77
Gardening ............................................................................................................... 78
Bushwalking, Hiking and Trekking ....................................................................... 78
Bird Observing ....................................................................................................... 78
Human Infrastructure Planning.............................................................................. 79
Risk Assessment..................................................................................................... 79
Landscaping............................................................................................................ 79
Wild Animals and Infrastructure............................................................................ 80
Building timbers..................................................................................................... 80
Aquatic and Marine Biodiversity............................................................................. 81
Conclusion.................................................................................................................. 82
Acknowledgements.................................................................................................... 83
References .................................................................................................................. 84
Index......................................................................................................................... 100
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Introduction
Plant and animal specimen data held in museums and herbaria, survey data and species
observational data provide a vast information resource, providing not only present day information
on the locations of these entities, but also historic information going back several hundred years
(Chapman and Busby 1994). It is estimated that there are approximately 2.5-3 billion collections
worldwide in museums, herbaria and other collection institutions (Duckworth et al. 1993, OECD
1999). In addition there are untold numbers of observational data records. Projects to digitise this
information are underway in many institutions, with others at either the discussion or planning
stage.
A key purpose of digital information in the biological sciences is to provide users of information
with a cost-effective method of querying and analysing that information. The biological world is
infinitely complex and must be generalised, approximated and abstracted in order to be represented
and understood (Goodchild et al. 1991). Ways of presenting biodiversity information to users is
through the use of geographic information systems, environmental modelling tools, decision
support systems, books, cds, images and on-line databases, specimens and their parts, DNA reports,
etc. Within these tools, however, it is essential that variation be sampled and measured, and error
and uncertainty be described and visualised. It is in this area that we still have a long way to go
(Goodchild et al. 1991).
The uses of primary species-occurrence data are wide and varied and encompase virtually every
aspect of human endeavour – food, shelter and recreation; art and history, society, science and
politics. The examples shown in this paper emphasizes the importance of having museum specimen
data digitized and made available to the wider user community. In this way, the collections will be
made even more valuable than they already are, and provide new opportunities for funding and
collaboration through their increased relevance and value to a much larger audience. With
dwindling resources being made available for the biological sciences, funding bodies are beginning
to ask the relevance of many natural history collections, and it is becoming increasingly more
difficult to obtain funds for collection maintenance. By making information available to the broader
scientific community for use in conservation and the many other areas of study covered in this
paper, institutions will have a much more robust and sustainable argument for continued funding. In
addition, it will rapidly add to the world’s knowledge of biodiversity and ecological systems and aid
in its future conservation and sustainable use and management.
The increased availability of data on species is opening up new and improved methods of dealing
with these issues. The information in museums is a storehouse going back hundreds of years, and
the new availability of that storehouse in on-line databases is improving science, reducing costs by
providing for more efficient and effective biological survey, freeing up scientists to spend more
time on research, and leading to a more rapid build-up of knowledge of our environments leading to
its improved conservation and sustainable use.
Taxonomic research is benefiting through the availability of images of specimens, including types,
data on the location of specimens in other museums, etc. But perhaps the greatest benefit of the
availability of distributed data is the study of the biogeography of species – their location in time
and space. “By reducing the costs of studying vectors of human disease, biological invasions, and
global climate change, biological collections provide direct financial and social benefits to society”
(Suarez and Tsutsui 2004).
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One of the things that will come out of a study of uses of species-occurrence data is the opening up
new requirements for recording information as part of future collecting events (Chapman 2005b).
This may even include a greater use of digital images (Basset et al. 2000), and video. But along
with all the positives of electronic data exchange, there is a tendency to divorce the data from the
objects, and it is important that those outside the museum community recognise that the objects
themselves remain important long-term repositories and sources of data that have yet be captured
and developed (Winker 2004). Ultimately, maintaining and developing the infrastructure of
biodiversity collections will produce unforeseen benefits (Suarez and Tsutsui 2004). Those benefits
to society will be multiplied through the ready availability of the information to those that need to
use them.
But primary species-occurrence data are not just the data held in museums and herbaria. There is a
massive amount of observational and survey data held in universities, by non-governmental
organisations and by private individuals and these data add valuable additional knowledge on our
environment. They are not competing data resources but complementary and each have their
strengths and weaknesses in supplying the information the world needs.
Some question the value of digitised museum specimen data for use in biogeographic and other
studies because much of the data are “outdated and unreliable”, with many records misidentified or
badly geo-referenced (Wheeler et al. 2004). That may be true for many records, but, as shown in
this paper, there are many other records that are not so unreliable, and that are being used by
researchers and others with great success. The museum community is aware of the problems
inherent in their data and are making concerted attempts to improve the quality of those data
(Chapman 2005a), and as stated by Edwards (2004), “one of the best ways to expose those errors is
to make the data visible, so that qualified researchers can compare and correct them”. All data have
errors, but that should not be a reason not to use the data, but to ensure that the error is documented
and that users are made aware of the errors so that they may determine the fitness for use of the data
(Chapman 2005b).
There are many uses for primary species data. Traditionally, collections in museums and herbaria
were only made with one main purpose in mind – that of taxonomic study. Their long-term mission,
however, is to document biodiversity and its distribution through time and space for research and
education (Winker 2004) and to serve the public. The introduction of computer processing and
computer databases have opened up this vast data store to many new uses (Chapman 1999). These
uses include biogeographic studies (Longmore 1986, Peterson et al. 1998), conservation planning
(Faith et al. 2001), reserve selection (Margules and Pressey 2000), development of environmental
regionalisations (Thackway and Cresswell 1995), climate change studies (Chapman and Milne
1998, Pouliquen and Newman 1999, Peterson et al. 2002a), agriculture, forestry and fishery
production (Booth 1996, Nicholls 1997, Cunningham et al. 2001), species translocation studies
(Panetta and Mitchell 1991, Soberón et al. 2000, Peterson and Veiglas 2001), etc., etc. These and
other uses will be elaborated further in this document. Many of these studies have used
environmental modelling using software such as BIOCLIM (Nix 1986, Busby 1991), GARP
(Stockwell and Peters 1999, Pereira 2002) or methods such as Generalised Linear Models (GLM)
(Austin 2002). Most of these species distribution models rely on specimen or observation records,
generally of a presence-only nature (usually including records from herbaria or museums as well as
observation data) or occasionally presence-absence data from systematic surveys.
Much of the data (both museum and observational) have been collected opportunistically rather
than systematically (Chapman 1999, Williams et al. 2002) and this can result in large spatial biases
– for example, collections that are highly correlated with road or river networks (Margules and
Redhead 1995, Chapman 1999, Peterson et al. 2002, Lampe and Riede 2002). Museum and
herbarium data and most observational data, generally only supply information on the presence of
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the entity at a particular time and says nothing about absences in any other place or time (Peterson
et al. 1998). This restricts their use in some environmental models, but they remain the largest and
most complete database of biological information over the last 200+ years we are ever likely to
have. The cost of replacing these data with new surveys would be prohibitive. It is not unusual for
a single survey to exceed $1 million to conduct (Burbidge 1991). Further, because of their
collection over time, they provide irreplaceable baseline data about biological diversity during a
time when humans have had tremendous impact on such diversity. They are an essential resource
in any effort to conserve the environment, as they provide the only fully documented record of the
occurrence of species in areas that may have undergone habitat change due to clearing for
agriculture, urbanization, climate change, or been modified in some other way (Chapman 1999).
But primary species data do not stop with just the information on the label, as there is information
contained within the collections themselves and this may be used for tissue sampling, chemical
analysis of contaminants, forensic information held in the DNA of individual specimens, etc. Living
culture collections of micro-organisms that cannot otherwise be preserved, images and even video
of individual birds and animals in the field, of preserved specimens in museums, or micrographs of
parts, and even drawn illustrations – some done before photography was invented – must also be
regarded as an integral part of the species-occurrence data record.
Data interchange and distributed data
As early as 1974, discussions on developing standards for electronic exchange of primary specimen
data between museums and herbaria were taking place. Although the Internet was restricted to
users in a limited research community and not generally available to biodiversity institutions
(Kristula 2001), and exchange via media such as floppy disks, and magnetic tape was occurring
around the world, no standards for doing so existed. As a result of these discussions, a standard for
the interchange of biotaxonomic information was developed in Australia in 1979 (Busby 1979).
Later, the Australian herbaria got together and extended this standard for use by botanical
institutions and the HISPID (Herbarium Information Standards for the Interchange of Data)
standard was developed (Croft 1989, Conn 1996, 2000). Although very few institutions used these
standards for interchange, many used them as a template for designing their databases. The HISPID
standard was later adopted as a TDWG (Taxonomic Databases Working Group) standard.
The development of the Internet, and especially the World Wide Web (Berners-Lee 1999), allowed
new opportunities for the interchange of data. Although the Environmental Resources Information
Network (ERIN) used distributed data for modelling on the Internet as early as 1994 (Boston and
Stockwell 1995), there were few other successful electronic data interchange projects that utilised
the internet until the Species Analyst (Vieglas 1999, 2003a) project began the late 1990s.
Since then, a number of distributed projects have begun, including the Red Mundial de Información
sobre Biodiversidad (REMIB) –The World Network on Biodiversity (CONABIO 2002), Australian
Virtual Herbarium (CHAH 2002), speciesLink (CRIA 2002), European Natural History Specimen
Information Network (ENHSIN) (Güntsch 2004), Biological Collection Access Service for Europe
(BioCASE 2003), the Mammal Networked Information System (MaNIS 2001), and the GBIF Portal
(GBIF 2004). These systems use on-line information retrieval to search databases maintained in the
home institutions, extracting data in a way similar to what Google does for web resources. Early
versions of these relied on the information retrieval standard developed primarily for library use –
Z39.50 (NISO 2002), but more recently the museums community have combined to develop new
standards, the Darwin Core Schema (Vieglais 2003b) along with the DiGIR protocol (SourceForge
2004) and the combined BioCASE protocol (BioCASE 2003) and ABCD (Access to Biological
Collections Data) schema (TDWG 2004) that are more fitted for interchange of primary species
information. More recently the Taxonomic Databases Working Group and others have begun
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working to develop a combined protocol (TAPIR - http://ww3.bgbm.org/tapir) treading a middle
path between the simplicity of DiGIR and the complexity of BioCASE.
Multiple uses
Most projects that use species-occurrence data incorporate more than just one type of use. As
evident from this paper, there is considerable overlap in uses within any one project. A project
might include mapped primary records, some taxonomic study (possibly involving the use of
character databases), environmental modelling and predictive distributional studies which may
involve endangered or migratory species, climate change impact studies as well as population
viability analysis and studies of species associations, ecology and evolutionary history. The project
may then involve species recovery studies and monitoring, as well as development of environment
protection legislation, reserve and conservation assessment, links to border and custom controls to
prevent illegal smuggling, and finally education and social links. It is sometimes difficult to identify
where one use stops and another begins, and I hope readers will excuse the inevitable overlap that is
evident throughout this paper.
The ability to search databases all around the world for spatially-referenced primary species-
occurrence data has opened up the information to a range of uses, many of which have previously
not been possible. This paper will elaborate on some of those uses and present examples. It should
be noted that it is beyond the scope of a paper such as this to cover every example of use –
examples given are just that – samples to illustrate the types of uses mentioned.
Some of this overlap in uses can be seen from the first GBIF Demonstration Project in 2003. (UTU-
Biota 2004).
GBIF Demonstration Project 2003
The first GBIF Demonstration Project (http://gbifdemo.utu.fi/) provided a number of user-friendly
examples of how primary biodiversity data can effectively be used, managed, exchanged and
disseminated via the Internet. It was prepared for GBIF by the University of Turku in association
with the Institute of Amazonian Research (IIAP). The project was divided into four sections or
“tours”. Tour 1 dealt with Neotropical species distributions, Tour 2 with multi-authored rainforest
trees inventories, Tour 3 with sub-arctic plant observations and Tour 4 on planning and
management of biodiversity.
In 2004, GBIF funded two more Demonstration projects (http://www.gbif.org). The first of these is
an Australian-based project to develop an internet-based tool for biogeographic analysis of
endemism and taxonomic distinctness. The second project is based in Mexico, and will demonstrate
the feasibility of estimating the rate of disappearance of species populations by estimating
distribution areas of species associated with primary vegetation on the basis of primary biodiversity
data. Both will use data extracted via the GBIF Portal.
Benefits of making species-occurrence data available
Many of the uses of species-occurrence data elaborated in this paper have required the user to visit
the collections institution – the museum or herbarium, etc. to seek access to the information, or to
obtain identifications. Staff of the musem then has to spend time and resources in identifying the
material for the user (which may be from hundreds to thousands a year for some collectors (Suarez
and Tsutsui 2004) or readying the data for the user. Huge resources are spent each year as scientists
travel to museums to use the collections, or as museums loan specimens to researchers. Between
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1976 and 1986, the Smithsonian's entomological collection loaned, on average, over 100,000
specimens each year (Miller 1991) and it, like most of the world’s larger museums, annually hosts
hundred of visiting researchers. Collections institutions are now beginning to realise that they can
save valuable time and resources by making available electronically as much of that data as is
possible. An example is with the Botanischer Garten und Botanisches Museum Berlin-Dahlem
where their herbarium loan system has been completely replaced with a digital loan system1
(http://ww2.bgbm.org/Herbarium/AccessLoanNew.cfm). Not only does it free up resources, more
often than not, those resources are the taxonomists and researchers that can then spend more time
on basic research and curation and less on administration and on helping others. The digitisation of
the hundreds of millions of collections held in natural history museums, however, is no small taksk
and will take many years, or even decades to complete.
The increased use of species data through distributed systems will provide a climate that will allow,
among others:
y Consolidation of collections infrastructure and holdings within museums, herbariums,
botanical gardens, zoological gardens, germplasm banks, etc.;
y A reassignment of resources toward increased research and curation;
y Improvements in the standardization, quality, maintenance and organization of important
biodiversity collections;
y Reduce physical handling of specimens, ensuring their longevity;
y Reduce costs of shipping, insurance, etc. of transferring loans and specimens between
institutions;
y The sharing of information between institutions and researchers, including with countries
of origin;
y A more rapid advancement of the biodiversity knowledge-base as researchers build on the
information in a more timely manner;
y Establishment of international biodiversity information networks between institutions
involved with biodiversity research, conservation, genetics, production, resource
management, tourism, etc.;
y Improvements in the management and availability of image, cartographic, genetic, and
other databases that will subsidize biodiversity research;
y Improvements in the management of conservation units as knowledge about biodiversity
becomes more readily available;
y Improved evaluation of the representativeness of existing conservation units and reserves,
and the identification of priority areas for the establishment of new ones;
y Development of projects to study problems that affect conservation, such as the effects and
consequences of habitat fragmentation and climate change on biodiversity;
y Improvements in border controls for managing and monitoring movements in endangered
species, pests and diseases as identification tools and knowledge about the distributions of
taxa are improved;
y Production and dissemination of checklists of all known biota of conservation areas,
regions, States, and countries, etc.;
y Increased and more efficient production of identification tools, keys, catalogues and
monographs (electronic and/or paper publications);
y More and improved inventories and studies for identifying biodiversity information gaps
(both taxonomic and geographic);
y Development of research projects that aim at understanding the temporal and spatial
distribution of biological diversity processes and functions;
1 Pers. comm.. Anton Güntsch, BGBM 2005.
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y Comparative and retrospective studies for estimating biodiversity loss within regions,
habitats, ecosystems, and across political and geographic boundaries;
y Comparative studies on environmental impact, such as climate change, urbanization,
agriculture, fisheries, etc. and establishment of reference patterns for evaluation and
monitoring of environmental impact with respect to biological diversity;
y Increased opportunities for bioprospecting, and the linking of programs with related and
similar interests;
y Improvements in capacity building in biodiversity and biodiversity-related subjects;
y The development of professionals in new fields of knowledge and in new interfaces, such
as biodiverty informatics, image services, and geographic information systems;
y Production of improved teaching material, such as field guides, identification keys, image
databases, and on-line information for students and educators;
y Improved guides and information resources for use in ecotourism;
y Improved rates of publishing in taxonomy as researchers spend less time on identifications
and on making data available on an individual basis;
y Improved linkages with local people for collecting, ecological research and preliminary
identification using parataxonomists;
y transfer of some of the burden of sorting and preliminary identification of field samples
from the extremely small number of highly-skilled taxonomists to technically-skilled
parataxonomists;
y Development of new sources of funding for supporting collections.
y Etc.
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Taxonomy
For hundreds of years, primary species-occurrence data have been used for taxonomic and
biogeographic studies. Data in museums and herbaria have primarily been used for the
determination and description of new taxa. Collections were also used, however, for such things as
studying pollination biology, evolutionary relationships, and phylogenetics. These uses continue,
and with users now having access to data from a greater geographic range, they are able to expand
on these studies
Taxonomic Research
There are thousands of published examples of uses of primary species-occurrence data in taxonomy
and in the elucidation of new taxa and phylogenetic relationships. Species data in museums are core
to the study of basic taxonomy – the elucidation of new taxa and their descriptions. The world has
about 1.4 million taxa already described (World Resources 1992) – nearly all based on collections
in museums and herbaria. Many more still need to be described and thus one of the basic uses of
species-occurrence data is the description and classification of plants, animals, algae, fungi, viruses,
etc. Without these data, these processes could not continue.
Taxonomic projects are carried out at virtually every natural history museum and herbarium in the
world with outputs in journals, monographs and electronically.
Examples:
y Biodiversity and Management and Utilization of West African Fishes is a project of
ICLARM examing the taxonomy and phylogeny of fishes in Ghana and other West African
states. <http://www.worldfishcenter.org/Pubs/ghana-proceedings/ghana-proceedings.htm>;
y Cicadas of South-East Asia and the West Pacific – research from the Institute for
Biodiversity Research and Ecosystem Dynamics of the Zoological Museum of Amsterdam
(Duffels 2003). <http://www.science.uva.nl/ZMA/entomology/CicadasSE.html>
y The taxonomy of Vietnam’s exploited seahorses (Syngnathidae) (Lourie, et al. 1999).
<http://seahorse.fisheries.ubc.ca/pubs/Lourie_etal_vietnam.pdf>.
y HymAToL – a project aimed at constructing a large-scale phylogenetic analysis of the
Hymenoptera of the world as part of the Tree of Life project.
<http://www.hymatol.org/about.html>.
y Phylogeny. A project from the University of Alberta in Canada.
<http://www.deer.rr.ualberta.ca/library/phylogeny/Phylogeny.html>.
Name and Taxonomic Indices
Primary species-occurrence data has been used to develop lists of names and taxa which are used in
one way or another by most of the projects throughout this paper. In much the same way as
dictionaries and thesauri are used in the spoken and written languages of the word, indexes of
names and taxa are used for the language of biodiversity. Collections institutions use them as
authority files for their databases, taxonomists use them to help determine the correct spelling and
the place of original publication, and scientists and amateurs use them to find the correct spelling of
a name of a species, its synonyms and other information. These indexes can vary from being just a
list of names, to detailed lists that include taxonomic information, synonyms, place of publication,
type specimen information, references to different uses of the names (taxonomic concepts), etc.
Examples:
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y Species2000 <http://www.species2000.org>;
y Integrated Taxonomic Information System (ITIS) <http://www.itis.usda.gov/>;
y International Plant Name Index (IPNI) <http://www.ipni.org/index.html>;
y Electronic Catalogue of Names of Known Organisms (ECat) program of GBIF
<http://www.gbif.org/prog/ecat>;
y Universal Biodiversity Indexer and Organizer (UBio) <http://www.ubio.org/>;
y Index Fungorum <http://www.indexfungorum.org/>;
y Index of Viruses <http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/index.htm>;
y Taxonomic Search Engine (TSE) <http://darwin.zoology.gla.ac.uk/~rpage/portal/>;
y Nomenclator Zoologicus <http://uio.mbl.edu/NomenclatorZoologicus/>;
y Global Lepidoptera Names Index <http://www.nhm.ac.uk/entomology/lepindex/>;
y Tropicos <http://mobot.mobot.org/W3T/Search/vast.html>;
y Gray Card Index of Harvard University <http://www.huh.harvard.edu/databases/>.
Floras and Faunas
The publication of floras and faunas is one of the first outputs from the results of taxonomic
research and their development is being greatly enhanced through access to species-occurrence data
on-line. Most published floras and faunas include location information, and more often than not a
simple mapped distribution. Traditionally, these maps were drawn by hand, and were invariable
created without access to the totality of collections available. With distributed systems such as the
GBIF Portal, and using a simple GIS, these maps can now be produced quickly and easily, and by
having access to many more collections, are more likely to cover the totality of the distribution.
Examples:
y Flora of Australia online (ABRS, Canberra)
<http://www.deh.gov.au/biodiversity/abrs/online-resources/abif/flora/main/>;
y Fauna of New Zealand (Manaaki Whenua Landcare Research)
<http://www.landcareresearch.co.nz/research/biodiversity/invertebratesprog/faunaofnz/>;
y FaunaItalia <http://faunaitalia.it/index.htm> ;
y Phanerogamic Flora of the State of São Paulo (Brazil) <http://www.cria.org.br/flora/>.
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Taxonomy and Ecological Biogeography
Fig. 1. Phylogenetic information from Pultenaea species in Australia showing geographic
patterns related to leaf morphology. Phylogenetic groups were determined using cluster
analysis from herbarium records with affinities hypothesized using leaf morphology and the
phylogenetic cladogram derived from molecular data (right). Data were collated through the
Australian Virtual Herbarium (AVH) (CHAH 2002). Image from West and Whitbread (2004)
with permission of the authors.
The availability of distributed data points from many collections agencies, now allows for quicker
and more detailed studies, for example by looking at provenance differences, locations of
collections with different characteristics (plotting location against leaf length for example), and the
mapping of different taxonomic concepts. Many of the products mentioned below (Floras, Faunas,
field guides, etc.) are the visible output from the basic taxonomic research.
Examples:
y A project at the Centre for Plant Biodiversity Research in Australia, maps patterns related
to leaf morphology in phylogenetic groups of the genus Pultenaea (figure 1). Groups were
identified on the basis of leaf morphology and a phylogenetic cladogram based on
molecular data (Bickford et al. 2004, West and Whitbread 2004).
y Another project at the Centre for Plant Biodiversity Research, uses data obtained from 8
Australian herbaria accessed through the Australian Virtual Herbarium (CHAH 2002) to
plot geographic patterns related to different taxonomic concepts (West and Whitbread
2004).
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Fig. 2. Map showing different interpretations of a group of species in the genus Corymbia
(previously part of Eucalyptus). Different taxonomic concepts of experts propose C.
umbonata and C. dichromophloia encompassing the total distribution of the group as
shown, as compared to another concept which interprets C. dichromophloia in a more
narrow sense and recognises a number of other species as mapped here. Image from West
and Whitbread (2004) with permission of the authors.
Field Guides
Most field guides incorporate a mapped distribution of the species under consideration. Again, like
Floras and Faunas, they have traditionally included hand-drawn maps derived from the author’s
knowledge of the species. The availability of distributed species data now makes the production of
maps and the inclusion of distributional information, that much easier and far more accurate.
Examples:
y Birds of Argentina and Uruguay. A Field Guide (Narotsky and Yzurieta 2003).
y Dragonfly Recording Network
<http://www.searchnbn.net/organisation/organisation.jsp?orgKey=6>;
y Catalogue of the species of the Annelid Polychaetes of the Brazilian Coast (Amaral and
Nallin 2004);
y Butterflies of North America
<http://www.npwrc.usgs.gov/resource/distr/lepid/bflyusa/bflyusa.htm>;
y Butterflies of Australia (Braby 2000);
y Tour 2 from GBIF Demonstration Project 2003: Access to multi-author rainforest
inventories <http://gbifdemo.utu.fi/>.
y BumblebeeID – find British species by colour pattern.
<http://www.nhm.ac.uk/entomology/bombus/_key_colour_british/ck_widespread.html>
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Integrated electronic resources
The development of character-based databases, interactive keys, and digital imaging, along with the
arrival of CD-ROMs and DVDs has led to the development of a number of integrated electronic
resources.
Examples:
y PoliKey (an interactive key and information system for polychaete families and higher
taxa) (Glasby and Fauchald 2003)
y Publications from the Expert Centre for Taxonomic Identification (ETI) produced using the
Linnaeus II software (Shalk and Heijman 1996).
o Searchable and Browsable Index to CD products produced using the Linnaeus
software <http://www.eti.uva.nl/Products/Search.html>. Some examples include:
y Catalogue of the Chalcicoidea of the World,
y Birds of Europe,
y Crabs of Japan,
y Davalliaceae,
y Fauna Malesiana, and
y Fishes of the North-Eastern Atlantic and Mediterranean.
y Arthropods of Economic Importance
y Bats of the Indian Subcontinent
y Key to Cotton Insects
y Publications using the Lucid Software (University of Queensland 2004):
o Searchable Index to published products using the Lucid software. Searches can be
conducted taxonomically, geographically and in a number of other ways
<http://www.lucidcentral.com/keys/keysearch.aspx>. Examples include:
y Key to Common Chilocorus species of India (J. Poorani). an economically
important genus of lady beetles,
y Key to the World Genera of Eulophidae Parasitoids (Hymenoptera) of
Leafmining Agromyzidae (Diptera),
y Key to Insect Orders,
y Pest Thrips of the World.
y Publications using DELTA and IntKey (Dalwitz and Paine (1986).
o Index to publications using DELTA and IntKey
<http://biodiversity.bio.uno.edu/delta/www/data.htm>. Some examples:,
y Beetle – Elateroformia (Coleoptera) – families – (adults and larvae separate).
Downloadable characters and descriptions for use in the Intkey program.
y Braconidae (Hymenoptera) of the New World – subfamilies, genera and
species >,
y Downloadable characters and descriptions for use in the Intkey program - in
English and Spanish.
y Commercial timbers (in English, German, French, and Spanish)
y Polychaete families and higher taxa
y Publications using XID Authoring System <http://www.exetersoftware.com/cat/xid.html>
y Weeds of North America. A comprehensive weed identification reference for
North America on CD, it contains 140 grass-like and 860 broadleaf weeds.
y CD-ROM Publications from the Australian Biological Resources Study (ABRS) and the
Centre for Plant Biodiversity Research in Australia produced largely through use of Lucid
Software (University of Queensland 2004)
Examples include
(<http://www.deh.gov.au/biodiversity/abrs/publications/cds/index.html>):
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o Acacias of Australia,
o Mites in Soil,
o AusGrass,
o Spiders of Australia,
o Australian Tropical Rainforest Trees and Shrubs
<http://www.anbg.gov.au/cpbr/cd-keys/rainforest-key/home_page.html>, and
o Eucalypts of Southern Australia <http://www.anbg.gov.au/cpbr/cd-keys/Euclid/>.
Check lists and inventories
Species checklists for regions, national parks, etc. can now be produced almost automatically, and
maintained through the use of distributed information systems. This is probably one of the least
used, but most powerful use of a distributed system.
Examples:
y Checklist of Amphibian Species and Identification Guide. An online Guide for the
Identification of Amphibians in North America north of Mexico.
<http://www.npwrc.usgs.gov/narcam/idguide/>;
y A Checklist of the Ants of Michigan
<http://insects.ummz.lsa.umich.edu/fauna/MICHANTS.html>;
y Checklist of the Amphibians and Reptiles of Rara Avis, Costa Rica
<http://www.rara-avis.com/herplist.htm>;
y Checklist and distribution of the liverworts and hornworts of sub-Saharan Africa, including
the East African Islands <http://www.oshea.demon.co.uk/tbr/tbrr3.htm>;
y The Australian Mammal Audit (McKenzie and Burbidge 2002) was part of biodiversity
audit for Australia
<http://audit.ea.gov.au/ANRA/vegetation/docs/national/FINAL_MAMMAL_REPORT.doc>.
Image Databases
The use of Image databases, especially of type specimens is reducing damage to natural history
collections as taxonomists use images of the specimens, or of the labels, rather than borrowing
specimens.
Examples:
y New York Botanical Garden Vascular Plant Type Catalog
<http://www.nybg.org/bsci/hcol/vasc/Acanthaceae.html>;
y Parasite Image Library <http://www.dpd.cdc.gov/dpdx/HTML/Image_Library.htm>;
y Natural History Museum (London) Specimen label images
<http://atiniui.nhm.org/gallery/album33>.
Phylogenies
The study of phylogenies, or evolutionary trees is enhanced by the use of primary species-
occurrence data.
Examples:
y Tree of Life – a collaborative Internet project containing information about phylogeny and
biodiversity <http://tolweb.org/tree/phylogeny.html>;
y The study of phylogenetic patterns in groups of Pultenaea (figure 1) (Bickford et al. 2004).
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Parataxonomy
Parataxonomists are used in a number of developing countries to do preliminary sorting of
collections. These parataxonomists rely on good species-occurrence data and products to be able to
carry out their work efficiently and effectively.
Examples:
y Parataxonomists have been extensively used in the Guanacaste Conservation Area in Costa
Rica (Janzen et al. 1993) <http://www.unep-wcmc.org/forest/restoration/docs/CostaRica.pdf>;
y Parataxonomists are being used to conduct biological surveys by the New Guinea Binatang
Research Centre <http://www.entu.cas.cz/png/parataxonomists.htm>.
Automated Identification Tools
Automated identification tools that use pattern recognition followed by clustering, ordination or use
of artificial neural network are being tested for use with insects, birds and frogs.
Examples:
y In Germany bees can be identified using pattern recognition with the Automatic Bee
Identification Software (ABIS)
<http://www.informatik.uni-bonn.de/projects/ABIS/ABIS_Contact.html>;
y In Japan, cicadas and grasshoppers are being identified using hand-held recorders to
recognise calls using the Intelligent Bioacoustic Identification System (IBIS)
<http://www.elec.york.ac.uk/intsys/users/ijf101/research/acoustics/grasshoppers.shtml>;
y In Britain, the Intelligent Bioacoustic Identification System (IBIS) is being used to identify
bats <http://www.elec.york.ac.uk/intsys/users/ijf101/research/acoustics/bats.shtml>; as
well as to identify sett occupancy in badgers underground
<http://www.elec.york.ac.uk/intsys/users/ijf101/research/acoustics/badgers.shtml>;
y In Finland, sinusoidal modelling of birdcalls allows for the development of automated
identification of birds (Härmä 2003).
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Biogeographic Studies
Natural history collections contain a unique and irreplaceable record of the natural and cultural
history of our world. Many of the specimens and ancillary data in collections were obtained prior to
the major modifications of the landscape and they are irreplaceable (Chapman 1999, Page et al.
2004). Indeed, the collections are the fundamental database on the changing landscapes and patterns
of species distributions (Page et al. 2004).
There are hundreds, if not thousands of biogeographic studies using species-occurrence data. Some
use simple distributions within a grid, others link to environmental data layers such as climate and
geology through environmental modelling tools, others look at various combinations to develop
indices of diversity and endemism, relative abundance, etc. All such projects benefit from being
able to access distributed data from multiple institutions. Examples will be included under
individual headings below.
The use of environmental modelling software such as BIOCLIM (Nix 1986, Busby 1991) GARP
(Stockwell and Peters 1999, Pereira 2002), and methods such as GLM (Austin 2002), GAM (Hastie
and Tibshirani 1990), Decision Trees (Breiman 1984), and Artificial Neural Networks (Fitzgerald
and Lees 1992), etc. to link individual locations of plants and animals to environmental criteria such
as climate to produce maps of potential distribution have been around for more than 20 years.
Because of the scale of environmental layers available at the time, some of the earlier studies
looked at broad-scale distributions of groups of plants or animals, such as used with the Elapid
Snakes (Longmore 1986), or more intensely on one species such as with Nothofagus cunninghamii
(Busby 1984). Because of the nature of the software available at the time, and the paucity of good
environmental layers, these studies were slow and took months to produce a model for just one
species, and were often carried out at a scale that allowed for only broad conclusions to be drawn.
The development of new software and vastly improved environmental layers (Hijmans et al. 2004)
has meant that models can now be produced in limited time, allowing for more intensive studies of
individual species, or studies on much larger numbers of species. Care, however, needs to be taken
in using any of these modelling methods, and it is best to seek advice from experts before using
them to ensure that the right model is being used for the right data etc. (Chapman et al. 2005).
Distribution Atlases
Traditional uses for geo-referenced primary species data have been for developing maps of species
distributions and the development of distribution atlases. In the past, these have often been as a
presence or absence within a geographic grid, from 5 km to 2.5-degree grids, or in a biogeographic
region. Many of these have not been made available electronically.
Examples of mapping by grid or region include:
y Fife Bird Atlas (2 km grid squares) <http://www.the-soc.fsnet.co.uk/fife_bird_atlas.htm>;
y Atlas of the British Flora (Perring and Walters 1962) (10 km grid squares);
y Millenium Atlas of Butterflies in Britain and Ireland (Asher et al. 2001) (10 km grid
squares);
y Ontario Herpetofaunal Summary Atlas (10 km grid squares)
<http://www.mnr.gov.on.ca/MNR/nhic/herps/about.html>;
y The Introduction and spread of the Asian Long-horned Beetle in the north America is
being studied using biogeographic analysis <http://www.uvm.edu/albeetle/> and Peterson
et al. (2004)
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<http://www.specifysoftware.org/Informatics/bios/biostownpeterson/PSH_AMN_2004.pdf
>.
y Atlas of Australian Birds (1st edition) (Blakers et al. 1984) (10-minute grid squares);
y Atlas Florae Europaeae (50 km grid squares)
<http://www.biologie.uni-hamburg.de/b-online/ibc99/IDB/afe.html>;
y Census of Australian Vascular Plants (Hnatiuk 1990) (97 biogeographic regions covering
all of Australia);
y Moths of North America (Counties or States)
<http://www.npwrc.usgs.gov/resource/distr/lepid/moths/mothsusa.htm>.
Fig. 3. Distribution of the Eurasian Curlew (Numenius arquata) in Fife, Scotland from the
Fife Bird Atlas (Elkins et al. 2003) using 2 km grid squares. Map reproduced with
permission of the authors.
Many of the early species distribution atlases were done by hand, and often without carrying out
full geo-referencing. Mapping distributions in a grid could be carried out without a GIS and were
easy to record merely as present or absent within each grid cell. The use of distributed database
searches and Geographic Information Systems (GIS) now allows species distribution mapping and
atlases to be produced much more accurately and with better presentation, and has allowed easier
mapping of individual specimen records.
Examples of mapping individual records include:
y Atlas of Elapid Snakes of Australia (Longmore 1986);
y Protea Atlas Project (South Africa) <http://protea.worldonline.co.za/default.htm>;
y The New Atlas of Australian Birds <http://www.birdsaustralia.com.au/atlas/>;
y Tour 1 from GBIF Demonstration Project 2003: Reliability and consistency of Neotropical
species distributions <http://gbifdemo.utu.fi/>;
y Atlas of the Birds of Mexico (Navarro et al. 2003).
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Fig. 4. Distribution of the Rainbow Bee-eater from The New Atlas of Australian Birds
(Barrett et al. 2003). Records are recorded as point records and mapped as a summary in 1-
degree grid squares (red) and on 0.25-degree grid squares (grey).
Species Distribution Modelling
In the mid 1980s, the concept of environmental species distribution modelling using environmental
data such as climate, started to become possible with the development of computer software such as
BIOCLIM (Nix 1986, Busby 1991). Since then, many new modelling methodologies and programs
have been developed, including Generalised Linear Models (GLM) (Austin 2002), Generalised
Additive Models (GAM) (Hastie and Tibshirani 1990), Genetic Algorithm for Rule-set Production
(GARP) (Stockwell and Peters 1999, Pereira 2002), DOMAIN (Carpenter et al. 1993) and many,
many others. These programs were stand-alone programs, but the availability of World Wide Web
in 1994, saw the development of modelling on the Internet – firstly with BIOCLIM and GARP
(Boston and Stockwell 1995), and later with modifications of these and other programs.
The development of these modelling techniques opened up primary species-occurrence data to
many more uses. One of the main drawbacks of these data are their lack of comprehensiveness and
completeness, and the use of models allows for gaps in the distributional knowledge of species to be
filled. There are now many projects using modelling techniques for determining the potential
distributions of species under present-day climatic conditions given various constraints, under
altered climatic conditions following climate change, and under past climatic conditions in earlier
epochs. Some of these uses will be covered under more specific topics below, but
Examples:
y Atlas of Elapid Snakes of Australia (BIOCLIM) (Longmore 1986);
y Atlas of Vertebrates Endemic to Australia’s Wet Tropics (BIOCLIM) (Nix and Switzer
1991);
y Use of Environmental Gradients in Vegetation and Fauna Modelling (GLM) (Austin
2002);
y Potential distribution of Anoplophora glabripennis (Asian Long-horned Beetle) in North
America (GARP) (Peterson et al. 2004);
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y Predicting distributions of Mexican birds (GARP) (Peterson et al. 2002b);
y In Africa, tsetse fly habitats were modelled using species data and remotely-sensed
vegetation data (Robinson et al. 1997).
Atlas of Elapid Snakes of Australia
Fig. 5. Left-hand image - Potential distribution for Tropidechis carinatis in Australia. Red
stars indicate known collections, dots show modelled distribution. Right-hand image shows
predicted numbers of species in each 1º x 1.5º cell. From Longmore (1986) with permission
of Australian Biological Resources Study.
The Atlas of Elapid Snakes (Longmore 1986) was a result of a pilot project conducted with the
Australian Museum in 1982 to examine uses for geo-referenced primary species data. In 1983, the
Australian Bureau of Flora and Fauna (now the Australian Biological Resources Study), decided
that it was wasting resources by funding the collection of new species records without first utilising
data already held by museums. Data for 17,000 records were then collected from all the major
Australian museums, integrated and modelled using the bioclimatic modelling software, BIOCLIM
(Nix 1986, Busby 1991). Many of the data were in a poor state of curation and required extensive
data validation and cleaning prior to use. The Atlas contained maps for all 77 species of front-
fanged, venomous terrestrial snakes (the family Elapidae) in Australia and was one of the first
attempts to collate, geo-reference, and document all records of an animal group for purposes of
biogeographic study. The project also saw the first detailed publication of the software program,
BIOCLIM (Nix 1986).
Environmental data layers for use in bioclimatic modelling were still quite primitive. Twelve
climate parameters were used at a scale of 0.5-degree resolution. Species data were geo-referenced
as accurately as possible, and altitude determined to the nearest 50 m. The species were modelled
using the 5-95 and 100 percentile ranges and mapped at a continental scale (figure 5).
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Predicting new species distributions
By using species-occurrence data in conjunction with species modelling tools, it is possible for
additional locations of species to be identified. In other cases, species modelling has identified
disjunctions in climate profiles that have indicated that two species are present where only one was
previously known.
Examples:
y Museum collections as well as new survey data were used to predict reptile diversity in
Madagascar and were successful in predicting locations of new chameleon species
(Raxworthy et al. 2003);
y In Australia, new locations of a rare Leptospermum species (Myrtaceae) were identified
using species modelling (Lyne 1993)
<http://www.anbg.gov.au/projects/leptospermum/leptospermum-namadgiensis.html>.
Studying species decline
By using locality information and collection information such as date of collection, primary species
data can help in the understanding of species declines over time.
Examples:
y AmphibiaWeb (Wake 2004) <http://amphibiaweb.org/>; Species Decline: Contaminants as
a Contributing Factor. Patuxent Wildlife Research Center Database
<http://www.pwrc.usgs.gov/pattee/select.htm>;
y The Red List Index has developed a tool for measuring global trends in the status of
biodiversity (Butchart et al. 2004).
<http://www.birdlife.org/print.html?url=%2Fnews%2Fpr%2F2004%2F10%2Fred_list_indices.html>;
y Australian Terrestrial Biodiversity Assessment is part of the Australian Natural Resources
Atlas v. 2.0
<http://audit.ea.gov.au/ANRA/vegetation/vegetation_frame.cfm?region_type=AUS&regio
n_code=AUS&info=bio_asses>.
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Species Diversity and Populations
The study of species diversity, species density and richness is a discipline that is being aided
enormously by the increasing availability of species-occurrence data. In the past, these types of
studies required months, if not years of data collection and preparation, and usually concentrated on
the data available from just a few museums or herbaria and thus seldom covered the totality of the
data. This new availability of data through distributed systems has meant that new tools are being
developed to cater for the increases in data availability and to allow for more rapid analysis and
assessment. As a result, the data can be used more effectively in biodiversity assessment projects, in
conservation assessment and for regional planning and management.
The increased availability of data is allowing for improved modelling and distribution of
associations and populations leading to improved understandings of species and how they interact
with their environments. This is allowing for better management of populations, and understandings
of threatened species and communities. This improved understanding, for example, is now allowing
Australia to list threatened ecological communities as well as species (DEH 2000, 2004).
Species Diversity, Richness and Density
The study of species richness, density and abundance and the identification of centres of endemism
have been key areas of research in biodiversity over the past 20 years. More recently, they have
been integrated into conservation assessment and planning and species protection. In many cases,
species diversity, and richness are used as surrogates for measuring biodiversity.
Species Richness Tools
New tools are being developed to assist in assessment of species richness and endemism and for use
as planning tools for conservation assessment.
Examples:
y WorldMap uses species distribution data to produce species richness maps, which can then
be used to carry out further analyses. (Williams et al. 1996)
<http://www.nhm.ac.uk/science/projects/worldmap/index.html>;
y Australian Heritage Assessment Tool, under development at the Australian Department of
the Environment and Heritage, can quickly generate maps of richness and endemism for a
broad range of Australian plant, vertebrate and invertebrate taxa through an easy to use
interface (figure 4);
y Pattern Analysis tools such as PATN (Belbin 1994) can be used to identify patterns in
species diversity and endemism <http://www.patn.com.au/>;
y EstimateS is another software package for estimating species richness. (Colwell 2000)
<http://viceroy.eeb.uconn.edu/estimates>;
y Species Richness bibliography
<http://www.okstate.edu/artsci/botany/ecology/richness.htm>.
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0 - 1.25
1.26 - 3.59
3.6 - 6.74
6.75 - 10.4
10.5 - 15.7
15.8 - 22.7
22.8 - 36.1
36.2 - 59.5
59.6 - 102
103 - 177
Amphibia - Weighted endemism score
Australian Heritage Assessment Tool
Department of the Environment & Heritage
Australian Government 2004
0 500 1,000250 Kilometers
Fig. 6. Endemism in Australian frogs showing peak areas for frog endemism highlighted in
red. Image from the Australian Heritage Assessment Tool; published with permission of
Cameron Slatyer and Dan Rosauer, Australian Department of the Environment and
Heritage, 2004.
Biodiversity Hotspots
Biodiversity hotspots or centres of endemism are regarded as the world’s biologically richest and
most important areas for conservation (Mittermeier et al. 2000). Conservation International has
been conducting a program to assess those areas of the world regarded as the most “species rich”.
Examples:
y Conservation International identifies the 25 most threatened biodiversity rich areas of the
world (Myers et al. 2000) <http://www.biodiversityhotspots.org/xp/Hotspots>;
y Birdlife International’s Endemic Bird Areas of the world (Stattesfield et al. 1998)
<http://www.birdlife.net/action/science/endemic_bird_areas/>;
y Biodiversity hotspots in Australia
<http://www.deh.gov.au/biodiversity/hotspots/index.html>;
y The Millenium Atlas of Butterflies is mapping the species richness of butterflies across the
United Kingdom
<http://www.butterfly-conservation.org/index.html?/bnm/atlas/index.html>.
Patterns of Species Richness
Species richness studies are conducted from the size of one vegetation community to a global scale.
Most species richness studies have implications for conservation, the identification of hot spots as
mentioned above and the identification of priority areas for conservation.
Examples:
y A study in central Brazil looked at the richness and abundance of caterpillars of one genus
of plant in the cerrado (savannah-like) vegetation (Andrade et al. 1999)
<http://www.scielo.sa.cr/scielo.php?pid=S0034-77441999000400005&script=sci_arttext&tlng=en>;
y A study in Africa is looking at species richness and endemism of insects in sub-Saharan
Africa (Miller and Rogo 2001);
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y Species richness and endemism in South American bird species was used to plan a network
of reserves (Fjeldsa and Rahbek 1997);
y The geographic relationships and constraints on species richness were studied using mid-
domain effects (Colwell and Lees 2000);
y Examining spatial patterns at the community level (Ferrier et al. 2002).
Studying Individual species
Species richness studies of single species – knowing where it occurs, and where it moves, and the
densities of individual populations, can aid in the conservation of that species. By using historical
data, changes in patterns of movement can be examined.
Examples
y The density of Elephants in the forests of central Africa is being studied using Geographic
Information Systems (Michelmore 1994).
Evolutionary patterns
One of the aspects of species richness studies is the detection of patterns of endemism and richness.
By looking at the patterns of species concentrations and endemism, historical evolutionary patterns
can be determined.
Examples:
y In a study of conservation in Africa, Brooks (2001) examined four groups of animals –
mammals, birds, snakes and amphibians and modelled species richness against
environmental conditions such as primary productivity potential evapotranspiration, solar
radiation, temperature, and rainfall.
Population Modelling — Population Viability Analysis
The modelling of populations can help track the dynamics of the population, and assist in
determining a minimum area for conservation, and examine interactions with predators and prey,
etc. Species observational data and data from intensive survey is an essential tool for these studies.
Population Viability Analysis (PVA) was originally used to determine how large a population must
be to have a reasonable chance of survival for a reasonable length of time.
Examples:
y At the Centre for Resource and Environmental Studies in Canberra, detailed studies have
been conducted on populations of a small threatened marsupial – Leadbeater’s Possum
(Gymnobelideus leadbeateri) in the forests of northern Victoria. (Lindenmeyer and
Possingham 1995, 2001. Lindenmeyer and Taylor 2001)
<http://incres.anu.edu.au/possum/possum.html>;
y Applied Biomathematics® is using the RAMAS software package to model extinction risk
in birds through use of Population Viability Analysis <http://www.ramas.com/birds.htm>;
y Many studies in China have used Population Viability Analysis to examine minimum
reserve size for maintenance of viable populations of the Giant Panda (Ailuropoda
melanoleuca) (Zhou and Pan 1997);
y An annual census of Southern Elephant Seals is conducted on sub-Antarctic Macquarie
Island on the 15th October every year, and annual populations’ estimates made (Burton
2001). It is estimated that around one-seventh of the world’s populations of Elephant Seals
live on the island, and that they forage over vast areas of the southern ocean from Heard
Island in the west to the Ross Sea in the east
<http://www.aad.gov.au/default.asp?casid=3802>.
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Species Inter-relations
The study of species interactions is another area where species-occurrence data is essential. Such
inter-relationships can include parasitic relationships, symbiotic relationships between species of
animals, species of plants or between animals and plants; predator-prey relationships, competition,
etc.
Examples:
y A project is being conducted in the Guanacaste Conservation Area in Costa Rica to make
an inventory of Eukaryotic parasites of vertebrates (Brooks 2002)
<http://brooksweb.zoo.utoronto.ca/FMPro?-DB=CONTENT.fp5&-Format=intro.html&-
Lay=Layout_1&-Error=err.html&content_id=1&-Find>;
y A project at Madang, in Papua New Guinea looked at host specificity of insect herbivores
on 60 species of rainforest trees. The project needed to cross-reference data on habitats,
hosts, insect species, patterns of host use, and sampling events (Basset et al. 2000);
y The Parasite Database at the University of Toronto maintains information on parasite-host
relationships <http://brooksweb.zoo.utoronto.ca/index.html>;
y A project at the European Network for Biodiversity Information (ENBI) in collaboration
with African countries, is studying Afrotropical Ceratitidine Fruit Flies using a queryable
web site on species distribution of insects and host plants.
<http://projects.bebif.be/enbi/fruitfly/>
y Another study in Costa Rica is looking at the parasites of freshwater turtles (Platt 2000)
<http://brooksweb.zoo.utoronto.ca/pdf/Neopolystoma%20fentoni.pdf>;
y In Canada, the predator-prey relationship between the nemertean (Crebatulus lacteaus) and
the soft-shell clam (Mya arenaria) is being studied (Bourque et al. 2002)
<http://pubs.nrc-cnrc.gc.ca/cgi-bin/rp/rp2_abst_e?cjz_z02-095_80_ns_nf_cjz>;
y The World Federation of Culture Collections (WFCC) is supplying data via GBIF on
interactions between parasites and hosts for many species
<http://wdcm.nig.ac.jp/hpcc.html> as is the Belgian Co-ordinated Collections of Micro-
organisms (BCCM) <http://wdcm.nig.ac.jp/hpcc.html>.
Protecting Communities
In Australia, new environmental protection legislation (DEH 2000) now allows for the listing of
threatened communities in a similar way to the listing of threatened species. Communities can be
listed as: critically endangered, conservation dependant or extinct in the wild and there are severe
penalties for any significant impact on them. Primary species-occurrence data are used to determine
boundaries and definitions prior to listing (Chapman et al. 2001).
Examples:
y Riverine aquatic protected areas: protecting species, communities or ecosystem processes?
(Koehn 2003).
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Life Histories and Phenologies
The study of life histories of both plants and animals is benefiting from the availability of species-
occurrence data. The use if primary species data also aids the study of phenologies – being able to
relate collections and records to the date and time of occurrence.
Life History Studies
Museum collections are a logical resource for life history studies. As stated by Pettit in 1991
Using existing collections for such studies often enables large amounts of data to be
accumulated in a short time on such things as fecundity/mortality patterns, host-parasite
relationships, estimates of breeding seasons, micro-growth increments (many organisms
show growth layers when sectioned, such as the 'rings' of a tree, and these can be used to
study past environmental conditions), food pests, life-cycle duration, larval growth pattern,
migration (museum collections have been used to locate locust outbreak sites and to track
traditional migration patterns), species that mimic other animals, and other polymorphisms,
plant fecundity, flowering and fruiting dates, periods of dormancy, and correlations of plant
growing sites with rainfall or altitude.” (Pettitt 1991).
Many animals and plants have completely different life stages, and species-occurrence data can
supply a wealth of information on the relationship between different stages in the life cycle, and
geographic locations or times of the year.
Examples:
y In the study of the North American Wood Stork (Mycteria americana) in Florida, museum
collections were used to show that clutch sizes had not significantly declined since 1875
(Rogers 1990). Herons and egrets have also been studied
<http://web8.si.edu/sms/irlspec/Cl_Aves3.htm>;
y Wingpad development in Plecoptera was studied in Italy using museum collections (Zwick
2003)
<http://www.unipg.it/maystone/PDF%202001%20proc/ZWICK2%20IJM%20proceedings.pdf>.
Phenology
Phenology is the study of the timing of naturally occurring events and their relationship of biotic
and abiotic variables. Examples include the flowering of plants, arrival and departure times of birds,
the outbreak of plagues of locusts, the time of egg laying by monotremes and birds, etc. Primary
species data are a major resource of information that can be used in phenological studies.
Examples:
y The study of the time of egg-laying of the codling moth (Cydia pomonella) an important
pest of apples and pears, is important in determining times of spraying, etc.
<http://www.ipm.ucdavis.edu/PHENOLOGY/ma-codling_moth.html>;
y In Kansas, a database of the times of flowering of wildflowers and grasses has been
compiled <http://www.lib.ksu.edu/wildflower/season.html>;
y In the United States, the flight speed and rate of migration of birds is being studied
<http://www.npwrc.usgs.gov/resource/othrdata/migratio/speed.htm>;
y Species data are being used in phenological studies of turtle nesting and migration
<http://www.natureserve.org/explorer/servlet/NatureServe?searchName=Chelonia+mydas
>.
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Endangered, Migratory and Invasive Species
Endangered, migratory and invasive species are three groups of species regarded as key groups in
biodiversity management. Indeed, in Australia, they are legislated as “nationally significant” (DEH
2000). Species-occurrence data are essential for the understanding and management of these groups
of species in the environment.
Endangered Species
Endangered species provide many challenges to biogeographers, modellers and conservation
biologists. There are usually so few records that environmental modelling techniques seldom work
well. However, threatened species are essential components of any conservation program and
species-occurrence records often provide the only available information. Primary species-
occurrence databases are important for the identification of endangered species, identifying the
reasons why they are endangered, for identifying external factors affecting the species, and for
assisting in the development of species recovery plans.
Examples:
y IUCN Red List of Threatened Species http://www.redlist.org/.
y Endangered Species Program of the U.S.A. – U.S. Fish and Wildlife Service
<http://endangered.fws.gov/>;
y Threatened Species Program – Australian Department of the Environment and Heritage
<http://www.deh.gov.au/biodiversity/threatened/index.html>.
Species Recovery Plans
Species Recovery Plans are becoming an integral part of threatened species management in many
countries.
Examples:
y Recovery Plan for the Angle-stemmed Myrtle (Austromyrtus gonoclada) Queensland
Parks and Wildlife Service
<http://www.deh.gov.au/biodiversity/threatened/publications/recovery/a-
gonoclada/index.html>
y Threatened Species Recovery Plans Australian Department of the Environment and
Heritage <http://www.deh.gov.au/biodiversity/threatened/recovery/list-common.html>;
y Threatened Species Recovery Plans New Zealand Department of Conservation
<http://www.doc.govt.nz/Publications/004~Science-and-Research/Biodiversity-Recovery-
Unit/Recovery-plans.asp> ;
y Recovery Plan Summaries from Environment Canada
<http://www.speciesatrisk.gc.ca/publications/plans/default_e.cfm>.
Threats
The study of threats to endangered species can also be enhanced through the use of primary species
data – especially when those threats are other species such as predators or competitors. In Australia,
key threatening processes are listed under legislation, and include such things as feral goats, the
root-rot fungus (Phyophthora cinnamomi), the Fire Ant (Solenopsis invicta), etc.
Examples:
y Threat Abatement Plans – Australian Department of the Environment and Heritage
<http://www.deh.gov.au/biodiversity/threatened/tap/index.html> ;
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y Threats to Albatrosses and Giant-petrels
<http://www.deh.gov.au/biodiversity/threatened/publications/recovery/albatross/index.html
>;
y The introduction of the red imported fire ant, Solenopsis invicta, has caused a reduction in
biodiversity of Australian native flora and fauna
<http://www.deh.gov.au/biodiversity/threatened/ktp/fireant.html>.
Species Decline
The study of the decline in species numbers and distributions is an important step in preventing
future endangerment and extinction in species and species habitats. Species-occurrence databases
are an important information source for the study of both past declines and for monitoring current
species numbers for prevention of future declines.
Examples:
y AmphibiaWeb <http://www.amphibiaweb.org/declines/declines.html>;
y FrogLog – Newsletter of the Declining Amphibian Populations Taskforce
<http://www.open.ac.uk/daptf/froglog/>;
y At Cornell University in the United States, the status of birds are monitored to identify
declining species
<http://www.scsc.k12.ar.us/2000backeast/ENatHist/Members/BryanM/page%202.htm>;
y Predicting risk of extinction in declining species (Purvis et al. 2000)
<http://www.bio.ic.ac.uk/evolve/docs/pdfs/Purvis%202000%20PRSLB.PDF>.
Invasive species and translocation studies
The spread of invasive alien and translocated species is one of the biggest environmental problems
faced by most countries today. It is regarded by the Convention on Biological Diversity as the
second most important threat to biodiversity after habitat change (CBD 2004). It is estimated that
there are as many as 120,000 introduced species in the six countries made up of the United States,
United Kingdom, Australia, India, South Africa and Brazil, alone (Pimentel 2002). Of these,
perhaps 20-30% is now regarded as a pest species. The cost in economic loss of the 30,000 non-
indigenous species in the United States has been estimated at close to $123 billion a year (Pimentel
et al. 1999, 2000).
Not all introduced species become invasive. In the history of the United States it is estimated that
approximately 50,000 non-indigenous species have been introduced (Pimental et al. 1999). Many of
these of these have been used as food crops, livestock and farmed animals such as cattle and
poultry, pets, biological control agents, landscape restoration, etc. However, those that have become
pests cost the world a lot of resources every year in lost production, control and disease.
Preventing future invasions and predicting the impact of already introduced species requires
accurate identifications and information on the natural distributions and ecological requirements of
those species as well as associated species that may have positive or negative impacts with them
(Page et al. 2004). The availability of species-occurrence data from different countries through
projects such as GBIF, allows researchers to identify the native locations of invasive species,
determine the niche characteristics in the form of climatic and environmental requirements, and
then use this information to predict likely spread in the country of introduction.
It also allows researchers to look at the distribution of possible biological control species, and to use
this information to examine the possible spread and environmental limitations of these before
introduction.
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The availability of this information now makes possible, studies into invasive species and biological
control agents that has not been previously possible, and this alone more than justifies the costs of
projects such as GBIF.
There are many studies already using such information, and links to over 80 case studies can be
seen on the web site of the Convention on Biological Diversity at
<http://www.biodiv.org/programmes/cross-cutting/alien/cs.aspx>.
Example:
y The Global Invasive Species Program (GISP) in an On-line toolkit that “provides advice,
references, and contacts to aid in preventing invasions by harmful species and eradicating
or managing those invaders that establish populations”
<http://www.cabi-bioscience.ch/wwwgisp/gtcsum.htm>;
y Predicting the Geography of Species Invasions using Ecological Niche Modeling (Peterson
2003) <
http://www.specifysoftware.org/Informatics/bios/biostownpeterson/P_QRB_2003.pdf>;
y In Kenya, the process of weed invasions have been tracked using herbarium specimens,
showing that the regional spread of weeds in Kenya was correlated with the change in
agricultural systems (Stadler et al. 1998);
y The spread if invasive Argentine Ants (Linepithema humile) across the United States over
the past 100 years was studied by Suarez and others (2001) using both museum collections,
and observations <http://www-biology.ucsd.edu/news/article_051500.html>;
y In New Zealand, bioclimatic prediction is being used to monitor the potential distribution
of weeds prohibited entry to New Zealand (Panetta and Mitchell 1991);
y In North America studies are being carried out on the introduced Saltcedar (Tamarix
ramossisima), which is becoming a major pest species in arid areas of Mexico where it is a
huge user of water, aggressively replaces native riparian vegetation, and reduces habitat for
birds and other animals. Distributions are being modelled in native and introduced habitats
to assist planning in control and eradication (Soberón 2004);
y In Brazil and North America, the invasive potential of Homalodisca coagulata an insect
vector of a bacteria of orchard-based crops was studied using distribution models with
GARP (Peterson et al. 2003a);
y In Australia, invasive species are now listed under legislation and species-occurrence data
are used to track their spread and to monitor their control
<http://www.deh.gov.au/biodiversity/invasive/index.html>;
y Species distribution models were used to assess the invasive risk of several bird and insect
species (Peterson and Vieglais 2001)
<http://www.specifysoftware.org/Informatics/bios/biostownpeterson/PV_B_2001.pdf>;
y Timely identification of pests can reduce need for costly control programs
<http://www.bionet-intl.org/case_studies/case17.htm>.
y Harlequin Ladybird (Harmonia axyridis) study – a survey of an invasive species in the UK
<www.harlequin-survey.org>
Arthropods and Annelids.
Approximately 4,500 arthropod species (2,582 species in Hawaii and more than 2,000 in the
continental United States) have been introduced to the United States (Pimental 1999). In addition
many aquatic invertebrates and earthworms have arrived. According to Pimental loc. cit., about
95% of the introductions were accidental.
Examples:
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y North American Non-Indigenous Arthropod Database (NANIAD) is an on-line database of
over 2,000 species of non-indigenous arthropods introduced into the Unites States of
America <http://www.invasivespecies.org/NANIAD.html>.
Ballast Water
Ballast water in ships is a major source of introduced alien species into coastal habitats around the
world. The identification of these species is an international problem as they may arise from
anywhere in the world. The ability to use on-line primary species databases provides a major step
forward in the identification and eventual regulation and control of these species.
Examples:
y The Northern pacific seastar (Asterias amurensis) has virtually wiped out a species of
shellfish and is a major threat to the marine environment. It is also adversely affecting the
Tasmanian and Western Australian fisheries. It was not identified as an introduced species
until 1992, and thus attempts to control it were delayed. Distributed primary species
databases may help to prevent such delays occurring in the future
<http://www.fish.wa.gov.au/hab/broc/invasivespecies/seastar/>;
y The Zebra Mussel (Dreissena polymorpha) originated in Poland and in the former Soviet
Union, and after introduction in Ballast water are now causing problems throughout
northern Europe and the United States, including in the Great Lakes between Canada and
the United States <http://nas.er.usgs.gov/taxgroup/mollusks/zebramussel/>;
y In Australia, the Ballast Water Management Strategy uses species-occurrence data to
identify, for example, where ballast water should not be taken on because of ‘hot spots’ of
particular species that may become pests
<http://www.affa.gov.au/content/output.cfm?ObjectID=6F3A6281-9705-4878-
9FA6836B5D6D5814>.
Biological control of pests
The use of biological control agents to control pests has been in operation for around 50 years, and
their use is increasing. Species-occurrence data are used to help find suitable biocontrol agents and
to monitor their effectiveness and possible spread.
Examples:
y Biocontrol of mealybugs in South Africa
<http://www.bionet-intl.org/case_studies/case2.htm>;
y Taxonomy is used in the selection of bio control agents in Hawaii
<http://www.bionet-intl.org/case_studies/case15.htm>;
y Weevils are being used to control Eichhornia crassipes in Australia and elsewhere
<http://aquat1.ifas.ufl.edu/hyacin.html>;
y Rabbits are controlled in Australia using various virus species
<http://www.csiro.au/communication/rabbits/qa1.htm>.
Biological control gone wrong
The use of biological control agents must be controlled, otherwise disasters can occur. Species-
occurrence data can be used to study locations of possible biological control agents, and to predict
their possible spread in the proposed country of introduction. Not all biological control
introductions in the past have worked.
Examples:
y In Australia, the Giant Cane Toad (Bufo marinus) was introduced into Australia in 1935 to
control two introduced pests of the sugar cane industry – the Grey-backed cane beetle and
the Frenchie beetle. CSIRO in Australia is mapping the spread through museum records
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and observations
<http://www.csiro.au/index.asp?type=faq&id=CaneToadControl&stylesheet=sectorInformationSheet>;
y Many species have been introduced into Australia and South Africa to control Lantana
species. The majority of these have not worked for a number of reasons, although some
have worked in Hawaii and elsewhere. Different biological control agents have different
effects on the different phenotypes of Lantana occurring in Australia, and the use of
species-occurrence data to map the origins and spread of those phenotypes and the
relationships of the bio-control agents in those areas can help improve success rates (Day
and Nesser 2000).
Opuntia species in Mexico and the biological control agent Cactoblastis cactorum
Opuntia is one of the most used genera of plants in Mexico and Central America (Soberón et al.
2001), and is 10th in agricultural importance in Mexico (Soberón et al. 2000). The moth
Cactoblastis cactorum is one of the best-known examples of a successful biological program when
it was used in Australia in the control of Opuntia species in Queensland and northern New South
Wales (Debach 1974). Fears have now arisen about the introduction of the Cactoblastis moth into
Mexico, and the Commission on the Conservation and Use of Biodiversity in Mexico (Conabio) is
modelling the potential spread and impacts of the moth there.
Examples:
y Using species-occurrence data and species distribution modelling to examine the potential
spread and impact of Cactoblastis cactorum on the more than 90 species of native cactus
species in Mexico and North America (Soberón et al. 2001)
<http://www.fcla.edu/FlaEnt/fe84p486.pdf>.
Studying coeveolutionary patterns
Museum collections have even been used to examine the rapid evolutionary response and
adaptation of weeds to new environments.
Examples:
y In North America, studies on the co-evolution of parsnip (Pastinaca sativa) with the
parsnip web worm (Depressaria pastinacella) have examined seeds from herbarium
specimens to compare chemical co-evolution of the plants with the insect (Berenbaum and
Zangerl 1998). http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=24890 .
Migratory Species
Migratory species, virtually by definition, range across political boundaries and thus their study
requires data from a range of jurisdictions. In the past, it has been difficult to obtain data from areas
of a species range that one may be studying from outside the researcher’s own country. The
availability of distributed data systems is now allowing for new opportunities for migratory species
studies. Various agreements are now in place around the world to track and monitor migratory
species and to exchange information, including species-occurrence data.
Examples:
y Convention on Migratory Species (Bonn Convention) <http://www.cms.int/>;
y Japan-Australia Migratory Bird Agreement (JAMBA)
<http://www.austlii.edu.au/au/other/dfat/treaties/1981/6.html> and China-Australia
Migratory Bird Agreement
<http://www.austlii.edu.au/au/other/dfat/treaties/1988/22.html>;
y African-Eurasian Migratory Water Bird Agreement
<http://www.unep-wcmc.org/AEWA/index2.html>;
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y Global Register of Migratory Species (GROMS) <http://www.groms.de/>.
y Migratory Birds know no Boundaries An extensive information resource from Israel on
migratory birds <http://www.birds.org.il/>
Tracking Migratory Species
The tracking of migratory species and where they move has been an ongoing process for many
years. One of the problems in the past has been the lack of access to species-occurrence data. With
the new availability of species-occurrence data, data from all the range states can be combined to
track and monitor changes in patterns of behaviour, decline in numbers, life spans etc. Tracking
may be through observation and counts, through banding and recapture, through use of satellite
tracking devices, or by use of radioactive isotopes.
Examples:
y European Union for Bird Ringing <http://www.euring.org/>;
y Australian Bird and Bat Banding Scheme (ABBBS)
<http://www.deh.gov.au/biodiversity/science/abbbs/>;
y The Monarch Butterfly (Danaus plexippus) migration is tracked from Mexico to the United
States each year through the use of banding
<http://www.uen.org/utahlink/activities/view_activity.cgi?activity_id=2030>;
y Hydrogen isotopes (heavy water or deuterium) are being use to track Monarch Butterfly
(Danaus plexippus) breeding and feeding grounds (Wassenaar and Hobson 1998)
<http://whyfiles.org/083isotope/2.html>;
y In Malaysia, sea turtles are being tracked across the world’s oceans using satellite tracking
devices <http://www.kustem.edu.my/seatru/satrack/>.
Monitoring Adelie Penguins in the Antarctic
The Adelie penguin has been identified as an important krill-dependent indicator species and is
being used to monitor changes in critical ecosystem components for use in assessment of the
conservation of marine living resources in the Antarctic. One project (Southwell and Meyer 2003)
is studying the degree to which the feeding range of the penguins overlaps with the krill fishery in
both time and space; variations in the penguins breeding success and food consumption from year
to year and the factors responsible; and how much krill can be fished without affecting the penguins
that depend on it.
Examples:
y Tracking Adelie penguins around Casey Station to monitor feeding habits (Kerry et al.
1999) <http://aadc-maps.aad.gov.au/aadc/metadata/metadata_redirect.cfm?md=AMD/AU/Tracking_SI>;
y Adelie penguin research and monitoring in support of the CCAMLR Ecosystem
Monitoring Project Antarctic Science Project No. 2205
<http://cs-db.aad.gov.au/proms/public/report_project_public.cfm?project_no=2205>.
Wandering albatrosses and petrels
Albatrosses wander for thousands of miles around the southern oceans and generally only ever
touch land to breed. Little is known of the movements of the different species and individuals –
how far they range, where do they over winter, etc. Primary species-occurrence data are being
gathered through the use of satellite tracking and observation (Croxall et al. 1993).
Examples:
y Platform Terminal Transmitters have been attached to Tasmanian Shy Albatrosses to track
albatrosses over a four month period
<http://www.wildlifebiz.org/The_Big_Bird_Race/152.asp>;
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y Two species of albatross were tracked around Heard Island in the Antarctic
<http://www.aad.gov.au/default.asp?casid=14718>;
y Satellite tracking of petrels and albatrosses from the tropics to the Antarctic (Catard and
Weimerskich 1998).
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Impact of Climate Change
Climate change threatens the survival of ecological communities, individual species, and human
health and wellbeing. There have been many studies on the impact of climate change on human
populations, on roads and dams, island populations, etc. Fewer studies, have examined the impact
of climate change on biodiversity, but the use of species-occurrence data in environmental models
to examine impacts is increasing, and studies have shown that impact is likely to be considerable.
Howden et al. (2003), for example, identified impacts on Australia’s coral reefs, on rainforests and
rangelands, and on the distribution of birds, plants and reptiles. Recent studies have indicated that
as many as 18-35% of species will become extinct before 2050 due to climate change (Thomas et
al. 2004).
On Native Species
The availability of species-occurrence records through distributed systems such as the GBIF Portal
has opened up new areas of research, and allows climate change impacts to be studies across ranges
of species, climates and regions.
Examples:
y Studies in Australia on the impact of climate change on threatened species, estimated
reductions in core climate habitat of between 82 and 84% with 12% of threatened species
predicted to become extinct by 2030 (Dexter et al. 1995), and even currently non-
threatened species with limited distributions, or with specific habitat or soil requirements
were likely to be significantly impacted (Chapman and Milne 1998);
y Studies in Mexico looked at the impact of climate change on the fauna (Peterson et al.
2002a)
<http://www.specifysoftware.org/Informatics/bios/biostownpeterson/Petal_N_2002.pdf>;
y A study in Brazil looked at the impact of climate change on cerrado species, and examined
implications for conservation assessment and reserve selection (Siqueira and Peterson
2003)
<http://www.biotaneotropica.org.br/v3n2/en/download?article+BN00803022003+item>;
y A study of 35 non-migratory European butterflies showed a major shift north in
distribution over the past century of from 35-240 km that the authors contributed to global
warming (Parmesan et al. 1999)
<http://www.biosci.utexas.edu/IB/faculty/parmesan/pubs/Parm_Ntr_99.pdf>;
y Studies in birds in America has shown a shift in breeding dates in tree swallows (Dunn and
Winkler 1999);
y A study of the adaptation of migratory birds to global climate change was conducted using
the European Pied Flycatcher (Ficedula hypoleuca) Coppack and Both 2003)
<http://www.rug.nl/biologie/onderzoek/onderzoekgroepen/dierOecologie/publications/803Pdf.pdf>
.
On Primary Production
Not all climate change is detrimental, and for agriculture, some species will benefit. Other species
will grow in places where they have previously been marginal.
Examples:
y In Australia, it is predicted that wheat yield may increase in some areas (Nicholls 1997);
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y Studies in Denmark have shown that global climate change is likely to increase yields at
high and mid-latitudes (Olesen 2001)
<http://glwww.dmi.dk/f+u/publikation/dkc-publ/klimabog/CCR-chap-12.pdf>;
y Research is predicting that different agricultural and forest species will need to be planted
in different areas, some areas will require the planting of new varieties, other species will
need to be planted earlier, pesticide controls will need to be altered and water regimes may
need to be examined <http://www.gcrio.org/gwcc/booklet2.html>.
Desertification
Climate change and desertification are two big issues facing the world. Priimary species data are
being used as indicators of diversification under climate change
Examples:
y Grassroots indicators for desertification. Experience and Perspectives from Eastern and
(Hambly and Angura 1996);
y Global Biodiversity Forum on Linking biodiversity and desertification: a strategic
perspective <http://www.gbf.ch/desc_workshop_old.asp?no=6&app=&lg=EN&now=2>.
y In Cuba, biodiversity data are being used to develop an index of desertification (Negrin et
al. 2003) <http://www.unccd.int/actionprogrammes/lac/national/2003/cuba-spa.pdf>;
y The trialogue of climate change, biodiversity and desertification
<http://www.gdrc.org/uem/Trialogue/trialogue.html>.
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Ecology, Evolution and Genetics
Primary species-occurrence data provides the raw material for revealing patterns, processes, and
causes of evolution and ecological phenomena (Krishtalka and Humphrey 2000). The study of
vegetation structure and composition is largely dependant on the availability of species-occurrence
data. Much of the world’s vegetation has been altered in recent centuries and thus the reconstruction
of pre-settlement vegetation cover requires a combination of primary species data and modelling
against soils, climate, and topography, etc.
Vegetation Classification
The classification and description of vegetation is a first step in understanding the vegetation, its
functions and attributes. Primary species-occurrence data are essential for both the classification
and description.
Examples:
y Gillison and Carpenter (1994) used functional attributes for the description and analysis of
vegetation <http://www.cifor.cgiar.org/publications/pdf_files/WPapers/WP-03n.pdf>;
y VegClass: Vegetation Classification tool
<http://www.cifor.cgiar.org/docs/_ref/research_tools/vegclass/>;
y UK Habitat Classifications <http://www.jncc.gov.uk/habitats/habclass/default.htm>;
y Vegetation Classification Standards (Federal Geographic Data Committee) <
<http://www.fgdc.gov/standards/status/sub2_1.html>;
y Vegetation of southern Africa <http://www.plantzafrica.com/vegetation/vegmain.htm>.
Mapping Vegetation
Vegetation mapping is a key process in understanding the environment, and in providing a context
for studying species and their associations. Vegetation mapping covers both the mapping of current
vegetation cover as well as interpretation of past vegetation cover in areas that may now be cleared
for urbanization, agriculture, etc.
Examples:
y Checklist of Online Vegetation and Plant Distribution Maps (Englander and Hoehn 2004)
<http://www.lib.berkeley.edu/EART/vegmaps.html>;
y Australian National Vegetation Information System (NVIS) is using species distribution
data from herbaria and on-ground survey to prepare a detailed vegetation map for the
continent
<http://audit.ea.gov.au/ANRA/vegetation/vegetation_frame.cfm?region_type=AUS&regio
n_code=AUS&info=NVIS_framework>;
y The Australian Natural Resources Atlas v. 2.0 examines native vegetation types and extent
in Australia, and looks at what the vegetation was like prior to European settlement
<http://audit.ea.gov.au/ANRA/vegetation/vegetation_frame.cfm?region_type=AUS&regio
n_code=AUS&info=veg_type>;
y USGS-NPS Vegetation Mapping Program <http://biology.usgs.gov/npsveg/>;
y Florida Coastal Everglades LTER Sited – Vegetation Map <http://fcelter.fiu.edu/maps/>.
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Habitat loss
Habitat loss (including fragmentation) is considered to be one of the largest threats to biodiversity.
The study of habitat loss is again dependant upon the availability of species-occurrence data –
including data from museums as well as survey.
Examples:
y The study of woodland birds in Australia has shown a major decline as habitat
fragmentation increases
<http://www.wilderness.org.au/campaigns/landclearing/nsw/birdecline/>;
y Museum collections were used to show a change in proportions between species of small
mammals in the prairies of Illinois coincided with habitat destruction (Pergams and Nyberg
2001) <http://home.comcast.net/~oliver.pergams/ratio.pdf>;
y A study of tropical forests in the Mbalmayo Forest Reserve in Camaroon, examined
species richness for eight groups of animals and compared them with increased disturbance
(Lawton et al. 1998) <http://invertebrates.ifas.ufl.edu/LawtonEtal.pdf>.
Ecosystem function
Ecosystem function describes the way in which ecosystem processes interact internally between its
component organisms and externally with the physical environment, and include such processes as
nutrient cycling, decomposition, water and energy balance, and flammability. Ecosystem health
(Costanza et al. 1992) is very dependant on efficient ecosystem function. Many ecosystems around
the world are currently undergoing dramatic changes in species composition due to the influence of
human activity. These changes often lead to a reduction in species diversity and species richness
and to changes in species composition. How these changes affect overall function of the ecosystem
and thus its health is the subject of on-going research. This research is very dependant upon the
availability of primary species-occurrence data.
Examples:
y The role of biodiversity in ecosystem function (Gillison 2001)
<http://www.asb.cgiar.org/docs/SLUM%5C05-
Ecological%20functions%20of%20biodiversity%5C05-
2%20Does%20biodiversity%20play%20a%20significant.ppt>;
y Biodiversity and ecosystem function online
<http://www.abdn.ac.uk/ecosystem/bioecofunc/>;
y BIODEPTH is a program looking at cosystem functioning in terrestrial herbaceous
ecosystems <http://www.cpb.bio.ic.ac.uk/biodepth/contents.html>;
y BIOTREE is a long term project looking at tree diversity and function in temperate forests
<http://www.biotree.bgc-jena.mpg.de/mission/index.html>;
y Soil microbiology is thought to have a key role in efficient ecosystem functioning (Zak et
al. 2003) <http://www.bio.psu.edu/ecology/calendar/Zak.pdf >.
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Survey Design - Finding the Gaps
Fig. 7. Environmental regions using climate classes derived from mean annual rainfall and
temperature were identified and mapped using GIS. The proportion of biological collections
was determined for each class, and surveys planned in areas that were relatively under-
surveyed (Neldner et al. 1995).
Species occurrence data are a key resource in determining priorities for planning future survey.
Although some scientists fear that making their data available electronically will reduce funding
support for new biotic surveys and collections (Krishtalka and Humphrey 2000), the opposite is
proving to be the case, with increased support for gap filling. By making the data available,
geographic, taxonomic and ecological gaps in knowledge are more easily identified, and thus new
surveys and survey locations can be planned efficiently and with increased cost-effectiveness
(Chapman and Busby 1994).
Examples:
y The U.S. GAP Analysis Program aims at identifying gaps in species conservation
<http://www.gap.uidaho.edu/>;
y In Australia, environmental and species modelling and biological regionalisation was used
to identify key areas of the Cape York Peninsula for further survey (figure 5). A program
called VISTR (Visualisation of Taxa, Samples and Regions) was developed (Neldner et al.
1995);
y Tour 1 from GBIF Demonstration Project 2003: on the reliability and consistency of
Neotropical species distributions can be used to determine appropriate sites for future
survey <http://gbifdemo.utu.fi/>;
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y A BIOCLIM analysis was used in Australia to predict likely habitat for Tarengo Leek
Orchid (Prasophyllum petilum) based on climatic parameters of the known populations
(NSW National Parks and Wildlife Services 2003)
<http://www.nationalparks.nsw.gov.au/PDFs/recoveryplan_draft_prasophyllum_petilum.pdf>;
y The South Dakota Gap Analysis program used distributions of native vertebrates to
determine survey locations <http://wfs.sdstate.edu/sdgap/sdgap.htm>.
Evolution, Extinction and Genetics
Species-occurrence data have been used to study evolution of species, to examine likely species
distributions under previous climates, to examine causes of extinctions and to study genetic
relationships.
Examples:
y Bioclimatic profiles of a species of Nothofagus (Nothofagus cunninghamii) were used to
estimate Holocene climates in Tasmania (McKenzie and Busby 1992);
y Pollen evidence was used to reconstruct palaeoenvironments in the lower Gordon River
valley in Tasmania (Harle et al. 1999);
y Species data are used to infer phylogenies
<http://evolution.genetics.washington.edu/book/datasets.html>;
y The use of Ring species and DNA can infer evolutionary patterns in a range of species
<http://www.origins.tv/darwin/rings.htm>;
y Studies in Australia are examining the reasons for extinction of the megafauna and the
evolution of modern Australian faunal species
<http://science.uniserve.edu.au/school/quests/mgfauna.html>;
y Evolution and Mass Extinction (Hunt 2001)
<http://cwx.prenhall.com/bookbind/pubbooks/freemanea2/chapter3/custom5/deluxe-content.html>;
y In Canada, a range of projects is looking at Molecular Systematics and Conservation
genetics. Projects include the conservation genetics of endangered species, evolution of
unisexuality in reptiles, detection of cryptic species using DNA, etc.
<http://www.rom.on.ca/biodiversity/cbcb/cbmolecu.html>;
y A study of the evolutionary history of amphibians used molecular data (Feller and Hedges
1998) <http://evo.bio.psu.edu/hedgeslab/Publications/PDF-files/101.pdf>;
y The evolution of pattern and mimicry is being studied with butterflies
<http://evo.bio.psu.edu/hedgeslab/Publications/PDF-files/101.pdf>.
Genomics
Genomics is the study of genes and their functions. Primary species-occurrence data are being used
in the study of genomics through frozen tissue collections, such as those at the American Museum
of Natural History,
Examples:
y Plant Genome Databases <http://www.nal.usda.gov/pgdic/>;
y Institute for Comparative Genomics, American Museum of Natural History
<http://www.amnh.org/science/facilities/hayden.php>;
y Using genetic data for conservation of the Arabian oryx (Marshall et al. 1999)
<http://www.latrobe.edu.au/genetics/staff/sunnucks/homepage/papers/AnimalCons/Marshalletal98.pdf>
;
y Ancient DNA techniques are being used to observe evolutionary processes and to construct
phylogenetic trees from fossil bones discovered in the permafrosts of Alaska (Shapiro and
Cooper 2003);
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y In Finland, adaptive variation is being studied using genomes
<http://cc.oulu.fi/~genetwww/plants/adaptive.html>;
y DNA bar-coding is being examined for use in biological identifications and conservation
(Herbert et al. 2003) <http://barcoding.si.edu>.
Bioinformatics
In genome terms, bioinformatics includes the development of methods to search databases quickly,
to analyse DNA sequence information, and to predict protein sequence and structure.
Examples:
y GenBank Database <http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html>;
y EMBL – European Molecular Biology Laboratory <http://www.embl-heidelberg.de/>;
y Bioinformatics: Sequence, Structure and Databanks – A Practical Approach (Higgins and
Taylor 2000).
Microbial diversity and speciation
James T. Staley2
Since bacteria are the most ancient group of living organisms it is not surprising that the Tree of
Life, based on small ribosomal RNA sequence analysis, indicates there are at least 40 kingdoms.
Considering this high degree of diversity and the fact that micro-organisms are found in all
ecosystems, some of which are extreme environments such as boiling hot springs and acidic
habitats at pH 1, it is noteworthy that only about 6,000 species of Bacteria and Archaea have been
described and named. One reason for the low number of species is that the species concept used for
bacteria is very broad in comparison with that for animals and plants. Scientists are now
questioning the microbial species concept not only because of its breadth, but because none of the
known bacterial species can be considered endemic to a specific location on Earth. Recently,
evidence for endemism has been reported when scientists look at the subspecies level.
Multi-locus sequence analyses of protein genes that are less highly conserved than ribosomal RNA
are being used for studies of endemism.
Example:
y One example is that of Helicobacter pylori a human pathogen that causes gastric ulcers
that may eventually lead to stomach cancer. Using sequence analysis of several protein
genes, it has been found that human migration patterns can be discerned by the strains of
H. pylori that have been harboured in Homo sapiens since they dispersed from Africa.
Thus, the Maori strains of H. pylori contain unique strains that are clearly different from
those of European ancestry whose populations migrated to New Zealand more recently.
African strains were found in high frequency in West Africa as well as in African
Americans. Other patterns have been discerned that can also be explained by human
migrations that have occurred in the past 50,000 years (Falush et al. 2003);
y Evidence that non-pathogenic bacteria are endemic to hot spring habitats has been recently
reported in this newly emerging field. If speciation events are occurring at the subspecies
level in micro-organisms, this argues for the need for a redefinition of microbial species.
Also, if endemic bacteria exist, this information could be very helpful in forensic studies,
because the microbiota on objects removed from an area may contain genetic information
about the source of the object;
2 This section was authored by James T. Staley, University of Washington, Seattle, WA, USA.
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y The study of speciation is the new revolution in microbiology. Eventually, the numbers of
microbial species may exceed many millions.
Archaeological studies
Primary species-occurrence data in the form of fossil collections in museums are used in studying
the archaeological history of species.
Examples:
y Researchers at the Illinois State Museum in Springfield are using museum-based fossil data
in the scientific literature to plot ranges of North-American mammals over the last 40,000
years on computer-generated maps (Cohn 1995);
y New fossils in Ethiopia open a window on Africa’s ‘missing years’ (Washington
University in St. Louis News and Information)
<http://news-info.wustl.edu/news/page/normal/575.html>;
y African Archaeological Database <
<http://www.archaeolink.com/african_archaeology.htm>;
y The Age of the Megafauna (Australian Broadcasting Commission)
<http://news-info.wustl.edu/news/page/normal/575.html>;
y The Zooarchaeology Laboratory Comparative Vertebrate Collection at the Arizona State
Museum provides a resource for archaeological studies <
<http://www.statemuseum.arizona.edu/zooarch/zooarch_browse.asp>.
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Environmental Regionalisation
The dividing of an area into regions with similar environmental conditions is possible with the use
of species information in conjunction with environmental data and remote-sensing images. Such
regionalisations can be used for environmental planning at scales from regional to continental.
National Planning studies
Environmental regionalisations are an extremely valuable tool for planning of conservation and use
of natural resources. In Australia, the Interim Biogeographic Regionalisation of Australia (figure 8)
is used extensively for conservation planning, sustainable resource management and environmental
monitoring.
Examples:
y Interim Biogeographic Regionalisation of Australia (IBRA) was developed using species
data, remote sensing data and climate data (Thackway and Cresswell 1995)
<http://www.deh.gov.au/parks/nrs/ibra/version5-1/index.html>;
y The Australian Government is using bioregions for setting of priority bioregions for
developing a national reserve system
<http://www.deh.gov.au/parks/nrs/ibra/priority.html>.
Fig. 8 The Interim Biogeographic Regionalisation for Australia (IBRA) is a framework for
conservation planning and sustainable resource management within a bioregional context.
Regions represent a landscape based approach to classifying the land surface using a range
of continental data on environmental attributes.
Regional Planning Studies
Bioregional planning involves the development of approaches for identifying and characterising
regional environmental patterns for use in environmental assessment and planning (Chapman and
Busby 1994).
Examples:
y Bioregions are being used in Zimbabwe for conservation planning and for erosion control
<http://www.lancs.ac.uk/fss/politics/people/esrc/pppage2.html>;
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y A New Biogeographic Regionalisation for Tasmania (Peters and Thackway 1998)
<http://www.gisparks.tas.gov.au/dp/newibra/Title&Background.htm>;
y The Australian Government is using bioregions for integrating conservation and regional
planning <http://www.deh.gov.au/biodiversity/planning/index.html>. An example is with
the Wimmera Catchment Management Authority Pilot Project (Birds Australia 2003)
<http://www.deh.gov.au/biodiversity/publications/wimmera/methods.html>.
Marine Regionalisations
Creating meaningful environmental regionalisations of marine areas is not as simple as for
terrestrial areas, however they are just as important for conservation planning.
Examples:
y The Interim Marine and Coastal Regionalisation for Australia was created using
environmental data such as bathymetry along with species data
<http://www.deh.gov.au/coasts/mpa/nrsmpa/imcra.html>;
y Global 200 Ecoregions: Marine
<http://www.nationalgeographic.com/wildworld/profiles/g200_marine.html>;
y Canada’s National Marine Conservation Areas System Plan
<http://www.pc.gc.ca/progs/amnc-nmca/plan/index_E.asp>.
Aquatic Regionalisations
Aquatic regionalisations are not as common as terrestrial or marine, but are used for managing
aquatic ecosystems
Example:
y The management of aquatic ecosystems using macroinvertebrate regionalisations (Wells et
al. 2002).
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Conservation Planning
In order to conserve biodiversity in a long-term sustainable manner, it is important to use species-
occurrence data to determine conservation priorities. It is not possible to preserve all populations of
all species on earth (Margules et al. 2002). It is not even possible to conserve representatives of all
species in traditional reserves. Biodiversity has only recently become the most important
consideration in reserve selection. Key elements of the priority setting process are complementarity,
replication, representativeness and irreplaceability.
Gaston and others (2002) identified six distinct phases in the conservation planning process. The
first of these is the compiling of data on biodiversity, reviewing existing data, collecting new data
where time and resources permit, and collecting details on locations of threatened and other priority
species in the region. The data are an essential first step, and none of the other processes will or can
operate without the relevant data.
Rapid Biodiversity Assessment
Most rapid biodiversity assessment projects require extensive amounts of species-occurrence data in
order to come up with a meaningful result. Such projects have been very expensive, and the
collection of data, and especially species-occurrence data, has been the most time-consuming aspect
of these projects (Nix et al. 2000)
Examples:
y The BioRap biodiversity assessment and planning study of Papua New Guinea
<http://www.amonline.net.au/systematics/faith5a.htm>;
y Papua New Guinea Country Study on Biological Diversity (Sekhran and Miller 1995);
y Amazonian Biodiversity Estimation
<http://www.amazonia.org/SustainableDevelopment/Jauaperi/Biodiversity/ALMA/ABDE/ABDE_3.htm>;
y Rapid biodiversity surveys in Indonesia
<http://www.opwall.com/Indonesia_biodiversity_surveys.htm>;
y Rapid Ecological Assessment in the Spanish Creek Wildlife Sanctuary in Belize
<http://biological-diversity.info/Spanish_Creek.htm>.
Identifying Biodiversity Priority Areas
Biodiversity conservation planning and assessment requires the identification of areas that represent
the biological diversity of a region, country or biome (Margules and Redhead 1995). Setting
priorities involves deciding what biodiversity to conserve and how much of each species, etc.
Examples:
y Tools for Assessing Biodiversity Priority Areas (Faith and Nicholls 1996);
y Practical application of biodiversity surrogates and percentage targets for conservation in
Papua New Guinea (Faith et al. 2001);
y Biodiversity World – conservation assessment using biodiversity modelling
<http://www.bdworld.org/index.php?option=content&task=view&id=16&Itemid=25>;
y The Biodiversity Toolbox for Local Government is designed to provide councils with the
tools, resources and contacts to integrate biodiversity conservation
<http://www.deh.gov.au/biodiversity/toolbox/index.html>;
y National Land and Water Resources Biodiversity Assessment (Identifying Priorities for
Conservation)
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<http://audit.ea.gov.au/ANRA/vegetation/vegetation_frame.cfm?region_type=AUS&regio
n_code=AUS&info=bio_asses>;
y Establishing marine priority areas <http://www.mcbi.org/marineprotected/Marine.htm>;
y Workshop on priority-setting for biodiversity conservation
<http://www.earth.nasa.gov/science/biodiversity/section_d2.html>;
y Papua New Guinea Conservation Needs Assessment (Alcorn 1993).
Reserve Selection
Once biodiversity assessment has been carried out, and priority areas for biodiversity identified, the
next step is to select appropriate areas for reserves.
Examples:
y Gap Analysis is used in Idaho in the United States for reserve selection
<http://www.gap.uidaho.edu/Bulletins/9/bulletin9/bulletin9html/aaoarsafipobanme.html>;
y The Australian Museum has a program to examine the use of genetic criteria in reserve
selection <http://www.amonline.net.au/evolutionary_biology/research/projects/gcrs.htm>;
y Another project at the Australian Museum is looking at using dung beetles as indicator
species to measure and compare genetic diversity and evaluating their use in reserve
selection
<http://www.amonline.net.au/evolutionary_biology/research/projects/ressel.htm>;
y A study in British Columbia examined sensitivities of reserve selection to decisions about
scale, biodiversity data and targets (Warman et al. 2004);
y Margules and Pressey (2000) stressed the importance of both off-reserve and on-reserve
conservation and the need to manage whole landscapes for production and protection;
y Gap Analysis and reserve selection reference list
<http://www.apec.umn.edu/faculty/spolasky/reserve.PDF>;
y Pattern analysis allows for environmental representativeness in reserve selection (Belbin
1993);
y Designing protected areas and using critical habitat corridors for giant pandas in China
(MacKinnon and De Wulf 1994).
Complementarity
The idea of complementarity is to select a set of conservation areas that together contribute a
representation of a maximum number of species (Margules et al. 1988). Complementarity is an
iterative process – for example if you are wanting every species represented, complementarity
chooses the first area with the most species, then it looks for the next area that has the most species
not already represented and so on. Species-occurrence data are essential in determining areas using
these algorithms.
Examples:
y Complementarity, biodiversity viability analysis and policy-based algorithms for
conservation (Faith et al. 2003);
y Identifying top priority areas as those that make the highest contribution to a representative
complementary set (Faith and Walker 1997);
y A new database on the distribution of vertebrate species in a tropical continent allows new
insights into priorities for conservation across Africa (Brooks 2001);
y In Oregon, reserve-selection algorithms were compared using terrestrial vertebrate data
(Csuti et al. 1997);
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y A recent whole-country planning study for Papua New Guinea illustrated the importance of
complementarity-based trade-offs in determining conservation priorities (Faith and Walker
1996) <http://www.ias.ac.in/jbiosci/jul2002/393.pdf>.
Ex-situ Conservation
Not all biodiversity conservation can occur in formally established conservation reserves. Off-
reserve or ex-situ conservation is also important and zoological and botanical gardens play an
important role in the conservation of rare and threatened species and in captive breeding programs.
Species-occurrence data are essential sources of information for institutions and individuals running
ex-situ conservation programs.
Zoological Gardens
Zoos now play a major role in conservation of rare species. Many zoos have captive breeding
programs, and some are being used to breed up populations of rare species for release back into the
wild.
Examples:
y The Przewalski horse is being bred in zoos around the world for release back into the wild
<http://www.imh.org/imh/bw/prz.html>;
y The IUCN is backing the captive breeding of foxes, wolves, jackals and dogs for
reintroduction to the wild <http://www.canids.org/1990CAP/10captvb.htm>;
y Reproductive tissue from endangered animals is being preserved in Australia for future
breeding programs <http://www.monash.edu.au/pubs/eureka/Eureka_95/freeze.html>;
y In 1995, zoological institutions around the world developed the World Zoo Conservation
Strategy <http://www.zoo.nsw.gov.au/content/view.asp?id=47>.
Botanical Gardens
Botanical gardens play a similar role to zoos, but with plants. Many rare plants are grown and bred
for release to nurseries, thus releasing pressure on wild populations, some species are reintroduced
into the wild, and others are conserved in the gardens themselves.
Examples:
y The Green Legacy - botanical gardens and conservation in Canada
<http://www.rbg.ca/greenlegacy/pages/botanical_pg2.html>;
y The growing of rare plants in Australian botanical gardens
<http://www.anbg.gov.au/chabg/bg-dir/collections.html>;
y The Weight of a Petal: The Value of Botanic Gardens (Bruce Rinker)
<http://www.actionbioscience.org/biodiversity/rinker2.html>;
y A Handbook for Botanic Gardens on Reintroductions of Plants to the Wild (Akeroyd and
Wyse-Jackson 1995);
y A Reference List for Plant Re-Introductions, Recovery Plans and Restoration Programmes
(Royal Botanic Gardens Kew) <http://www.rbgkew.org.uk/conservation/reintro.html>;
y The location of the Wollomi Pine (Wollemi nobilis) in Australia was kept secret while
botanic gardens grew stock for distribution to nurseries to reduce pressure on wild stocks
<http://home.bluepin.net.au/yallaroo/conservationandcult.htm>.
Wildlife parks
Wildlife parks – both zoological and botanical – are another place where ex-situ conservation is
occurring.
Examples:
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y The South Lakes Wild Animal Park in the UK has a large conservation program
<http://www.wildanimalpark.co.uk/>;
y San Diego Zoo’s Wild Animal Park also has some major conservation programs
<http://www.sandiegozoo.org/conservation/zooprojects.html>;
y Cleland Conservation Park in South Australia aims to conserve both animals and plants
<http://www.environment.sa.gov.au/parks/cleland/>;
y Many private sanctuaries are being established for the preservation of plants and animals
<http://www.environment.sa.gov.au/biodiversity/sanctuary.html>.
Sustainable Use
There is an increasing move towards mixing conservation and sustainable use. Not all countries can
lock up land in traditional conservation reserves, and are developing sustainable use areas ustilising
local communities and biodiversity data.
Examples:
y In South Africa, the Ezemvelo Nature Reserve is being proposed as a economically
independent conservation-based reserve that utilises its natural resources in a sustainable
manner (Sonnekus and Breytenbach 2001);
y In Costa Rica, the Guanacaste Conservation Area has been set up as a sustainable-use
reserve with the support of the local community (Janzen 1998, 2000);
y The United Nations Man and the Biosphere Programme aims to reconcile the conservation
of biodiversity with its sustainable use <http://www.unesco.org/mab/>.
Seed Banks and Germplasm Banks
The conservation of biodiversity through the long-term storage and preservation of seeds and
germplasm is another use to which species data is being put.
Examples:
y Millenium Seed Bank Project is a global collaborative project to safeguard plant species
from extinction <http://www.kew.org/msbp/>;
y The Chinese Academy of Sciences is developing a germplasm bank for wildlife of SW
China <http://english.cas.ac.cn/english/news/detailnewsb.asp?infoNo=24630>;
y GenBank Database
<http://www.psc.edu/general/software/packages/genbank/genbank.html>.
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Natural Resource Management
Improved information on biodiversity will enhance the ability of resource managers to identify
areas of high species diversity, high endemism, and exploitable resources, and improve efforts at
protecting and managing natural resources. (Page et al. 2004)
Land Resources
The need for management of land resources in a sustainable manner is becoming recognised as an
increasingly important issue. The increasing wealth of high-resolution biodiversity data is essential
for landuse planning and management decisions.
Examples:
y Natural resource management and vegetation – an overview – Australia.
<http://audit.ea.gov.au/ANRA/vegetation/vegetation_frame.cfm?region_type=AUS&regio
n_code=AUS&info=NRMV_overview>;
y Regional Land Use Plans and Land Resource Management Plans (LRMPs) in British
Columbia <http://srmwww.gov.bc.ca/rmd/lrmp/>;
y In Cuba, biodiversity data are being used to fight against desertification (Negrin et al.
2003) <http://www.unccd.int/actionprogrammes/lac/national/2003/cuba-spa.pdf>;
y Managing Natural resources in Africa and the Middle East
<http://web.idrc.ca/en/ev-3313-201-1-DO_TOPIC.html>;
y The IUCN Sustainable Use site <http://www.iucn.org/themes/sustainableuse/>;
y South African Institute for Natural Resources <http://www.inr.unp.ac.za/>.
Water Resources
Water resource management, involves sustainable management and use including the development
of water quality indicators and the biological control of weeds.
Examples:
y Population growth (with demands for agriculture and hydroelectric power) is combining
with climate change to create water stress in Africa (Schultze et al. 2001);
y The World Bank – Water Resource Management site
<http://lnweb18.worldbank.org/ESSD/ardext.nsf/18ByDocName/WaterResourcesManagement>;
y US-China Water Resource Management Program
<http://www.lanl.gov/projects/chinawater/main.html>;
y Macroinvertebrates are used as indicators of water quality (Maryland Department of
Natural Resources)
<http://www.dnr.state.md.us/streams/pubs/freshwater.html#Where%20and%20when%20a
re%20freshwater%20benthic>;
y The U.S. EPA water quality and aquatic biology program
<http://www.epa.qld.gov.au/register/p00736ad.pdf>.
Environment Protection
Environment protection covers a broad area, and is mostly thought of as protecting the environment
from human-induced pollution. But it is much broader than that, and involves protecting the
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environment from all forms of human-induced impact such as climate change, impacts of the built
environment on the natural environment, etc.
Examples:
y Australia’s Environment Protection legislation uses an on-line decision support system to
monitor impacts of development, agriculture and fishing, etc. on matters of environmental
significance such as World Heritage sites, threatened and migratory species, important
wetlands. Primary species-occurrence data are a major source of background information
for the decision support system (Chapman et al. 2001)
<http://www.deh.gov.au/erin/ert/epbc/index.html>;
y The US Environment Protection Authority uses species-occurrence data for many aspects
of environment protection <http://www.epa.gov/>.
Environmental Monitoring
Monitoring of the environment through time is an often-neglected issue, but one that is essential for
continual management of environmental resources.
Examples:
y Long-term Monitoring of Australia’s Biological Resources (Redhead et al. 1994);
y Environmental monitoring in Sweden
<http://www.svenskamiljonatet.se/cbd/eng/hav/miljoovervakning.htm>;
y University of Waterloo students collect data in forest biodiversity plots every summer as
part of a third year course in Environmental Monitoring
<http://www.escarpment.org/Monitoring/mon_forestbio.htm>;
y The Albufera International Biodiversity Group (TAIB) uses volunteers to collect data for
monitoring environmental change
<http://www.medwetcoast.com/article.php3?id_article=200>;
y Birdlife International uses biodiversity indicators for environmental monitoring
<http://www.birdlife.net/action/science/indicators/>.
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Agriculture, Forestry, Fisheries and Mining
The fields of agriculture, forestry, fisheries and mining have been among the greatest users of
primary species-occurrence data. The identification of appropriate areas for growing crops, the
identification of wild relatives of key crop species for genetic breeding, the identification of new
species for food, forestry, shelter, fibre and industrial uses, the identification of provenances for use
in planting in different areas, the identification of biological control agents for weeds and diseases,
the identification of key areas for forestry production and protection, both for plantation and native
harvesting, identification and management of fisheries production, the identification of by-catch, the
study of feeding habits, pesticides, contaminants, and the identification of possible mine sites; etc.
Agriculture
A new term, ‘agrobiodiversity’ or ‘agricultural biodiversity’, has recently been defined by Decision
V/5 of the Fifth Conference of the Parties to the Convention on Biological Diversity, as including
… all components of biological diversity of relevance to food and agriculture, and all components
of biological diversity that constitute the agro-ecosystem ” (http://www.biodiv.org). This includes
ecological services such as nutrient cycling, pest and disease regulation (natural biological control),
pollination, wildlife habitats, hydrological cycles, carbon sequestration, and climate regulation as
well as cultural aspects, including tourism (Miller and Rogo 2001).
The food industry in the United States alone is estimated to be worth $800 billion per year
(Pimental et al. 1999). All of this is based on biological species whether they are plants such as
corn, wheat, rice, soybeans, or other food crops, animals like cows, pigs and poultry, or fungi such
as mushrooms. Biological species are also used in the agricultural industry for landscape
restoration, biological pest control, sport, pets and food processing. Primary species-occurrence
databases are a key source of information for use by agriculturalists.
New crops and wild relatives
The world is always looking out for new species for use in agriculture. Primary species databases
are being used to identify wild relatives of species currently being used for agriculture, or new
species that may have been used by indigenous peoples. In addition, wild relatives of cultivated
crops are being examined for genetic transfer to control weeds, improve growth rates, reduce water
use, etc.
Examples:
y Close relatives of cultivated rice, including Oryza rufipogon, O. nivara, O. longistaminata,
and O. glumaepatula are commonly found or coexist in rice farming systems of many
Asian, African, and American countries. The use of these species in cross breeding has
been in practice for hundreds of years, and more recently biotechnology has been used to
transfer specific genes to increase levels of beta-carotene, protein content, disease and
insect resistance, herbicide resistance, and salt tolerance (Lu 2004);
y In Brazil, controlled and natural hybridisation is occurring between cassava (Manihot
esculenta) and its wild relatives. Studies are being carried out to look for, or breed, new
hybrids for improved production and fertility (Nassar 2003)
<http://www.funpecrp.com.br/gmr/year2003/vol4-2/gmr0047_full_text.htm>;
y The Desert Quandong (Santalaum acuminatum) is a plant traditionally used by Australian
aborigines. It is now being developed as a commercial food source
<http://sres.anu.edu.au/associated/fpt/nwfp/quandong/Quandong.html>.
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Provenances and wild relatives
The identification of new provenances of cultivated species has been a tradition going back many
hundreds of years. Primary species-occurrence databases can now help in that search as point
records are extracted over the Internet, allowing the identification of new populations and areas for
study.
Examples:
y In New Zealand, four new provenances of the plant Cordyline australis were selected to
examine their suitability for fructose production (Harris 1994);
y In Australia, suitable provenances of species of Acacia are being sought for use for grazing
livestock (Dynes and Schlink 2002);
y In Central Africa, germplasm of eighty-five provenances of Eru (Gnetum africanum and
Gnetum buchholzianum), species that are valued as highly nutritious green vegetables,
have been selected for genetic improvement and ex-situ cultivation and management
(Shiembo 2002) <http://www.fao.org/docrep/X2161E/x2161e06.htm>;
y Potential for Seed Gum production in Cassia brewsteri (Cunningham et al. 2001)
<http://www.rirdc.gov.au/reports/NPP/UCQ-12A.pdf>;
y Seeds for Success program in the United States is collecting seeds of species for use in
stabilisation, rehabilitation and restoration of degraded land
<http://www.nps.gov/plants/sos/>.
Food processing
The use of species in food production goes back many thousands of years with the use of yeasts in
the production of alcohols and bread, and bacteria for cheese production. For example, the many
varieties and flavours of wine come from the extensive selection of possible grapes to be fermented
and from the vast array of yeasts and bacteria that may be used. Winemakers and beer brewers are
always on the lookout for new and improved yeast varieties.
Examples:
y The Role of Yeast in Production of Alcoholic Beverages.
<http://www.botany.hawaii.edu/faculty/wong/BOT135/Lect14.htm>;
y Bacteria are used in the production and processing of sour creams, buttermilk, yoghurt,
cheese, sauerkraut, pickled vegetables, chocolate, coffee, vinegar, etc. and manufacturers
are always on the lookout for new and improved species to use to introduce new flavours
and products <http://www.bacteriamuseum.org/niches/foodsafety/goodfood.shtml>.
Harvesting of wild populations
The harvesting of wild populations of plants and animals for food and ornament is another major
industry that benefits from the availability of species-occurrence data and databases. The
harvesting of native animals is a controversial subject, but it is an industry that is important in many
developing countries. The use for forestry is considered elsewhere, but the harvesting of flowers
from wild areas is a large industry in countries like South Africa and Australia. Species-occurrence
data are used in the identification of species suitable for harvesting, and for determination of areas
with sustainable populations.
Examples:
y Wildlife harvesting in the Fynbos area of South Africa provides income for 20,000 people
(Lee 1997) <http://www.ars.usda.gov/is/pr/1997/971010.2.htm>;
y Some South American fruits and yams are grown under “semi-wild” cultivation, for
example Spondias mombin (Campbell 1996)
<http://www.hort.purdue.edu/newcrop/proceedings1996/V3-431.html>;
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y Twenty two species of animal are harvested from the wild in Africa (Ntiamoa-Baidu 1997)
<http://www.fao.org/docrep/W7540E/w7540e00.htm>;
y In Brazil, many native fruits are used for flavouring ice-creams and as fruit juices
<http://www.maria-brazil.org/brazilian_sherbets.htm>.
Beneficial Insects in agriculture
As well as their huge detrimental impact on agriculture, insects are also a important positive
contributor.
Examples:
y Honey industry profile (Saskatchewan Agriculture, Food and Rural Revitalization)
<http://www.agr.gov.sk.ca/docs/crops/apiculture/HoneyIndustry.pdf>;
y Silk Business in Iran
<http://www.iccim.org/English/Magazine/iran_commerce/no1_1999/17.htm>;
y The economics of apiculture and sericulture modules for income generation in Africa
(Raina 2000);
y Cash crops (e.g. butterflies or chemical extraction), mini-livestock (Odhiambo 1977);
y Termite nests are also used for building materials (Swaney 1999: 435);
y Species-occurrence data was used to improve pollination in Oil Palms in Malaysia
<http://www.bionet-intl.org/case_studies/case14.htm>.
Weeds and Pests
The financial impact of weeds, pests and diseases on agricultural production is enormous (Suarez
and Tsutsui 2004). Species that generally cause the greatest impact are introduced from other areas
(Pimental et al. 1999), and these are covered separately under the section on invasive species,
above. Not all pests and diseases are introduced, however, and their identification, control and
management can be important issue for farmers. Weeds for example can provide valuable food
resources for pollinating insects. Often, past clearing of land for agriculture has meant increased
grassland for grazing animals and seed-eating birds such as Kangaroos and Corellas in Australia.
Primary species-occurrence databases can be important in the identification of weeds and pests of
agriculture and for studying their distributions.
Examples:
y Some animals have adapted well to the changed landscape of Australia and their
numbers continue to increase. These include western grey kangaroos (Macropus
fuliginosus), galahs (Cacatua roseicapilla), ravens (Corvus coronoides), Australian
magpies (Gymnorhina dorsalis), corellas (Cacatua tenuirostris) and the Port Lincoln
Parrot (Barnardius zonarius). Other, related species can be very rare, so identification
is important for their management (Hindmarsh
2003).<http://portal.environment.wa.gov.au/pls/portal/docs/PAGE/DOE_ADMIN/TE
CH_REPORTS_REPOSITORY/TAB1019581/WRM33.PDF>;
y Only 5 of 43 species of macropods (kangaroos) in Australia can be harvested, and
counts are made every year to determine the numbers allowed for harvesting.
Identification is important so as to get accurate numbers and so that more threatened
species aren’t killed by mistake <http://www.dfat.gov.au/facts/kangaroos.html>;
y Correct identification of a fungus of wheat in the USA saved $5 billion/year in wheat
exports <http://www.bionet-intl.org/case_studies/case8.htm>.
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Invertebrate pests
Invertebrate pests, especially insects, cause massive losses to production every year, and are a major
cause of famine (plague locusts) in many parts of Africa and elsewhere. The identification of pests
is another role where species data plays an crucial role.
Example:
y The National Centre for Integrated Pest Management in India, has developed a program to
map the geographical distribution of all pests of major crops in the country
<http://www.ncipm.org.in/Maps.htm>;
y The International Development Research Centre is setting up an insect identification and
biosystematic service for agriculture Africa south of the Sahara
<http://web.idrc.ca/en/ev-26155-201_870175-1-IDRC_ADM_INFO.html> ;
y Intercropping increases parasitism of pests (Khan et al. 1997).
Plant and animal pathogens
There are an estimated 50,000 parasitic and non-parasite diseases of plants in the United States
alone, most of which are caused by fungus species. Mycological species databases, including living
collections, can be important for the identification and control of many of these species.
Examples:
y The Ecological Database of the World’s Insect Pathogens offers information on fungi,
viruses, protozoa, mollicutes, nematodes, and bacteria that are infectious in insects, mites,
and related arthropods <http://cricket.inhs.uiuc.edu/edwipweb/edwipabout.htm>;
y With links to primary species-occurrence databases, Kansas State University uses
geographic tools to track plant pathogens
<http://www.innovations-report.de/html/berichte/agrar_forstwissenschaften/bericht-27646.html>;
y Modelling the spatial distribution of important South African plantation forestry pathogens
(van Staden et al. 2004).
Forestry
The forestry industry is an enormous industry around the world. It is an industry that has
traditionally utilised native and wild populations, but one that is gradually moving toward
plantation forestry. Primary species-occurrence data play a role in both areas, firstly through
identifying species and areas for forest production, and attempting to balance that with
conservation, and secondly in determining what species and provenances will most suitably grow
where.
Balancing forestry and conservation
Native forest industries rely on species distribution data to find locations of new species and areas
for forest production. Species-occurrence data are also used to develop sustainable forestry
management processes through setting aside restricted areas for native harvest, and using methods
described elsewhere in this paper (see Conservation Assessment) for determining those areas to be
set aside for conservation.
Examples:
y National Indigenous Forest Inventory for South Africa (Wannenburgh and Mabena 2002)
<http://www.dwaf.gov.za/Forestry/FTIS/symp2002/inventory.doc>;
y The National Forestry Programme for Swaziland examines biodiversity values and multi-
uses of forestry land <http://www.ecs.co.sz/forest_policy/fap/index.htm>;
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y Regional Forest Agreements in Australia. Government of Tasmania & the Commonwealth
of Australia <http://www.affa.gov.au/content/output.cfm?ObjectID=89389274-95D8-
4380-BD9BB177D644820A&contType=outputs>;
y Using process-based and empirical forest models in eucalypt plantations in Brazil
(Almeida et al. 2003);
y Studies in Australia use species-occurrence data in modelling and conservation assessment
to balance forestry and biodiversity (Faith et al. 1996).
Plantation forestry
The use of plantation forestry is increasing throughout the world, and techniques are being used to
determine the most suitable location for species to be grown. Species-occurence data are linked
with environmental modelling to determine climate profiles from native areas and then applying
those profiles to areas and countries where the plantation is to be grown.
Examples:
y Matching Trees and Sites using environmental modelling (Booth 1996)
y Modelling Forest Systems. This book looks at forest models, tools and approaches to forest
modelling, including distribution modelling – some of it using species-occurrence data.
(Amaro and Soares 2003).
Provenance identification
The selection of the most appropriate provenance of a species to grow in a new plantation area is
extremely important. The selection can not only use present-day conditions, but can model and
select for future climate conditions, etc.
Examples:
y Selecting species and provenances of Australian trees for growing in Australia, China,
Thailand, Laos, Cambodia, Vietnam, Indonesia, Philippines and Zimbabwe, as well as
regions such as Southeast Asia, Africa, and Latin America (CSIRO Australia)
<http://www.ffp.csiro.au/pff/species/>;
y Matching Trees and Sites using environmental modelling examines the provenances of tree
species from Australia for planting in China and South-east Asia (Booth 1996);
y In India, new provenances of the genus Leucaena are being sought with the aim of finding
provenances that can introduce straighter stems, later flowering and lower seed set.
<http://www.forests.qld.gov.au/resadv/research/qfriconf/qfri6.htm>;
y In Vietnam, Acacia species and provenances are being selected for large-scale plantings
(Ngia and Kha 1996). Between 1982 and 1995, 18 species and 73 provenances from 5
species of Acacia were trialed at 8 localities across Vietnam
<http://www.forests.qld.gov.au/resadv/research/qfriconf/qfri6.htm>;
y Climate change studies in the UK, have concluded that new provenances of existing
species will need to be found in order that new plantations may be adapted to the warmer,
and possibly drier conditions expected in the future (Cannell et al. 1989).
Fishing
Fishing and fisheries are an important industry and user of species distribution data. With ever
increasing pressure on fishing stocks as evidenced by the decline in stocks of Cod fish in the
Northern Atlantic (Crosbie 1992, Meisenheimer 1998). Being able to track stocks and movement of
fish throughout marine and fresh waters is essential to the long-term sustainable management of
commercial fish stocks. The identification of species caught in by-catch is also important for
conservation and resource management.
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Resource management
Resource management of both marine and fresh-water fisheries is become a critical issue around the
world. A large proportion of the world’s coastal population is almost entirely dependant on the
fishing industry for their livelihood. The use of distributed data and information to make important
resource decisions is becoming increasingly important.
Examples:
y The Gulf of Maine Biogeographic Information System is developing a methodological
framework for accessing and distributing marine biogeographic data. The system will
provide information and tools for better understanding and regulating fish populations
(Tsontos and Kiefer 2000)
<http://gmbis.marinebiodiversity.ca/aconw95/aconscripts/gmbis.html>;
y The US National Marine Fisheries Service provides automated data summaries of US
commercial fisheries landings for fish and shellfish. The volume and value of landings
from 1950-2002 landings can be summarized by: years, states and species
<http://www.st.nmfs.gov/st1/commercial/>;
y FAO Species Identification and Data Programme (SIDP)
<www.fao.org/fi/sidp/products.htm>;
y Studies in the Bering Sea have examined long-term oceanic primary production and
ecosystem changes and shown significant declines in productivity by as much as 25-45%
between 1947 and 1997 (Schell 2000)
<http://www.alaskasealife.org/documents/Education/Teacher_guide.pdf>
y The identification of marine hotspots in New Zealand, allows for protection of valuable
spawning grounds <http://www.bionet-intl.org/case_studies/case25.htm>.
Overfishing
Overfishing of native stocks is becoming an ever-increasing issue. Overfishing of cod in the
northern Atlantic has caused major disruption of whole populations of people, for example on
Newfoundland where people have had to find new occupations. Species-occurrence data are used
for monitoring stocks.
Examples:
y Closure of cod fishing Action Plan (CNLBSC 2003)
<http://www.cbsc.org/nf/search/display.cfm?Code=6145&coll=NF_PROVBIS_E>;
y What is the problem with cod? (Meisenheimer 1998)
<http://www.imma.org/codvideo/whatproblemcod.html>;
y A study of the effects of fishing on deep-water fish species to the west of Britain was
carried out in the 1970s and 1980s (Basson et al. 2002).
Freshwater
Commercial freshwater fisheries are also important in many parts of the world. In many countries,
freshwater fishing is largely recreational, but commercial fishing is still an issue in those countries,
as well as in countries with large inland lakes, and large inland fishing industries.
Examples:
y Freshwater Fisheries Management Policy of the Victorian Government in Australia
<http://www.nativefish.asn.au/fwpolicy.html>;
y Fish and Fisheries of the Great Lakes Region, Canada with information on species,
ecology, etc.<http://www.great-lakes.net/envt/flora-fauna/wildlife/fish.html>;
y “Farming Freshwater Prawns” is an FAO technical paper that examines nomenclature and
distribution as well as providing a manual for culture of the Giant River Prawn
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(Macrobrachium rosenbergii).
<http://www.fao.org/DOCREP/005/Y4100E/y4100e00.htm#TOC>;
y Inland capture fisheries and enhancement: status, constraints and prospects for food
security (Coates 1995).
Bycatch
The identification and reduction of bycatch from commercial fishing is becoming an international
issue as more and more marine species are becoming endangered. The monitoring of bycatch has
become a requirement of some governments, and methods to reduce the numbers of species and
amount of bycatch have been put in place.
Examples:
y A program in the Gulf of Mexico looks at the effects of bycatch on the conservation of
fisheries resources in the Gulf (Burrage et al. 1997).
<http://www.rsca.org/docs/ib324.htm>;
y Tuna Bycatch Action Plan stresses the need for correct identification of turtles, and the
need for species identification posters and booklets.
<http://www.afma.gov.au/fisheries/etbf/mac/mac54/item3_2.pdf>;
y The CSIRO Fact Sheet on Conserving Australian Sharks and Rays also stresses the need
for “identification guides to assist in the collection of comprehensive information on
bycatch species to underpin sustainable management”
<http://www.marine.csiro.au/LeafletsFolder/53guide/53.html>.
Contaminants
The identification of contaminants in fish and their monitoring through time to determine suitability
for human consumption is another use for species-occurrence data. Fish are also good organisms for
testing of water quality through the accumulation of toxins.
Examples:
y Testing for Persistent Environmental Contaminants in Fish and Wildlife (Schmitt and
Bunck 1995);
y Integrated Fish Monitoring in Sweden (Sandström et al. 2004);
y Use of fish specimens from Richter Museum to analyse historic DDT levels in avian food
webs <http://www.uwgb.edu/davisj/biodiv/richter/resources.htm>;
y National Contaminant Biomonitoring Program of the USGS studies concentrations of
arsenic, cadmium, copper, lead, mercury, selenium, and zinc in freshwater fishes of the
United States <http://www.cerc.cr.usgs.gov/data/ncbp/ncbp.html>.
Nursery and Pet Industry
Plant nurseries
The Nursery industry is a large user of species names and thus benefits greatly from the use of
species-occurrence data. Nurseries are always looking for the names of the plants they sell, and
information on their distributions for adding to the labels.
Examples:
y The Society for Growing Australian Plants tracks name changes for informing growers and
nurseries that sell Australian plant species
<http://farrer.csu.edu.au/ASGAP/changes.html>;
y The Ornamental Plants database provides details on hundreds of cultivated plants with
names and information <http://www.msue.msu.edu/msue/imp/modzz/masterzz.html>.
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Orchids and mycorrhiza
The cultivation of many terrestrial orchids requires an association with specific mycorrhiza and
species databases can assist with the identification of these associations.
Examples:
y Many studies have been carried out at the Australian National Botanic Gardens on the
symbiotic germination of terrestrial orchid species (Clements and Ellyard 1979)
<http://www.anbg.gov.au/cpbr/summer-scholarship/2003-4-offer-clements.html>;
y In Costa Rica, studies on the relationship of mycorrhiza and orchid cultivation are being
carried out at the Lankester Botanical Gardens (Rivas et al. 1998).
Pets
The pet industry is a huge industry world wide. Pet shops, etc. require information on the names
and original localities of many of the animals they sell.
Examples:
y In the US alone, 19 million birds live as household pets <http://www.birdsnways.com/>;
y Index of exotic pets
<http://exoticpets.about.com/cs/resourcesgeneral/a/exoticpetsatoz.htm>.
Mining
The mining industry would seem to be an unlikely user of species-occurrence data, but there are
two major areas of biodiversity use in the mining industry. Some species are indicators of high
mineral concentrations and are even used in mining in some rare cases; others are used in mine site
regeneration.
Examples:
y Terminalia alata is used in India to indicate Copper mineralisation (Pujari and Shrivastava
2001);
y Phyto-mining is the use of plants to extract valuable heavy-metal minerals from soils
<http://www.ars.usda.gov/is/pr/2000/000622.htm>;
y Phyto-mining of gold in New Zealand and Brazil
<http://www.gold.org/discover/sci_indu/gold2003/pdf/s36a1355p976.pdf>;
y Phytoremediation uses plants to clean up soils
<http://www.ars.usda.gov/is/AR/archive/jun00/soil0600.htm>;
y The influence of insects on soil chemistry may even be utilised in prospecting for minerals
(e.g. Watson 1974);
y Rehabilitation of mines and other disturbed sites
<http://www.otago.ac.nz/geology/features/restoration/wangaloa/wangaloa.html>;
y Species of the genus Polycarpaea have been used to indicate copper as they generally only
grow on copper rich soils (Nicholls et al. 1965).
Mining and waste
Species-occurrence data are being used for biotechnology uses such as mining and pollution
monitoring and control.
Examples:
y Bacteria are being used to clean up toxic waste sites including nuclear sites
<http://sfgate.com/cgi-bin/article.cgi?f=/c/a/2003/07/14/MN103893.DTL>;
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y Bacteria are being used to extract ore including copper, gold and iron and in waste
management leading to cleaner mining technologies
<http://www.bioteach.ubc.ca/Bioengineering/microbialmining/>;
y Plants are used as detectors for air pollution and as scavengers of air pollutants (Omasa et
al. 2002) <http://www.cplpress.com/contents/C808.htm>;
y Lichens are used as pollution indicators <http://www.earthlife.net/lichens/pollution.html>.
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Health and Public Safety
The importance of species data and their contribution to public health and safety, although
increasing in importance, is still largely unknown by the general populace. As mentioned by Suarez
and Tsutsui (2004) species-occurrence data “play a critical role in public health and safety as
cornerstones in studies of environmental health and epidemiology”. They also play a key role in
security through their importance in the prevention, detection, and investigation of various types of
bioterrorism (NRC 2003).
Health, both human and environmental, is being impacted upon by climate change along with the
recent increase in terrorism and human, animal and plant migrations. Species-occurrence data can
contribute valuable insights into the study of pathogens, vectors of diseases, and environmental
contaminants (Suarez and Tsutsui 2004). Many diseases (human, animal and plant) are biodiversity-
related, and the distribution of both the vectors and the disease agents themselves can be studied
using species-occurrence data. When linked to biodiversity modelling programs, the potential
spread and rate of spread of some of these species can be predicted, both under present day
conditions and under altered climate change regimes, etc.
Diseases and disease vectors
Studies of the West Nile Virus in the Dominican Republic (Komar et al. 2003) examined the
presence of West Nile virus in bird species and hypothesised possible linkages to migration routes
of migratory bird species. The use of distribution modelling (Peterson et al. 2003b) successfully
tested hypotheses that West Nile virus transmission on large geographic scales was by migratory
birds, and using this information in conjunction with a simulation model allowed for new outbreaks
and spread to be predicted (Peterson et al. 2003b).
Many other viruses are also transmitted by vectors, and entomological collections around the world
include many records of mosquitoes which are responsible for the transmission of diseases,
including malaria, avian malaria, dengue fever, equine encephalitis, and the already mentioned
West Nile virus.
Species-occurrence data have also been used to construct evolutionary histories of viruses in order
to develop more robust vaccines (Ferguson and Anderson 2002), to study the origins of HIV
(Siddall 1997), to study the origins and track the movement of Avian Influenza (Bird Flu) in native
and domestic bird populations (Perkins and Swayne 2002) and studying possible cross-
susceptibility of the Rabbit CaliciVirus (RHD) in other animals (Munro and Williams 1994).
In addition, we now have the issue of emerging infectious and parasitic diseases, and the need to
document transmission patterns. This cannot be done without species-level identifications of both
adults and infective stages (larvae/juveniles) (Brooks and Hoberg 2000).
Examples
y West Nile Virus (Komar et al. 2003).
<http://www.specifysoftware.org/Informatics/bios/biostownpeterson/Ketal_EID_2003.pdf>;
y Mosquito-borne diseases (Rutgers University and CDC)
<http://www.rci.rutgers.edu/~insects/disease.htm>;
y Rabbit Haemorrhagic Disease (Munro and Williams 1994);
y Origins of HIV (Siddall 1997).
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Bioterrorism
A key role in the use of species-occurrence data in controlling terrorism is in tracking the history of
infectious diseases and in identifying their sources. Among some of the most important public
health-related collections of species-ocurrence data are the examples of known viruses and bacteria
that are retained and used for comparison with outbreaks of new infections. A recent example of
their use was with the anthrax attack on the United States in 2001 where researchers at various
Centers for Disease Control and Prevention used specimen collections from the 1960s and 1970s to
attempt to identify the anthrax strains used (Hoffmaster et al. 2002).
One of the identified challengers to the museum community in the face of national threats of this
nature is to be able to provide swift and accurate identifications of possible bioterrorism agents
(Page et al. 2004).
Examples:
y Anthrax attack on the United States 2001 (Hoffmaster et al. 2002);
y Biological terrorism Risk Assessment (University of Kansas, Biodiversity Research
Center) <http://www.specifysoftware.org/Informatics/informaticsbtra/>.
Biosafety
The flow of genes from modified organisms to their wild relatives is a recognised risk associated
with genetically modified crops (Soberón et al. 2002). As noted by Soberón et al., the risk is
greatest when a crop “spontaneously hybridises with its taxonomically related species”. Species-
occurrence data are a necessity if scientists are going to be able to assess these risks by tracking
spatial relationships between GMO crops and wild relatives, their potential distributions under
various climatic conditions, and the reproductive biology of both groups of plants (Soberón et al.
2002).
Examples:
y The Mexican Comisión Nacional para el Conocimiento y Uso de la Biodiversidad
(Conabio) (http://www.conabio.gob.mx/), is using species-occurrence data obtained from
herbaria around the world to study and model potential distributions, and to study the
likelihood of genetic transfer (Soberón et al. 2002). This information is used several times
a week to inform the Mexican Ministry of Agriculture (Soberón pers. com. Aug. 2004).
Environmental Contaminants
The monitoring of environmental contaminants in natural populations is another important health-
related use for primary species-occurrence data. An example is the use of the Swedish Museum of
Natural History’s Environmental Specimen Bank to monitor contaminants in faunal species and to
study the effects of noxious substances on endangered and threatened species. Another example is
the tracking of pesticides, fungicides, etc. in streams through studying contaminants in populations
of native amphibia. In conservation studies on the Californian Condor (Gymnogyps californianus),
it was found that contamination with lead (and possibly DDT) were major causes of its decline
towards extinction through increased mortality (Janssen et al. 1986). Museum collections have been
used to examine lead and DDT levels through both time and space (Ratcliff 1967). Other studies
have looked at increasing mercury levels in marine ecosystems by examining mercury levels in the
feathers of seabirds breeding in various areas of the world and compare the levels achieved with
historic specimens from the same localities held in natural history museums (Monteiro and Furness
1998, Thompson et al. 1998). Birds accumulate heavy metals from their food and secrete them into
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their growing feathers during molt (Green and Scharlemann 2003). Long-term changes and spatial
variation in heavy metal concentrations can easily be studied using such collections.
Examples:
y Environmental Specimen Bank (Swedish Museum of Natural History)
<http://www.nrm.se/mg/mpb.html.en>;
y Environmental Contaminants of Amphibians in Canada (Froglog 16: 1996)
<http://www.open.ac.uk/daptf/froglog/FROGLOG-16-5.html>;
y Mercury in Feathers from Birds of the Southeastern Pacific: Influence of Location and
Taxonomic Affiliation
<http://cars.er.usgs.gov/posters/Ecotoxicology/Mercury_in_Bird_Feathers/mercury_in_bir
d_feathers.html>.
Antivenoms
Snakebite and spider bite are common in many parts of the world, and nowhere more so than
Australia where more than 3000 cases are reported annually (Queensland Museum 2004). Many of
the world’s most venomous snakes are found in Australia. The accurate identification of a snake
responsible for a bite allows for the correct antivenom to be administered. Species-occurrence data
can limit the areas for which specific antivenoms may need to be stored, and assist in quicker
identification of the snake through geographic sifting. This can be important from both from a
health point of view, and because of cost. An ampoule of polyvalent antivenom (a cocktail of
separate antivenoms) costs $1600 in Australia, compared to $300 to $800 (depending on the species
of snake) for an ampoule of specific antivenom (Queensland Museum 2004). Victims of snakebite
may require up to eight ampoules of antivenom, so the cost saving of an accurate identification can
be significant, and in addition there are significant health benefits.
Examples:
y Queensland Museum antivenom project
<http://www.qmuseum.qld.gov.au/features/snakes/saving.asp>.
Parasitology
Parasites are becoming recognised as significant components of the environment and are good
models for evolutionary studies (Brooks and Hoberg 2001). Parasites are agents of disease in
humans, domestic livestock and native wildlife, and maintain a significant role in ecosystem
integrity and stability (Brooks and Hoberg 2000). Parasite collections have traditionally been held
in large personal collections and have thus been less available to researchers than they may
otherwise have been (Hoberg 2002). This is now being rectified with new distributed systems like
the GBIF Portal. Specimen-based data can serve as historical and temporal baselines for
understanding environmental change and human intervention on the distribution of parasites and
pathogens (Hoberg 2002).
Examples:
y The United States National Parasite Collection (USNPC) is providing a major resource for
systematic, taxonomic, diagnostic ecological and epidemiological research
<http://www.anri.barc.usda.gov/bnpcu/>;
y The distributions of rodents have been used to study reservoirs and vector sites for a range
of parasitic diseases, including Lyme disease – a parasitic disease transmitted to humans
via tick bite, Lassa fever in Africa associated with multimammate rats, various hanta
viruses in Argentina and Chile (Mills and Childs 1998)
<http://www.cdc.gov/ncidod/eid/vol4no4/mills.htm>;
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y Parasites are being used in studies of evolutionary biology (Dimigian 1999)
<http://www.baylorhealth.edu/proceedings/12_3/12_3_dimijian.html>;
y Epidemiology of amoebiasis: an age-old problem solved by taxonomy
<http://www.bionet-intl.org/case_studies/case1.htm> .
Safer Herbal Products
Many new herbal medicines are becoming available and being sold through pharmacists and health
stores. The safety and purity of these medicines needs to be monitored and tested. To this
information on their geographic distribution can be important.
Examples:
y Authentication of Chinese herbal medicines helps to deliver safer medicines
<http://www.bionet-intl.org/case_studies/case3.htm> ;
y Testing and standardisation of herbal medicines
<http://www.frlht-india.org/html/lab.htm#testingmedicines> .
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Bioprospecting
Bioprospecting is the search for, and identification of, plants and animals that may provide products
with potential economic value, such as new pharmaceuticals, foods, and other as yet-undiscovered
uses. Species-distribution data are needed to assist in determining sites and likely species and
requires taxonomic and phylogenetic research and distributional information from natural history
collections (Page et al. 2004).
Pharmaceuticals
For centuries, plants and animals have been the source of healing products. Today, they are the
basis of many of the world’s pharmaceutical drug products. Primary species data are used to
identify relatives of species that are already sources of active products and to find locations of those
and other species for assay.
Examples:
y In Costa Rica, the National Biodiversity Institute (Inbio) is a major player in
bioprospecting for pharmaceutical products in the forests of Costa Rica (Janzen et al.
1993) <http://www.inbio.ac.cr/en/>;
y Natural products research, especially novel chemical aspects of insect-plant interactions
and arthropod venoms in Africa (Iwu 1996; Torto & Hassanali 1997; Weiss and Eisner
1998);
y Using plants to produce pharmaceuticals (Council for Biotechnology Information)
<http://whybiotech.ca/canada-english.asp?id=3352>;
y In Brazil, the FAPESP-Biota program is funding a project to examine plants of the Mata
Atlantica (Coastal rainforest) and Cerrado (savannah) for chemical and pharmacological
products <http://www.biota.org.br/projeto/index?show+229>;
y The Amazon Rainforest is a source for present and future drugs <http://www.rain-
tree.com/>;
y Ants as a source of pharmaceuticals (Majer et al. 2004)
y Plant-derived Drugs: Products, Technology, Applications
<http://bcc.ecnext.com/coms2/summary__0002_001960_000000_000000_0002_1>;
y Chemotaxonomy of Xylariaceae uses bioprospecting to attain information on species of
fungus. <http://pyrenomycetes.free.fr/xylariaceous/keydir/chemotaxonomy.htm>;
y Screening for bioactive compounds from Fungi using PCR (Polymer Chain Reaction)-
based data (Stadler and Hellwig 2005).
y In Australia, chemical prospecting for pharmaceuticals in molluscs is being studied as a
tool for conservation (Benkendorff 1999)
<http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20011204.154039/>;
y The mining for biodiversity products can be carried out in conjunction with deep sea
mining <http://www.theworx.com/deepsea/mining.html>;
y Herbal medicines <http://hcd2.bupa.co.uk/fact_sheets/html/herbal_medicine.html>.
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Forensics
Primary species-occurrence data are a source of information for use in forensic research. Forensic
science is based on protocols that require accurate identifications of organisms and precise
distributional information (Page et al. 2004). Collections in natural history museums contain a
massive store of DNA information that can be used in profiling and in determining locations, etc.
Gene Fragments
The identification of genetic fragments using DNA and comparing that with information held in
museums or primary species databases is a key use in forensics.
Examples:
y Gene fragments were used to track rhino poachers by looking for genetic signatures in
products such as powdered Asian medicines and Yemeni ornamental daggers. Fragments
were able to identify not only the species, but individual game reserves that the horn came
from. New Scientist 2411 (2003).
<http://www.newscientist.com/article.ns?id=mg17924110.700>;
y Blood evidence from dogs has been used to convict murderers and rapists
<http://www-ucdmag.ucdavis.edu/sp02/feature_2.html>;
y Analysis of DNA from an asthma inhaler was used to identify the administration of
performance enhancing drugs to a race horse
<http://www-ucdmag.ucdavis.edu/sp02/feature_2.html>;
y Forensic DNA sampling has established that an introduced colony of tammar wallabies
living on Kawau Island, in New Zealand, is almost certainly comprised of the descendants
of a wallaby subspecies that vanished from mainland South Australia in the early 1900s.
The subspecies is now being reintroduced to its original location
<http://www.bio.mq.edu.au/school/mag/intro/98bytes/may98/Bytes_May98.html>;
y DNA evidence is commonly used to convict for illegal trade in endangered species
<http://genetics.nbii.gov/forensics.html>;
y DNA was used to identify contraband meat smuggled into the USA as red colobus
monkeys (Nash 2001).
Plant material
The identification of plant material and the use of herbarium collections to identify them, is used in
legal cases involving endangered species – plants that are the source of rugs, plants that help
identify the scene of the crime, etc. Herbs and grasses on clothing can track the movement of
criminals, or the origin of illegally transported objects, etc. Only by comparison with known
material can definitive locational and taxonomic information be determined.
Examples:
y By using a mass spectrometer to measure the ratios of carbon-12 to carbon-13, and
nitrogen-14 to nitrogen-15, species of rhinoceros were identified in tracking poachers. The
ratios vary depending on diet, and reveal whether horn came from white rhinos, which eat
grasses, or black rhinos, which eat herbs and woody plants. Also by using optical emission
spectrometers, the ratios of common trace elements such as iron and copper can identify
locations where the material may have arisen New Scientist 2411 (2003).
<http://www.newscientist.com/article.ns?id=mg17924110.700>;
y The identification of plant material, including cannabis is a common forensic use;
y The identification of leaves and fruits that may be found at a murder scene, or in a suspects
car, etc. can help lead to a conviction <http://www.sfu.ca/biology/faculty/mathewes/>;
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y The identification of plant parts in the intestinal tract of victims can aid in homicide
investigations (Norris and Bock 2001);
y The identification of plant materials can be important in solving crimes (Lane et al. 1990).
Pollen
The pollen provides a key identification resource for use in forensic palynology. Forensic
palynology is the study of pollen and powdered minerals. Their identification and location can be
used to ascertain that a body or other object was in a certain place at a certain time.
Example:
y The Swedish Museum of Natural History maintains an international slide collection with
more than 25000 pollen samples of different plant families
<http://www.nrm.se/pl/samling.html.en>;
y The background and use of environmental profiling and forensic palynology (Wiltshire
2001) <http://www.bahid.org/docs/NCF_Env%20Prof.html>;
y The first conviction that used pollen analysis was in Austria in 1959. Pollen was used to
identify a location where a body was buried using pollen in the mud on a suspect’s boots
<http://www-saps.plantsci.cam.ac.uk/osmos/os23.htm>;
y Pollen was used to identify the origin of a shipment of stolen Persian Rugs, although lack
of suitable comparative species-occurrence data from Iran led to a failure to convict
(Bryant and Mildenhall 2004) <http://www.crimeandclues.com/pollen.htm>.
Insects
Forensic entomology is used extensively to identify the time elapsed since the death of victims
(Post-mortum Interval - PMI), to study whether bodies have been moved since death, to detect
chemicals and poisons in bodies through the study of maggots, to track the movement of vehicles,
and to determine the source of pest outbreaks (using houseflies and lesser houseflies) for city
councils and health departments.
Examples:
y The use of forensic entomology
<http://www.expertlaw.com/library/attyarticles/forensic_entomology.html>;
y Insects in legal investigations <http://www.forensic-entomology.com/>;
y The American Board of Forensic Entomology
<http://www.missouri.edu/~agwww/entomology/>;
y Coleoptera and their significance in forensic entomology
<http://www.beetlelady.com/hister.html>;
y Correct taxonomic identification of many insects and other Arthropoda can provide vital
clues to the time and location of a death
<http://www.bionet-intl.org/case_studies/case24.htm>
y The use of insects for determining Post-mortum Interval <
http://www.absoluteastronomy.com/encyclopedia/F/Fo/Forensic_entomology.htm>;
y The use of maggots to determine time of death and to detect poisons and chemicals <
http://www.benecke.com/suntel.html>.
Bird and Mammal Strikes
Bird strikes are a major problem with the safety of aircraft, etc. (Bird Strike Committee of the USA-
<http://www.birdstrike.org/events/signif.htm>. The identification of these birds is essential to
preventing future strikes, and species-occurrence data is an important tool in these identifications.
Mammal strikes (e.g. large animal strikes with trains and road transport, etc.) can also be a problem
in some areas.
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Examples
y Bird Identification from the Smithsonian Institution (Dove et al. 2003).
<http://wildlife.pr.erau.edu/BirdIdentification.htm>;
y Bird/Wildlife Strike Report Database, Environment Canada.
<http://www.tc.gc.ca/aviation/applications/birds/en/default.asp>;
y Bird Strike Links from the International Bird Strike Committee
<http://www.int-birdstrike.com/links.html>;
y German Bird Strike Committee (includes BIRDTAM). <http://web.tiscali.it/birdstrike/>;
y Bird Remains Identification System (BRIS) (Zoological Museum, Amsterdam)
<http://www.christ-media.de/cgibin/auswahl.cgi?basket=180757&wahl=___2454629>;
y Effect of bird strikes and the Bird Strike Information System (IBIS)
<http://www.icao.int/icao/en/jr/5308_ar1.htm>.
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Border Control and Wildlife Trade
Wildlife trade is a large industry, but one that invites illegal activities. Border control is used to
prohibit the entry into countries of diseases, illegally traded wildlife such as endangered species, or
products from endangered species such as ivory, pests such as might be transported unintentionally
in wooden products, drugs, etc. Species-occurrence data are used to provide border control agents
with identification tools and means of identifying illegally traded and imported goods and to help
them determine where they originated.
Border Controls and Customs
It is difficult for customs officers to know what is being illegally traded or not – what are pests that
are prohibited etc. without good identification tools and access to primary species-occurrence data.
CITES
The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES)
(http://www.cites.org/) aims to ensure that international trade in specimens of wild animals and
plants does not threaten their survival. There are many listed species and groups of species, and it is
difficult for customs officers to identify what might be an endangered species or not, and especially
if a manufactured product or food has been derived from a CITES listed species.
Examples:
y Illegal bear parts seized by Customs Australia
<http://forests.org/articles/reader.asp?linkid=32880>;
y Federal agents target illegal bird trade
<http://www.internationalparrotletsociety.org/smuggle.html>;
y Illicit trade in orchids and wild plants (Cites World No 9, July 2002)
<http://www.cites.org/eng/news/world/9.pdf>;
y An illegal shipment of 9,300 live turtles was made in Hong Kong (Traffic Bulletin vol. 19
2002) <http://www.traffic.org/bulletin/Nov2002/seizures3.html>;
y CITES Identification tools and Guides <http://www.cites.ec.gc.ca/eng/sct5/sct5_1_e.cfm>;
y Controlling the Shahtoosh trade in Tibet
<http://www.met.police.uk/wildlife/new%20site%20docs/docs/shah.htm>;
Illegal Fishing
Illegal fishing is of major concern to most maritime countries. Many of the species taken are CITES
species, but others not.
Examples:
y Ecuador seizes illegal Galápagos Island shark fins
<http://www.planetark.com/dailynewsstory.cfm/newsid/22244/newsDate/16-Sep-2003/story.htm>;
y Illegal fishing threatens Galápagos Islands Waters
<http://news.nationalgeographic.com/news/2004/03/0312_040312_TVgalapagos.html>;
y Illegal fishing continues to grow (FAO)
<http://www.fao.org/newsroom/en/focus/2004/47127/>.
Drugs
Drugs and drug interception is another role for border control agents. The identification of drug and
drug products is another use for primary species data.
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Examples:
y Indian authorities have developed a database of Indian Medicinal Plants and species being
traded as botanical drugs <http://www.frlht-india.org/html/crg.htm>;
y Regulating export of endangered medicinal plant species–Need for scientific rigour (Ved
1998) <http://www.ias.ac.in/currsci/aug/articles8.htm>.
Quarantine
Pests and Diseases
The importation of diseases and pests is of major interest and importance to agricultural industries
as well as the general public. Again, the identification of pests and diseases can often be a problem
for border control agents.
Examples:
y “Interception of potential agricultural, forest or medical pest species at U.S. borders will be
greatly facilitated by access to a distributed network of taxonomic resources” (Page et al.
2004);
y Nematodes threaten US farmers <http://www.hqusareur.army.mil/opm/aug04.htm> and
Mexican pecans
<http://southwestfarmpress.com/mag/farming_nematodes_threaten_new/>;
y Please... don't bring pests or diseases with you to Australia
<http://www.aust-immig-book.com.au/in_quarantine.html>;
y Australian Plant Pest Database <http://appd.cmis.csiro.au/>;
y In Namibia, identififcation of fruit flies allowed for more effective bilateral trade
<http://www.bionet-intl.org/case_studies/case6.htm>.
Imported pets
The migration of people also means that pets are being transported across borders. Quarantine
authorities need to monitor these for illegal importation, diseases, etc.
Wildlife Trade
Not all trade in wildlife is illegal, but controls of export and import permits requires knowledge and
information on what species are being traded, and this requires primary species-occurrence data.
Examples:
y Wildlife trade and conservation in Australia
<http://www.deh.gov.au/biodiversity/trade-use/index.html>;
y As part of its Wildlife Conservation Program, WWF Guianas is working with wildlife
exporters and local governments to ensure that trade in wildlife is properly managed and
based on the best scientific knowledge available. New Wildlife ID Manual
<http://www.wwfguianas.org/Wildlife_IDman.htm>;
y Seahorses as wildlife trade – identification manuals
<http://www.worldwildlife.org/trade/seahorses.cfm>;
y EU faces challenges in controlling Europe’s demand for wild animals and plants
<http://www.traffic.org/news/enlarge_european.html>.
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Education and Public Outreach
Education at all levels; along with public outreach are regular uses for primary species-occurrence
data.
School level education
School level education at all levels benefits from integration with museums as well as being
involved in school-level biodiversity data projects.
Examples:
y Museum School Partnership program (Doctoral Dissertation) (King 1998)
<http://home.iag.net/~ksking/muslearn.html>;
y The GLOBE Program – hands on education and science program
<http://www.globe.gov/globe_flash.html>;
y The Waterwatch program in Australia is a program conducted between museums,
government, schools and the community to carry out biodiversity and habitat assessments
of wetlands in their area <http://www.waterwatch.org.au/>;
y The Natural History Museum in London has an extensive education program – Exploring
Biodiversity <http://internt.nhm.ac.uk/eb/messages/probbrowser.shtml>;
y In America, the National Zoo Biodiversity Monitoring Project works with school children
to survey and monitor biodiversity in their area
<http://nationalzoo.si.edu/Publications/PressMaterials/BMPSchoolProjects.cfm>;
y In Hungary, the Toad Action Group monitors amphibians with the aid of school children
<http://www.virtualfoundation.org/publicboard/display.cgi?_Hungarian_amphibian_biodiv
ersity_monitoring_EPCE_Hungary+archive>;
y In England, as part of the Stag Beetle Biodiversity Action Plan, schools were involved in
recording and mapping the location of stag beetles across the country
<http://www.lbp.org.uk/03action_pages/ac30_comms8.html>;
y Biodiversity for kids’ teacher’s kit
<http://www.bookshop.nsw.gov.au/pubdetails.jsp?publication=3403>.
University level education
Universities are the training centers for the world’s biodiversity specialists and most maintain
museum and herbarium collections, and collect species-occurrence data as part of many of their
courses.
Examples:
y Duke University hosts undergraduate students in a summer research program
Bioinformatic and Phylogenetic Approaches to the Study of Plant and Fungal Biodiversity.
http://www.biology.duke.edu/reu/
y The Xishuangbanna Tropical Botanical Garden in China runs a graduate student training
courses in Asia in conjunction with a number of international universities
http://www.xtbg.ac.cn/english/PDF/gsxtbg.pdf
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Training of Parataxonomists
The training of local peoples to be parataxonomists, requires extensive primary species data,
including information on names, distributions, and often good image databases.
Examples:
y Training programs for parataxonomists have been developed by the National Biodiversity
Institute (Inbio) in Costa Rica for use in the Guanacaste Conservation Area (Janzen et al.
1993, Janzen 1998);
y Training of local indigenous people has been carried out with insects in the Madang region
of Papua New Guinea and in Guyana (Basset et al. 2000);
y In Hawaii parataxonomists are trained using insect processing by the Bishop Museum
<http://www.bishopmuseum.org/research/natsci/guyana/LOGGING4.HTM>;
y Brazilian Pollinators Initiative <http://www.mma.gov.br/port/sbf/chm/doc/pollinas.pdf>;
y Taxonomic tools allow rapid problem solving by non-specialists
<http://www.bionet-intl.org/case_studies/case5.htm>.
Public awareness
The public are increasingly aware and becoming involved in their local environment (see also
public participation programs below). Many organizations are now attempting to make it easier for
people to find out about their natural environment and what is in it. This can be as simple as making
available guidebooks so that people can identify the birds that visit their gardens, through to much
more detailed environmental descriptions of their local areas.
Examples:
y The National Biodiversity Network (NBN) aims to make it easier for people to find out
about their natural environment <http://www.nbn.org.uk/>;
y The North Australian Frogs Database System (Frogwatch) provides information to the
public about frogs, cane toads and frog diseases to the Northern Territory public
<http://www.frogwatch.org.au/>;
y The Biodiversity Conservation National Strategy and Action Plan of Uzbekistan aims to
increase public awareness in biodiversity
<http://bpsp-neca.brim.ac.cn/books/actpln_uzbek/>.
Books and materials
The publication of books and materials – local guide books to plants and animals, posters, screen
savers and calendars all help in improving public awareness of biodiversity. Primary species-
occurrence data are essential in helping develop these materials.
Examples:
y Australian mammals poster
<http://www.bookshop.nsw.gov.au/pubdetails.jsp?publication=492>;
y Fish Posters of the World <http://www.fishposters.com/index.html>;
y Animal Posters <http://www.realtime.net/~raintree/gallery/posters.htm>;
y Animal Screen Savers <http://www.tnpsc.com/ssaver/animals.htm>;
y NatureBase Screensavers of Western Australia
<http://www.calm.wa.gov.au/screensavers/>;
y Wildlife calendars from Africa
<http://www.wildlife-pictures-online.com/wildlife-shopping-1.html>;
y Lifemapper screensaver produces distribution maps
<http://www.npaci.edu/online/v6.14/lifemapper.html>.
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Museum displays
Museum displays are a major source of education and public awareness. In recent years, museum
displays have taken on the education role with increased vigour. Primary species-occurrence data
play a key role in the development of these displays.
Examples:
y As early as 1995, the Field Museum saw benefits of automating collections records beyond
scientific research. The integration of audio and textual data with visual images allows
people to see exhibits from different museums and consider alternative interpretations from
their homes or offices (Cohn 1995).
y North Carolina Nature Museums and Science Centers
<http://www.unc.edu/depts/cmse/museums.html>;
y Australian Museum “What’s on” <http://www.austmus.gov.au/visiting/whatson/>.
Image Databases
Image databases are a valuable resource for development of virtual reference systems and on-line
identification tools for biodiversity assessment (Oliver et al. 222). For example, by linking to an
on-screen reference system of insect specimen images, several parataxonomists working on the
same taxon in remote laboratories can make identifications simultaneously, limiting the need for
repeated handling and damage to valuable reference specimens (Oliver et al. 2000).
Examples:
y High-definition images are a core component of an on-line invertebrate identification
network being established at the Macquarie University in Sydney (Oliver et al. 2000);
y Australian Plant Image Database <http://www.anbg.gov.au/anbg/index-photo.html>;
y Type Photos at the New York Botanic Gardens
<http://sciweb.nybg.org/science2/hcol/vasc/index.asp>;
y Woodpecker images and sounds
<http://www.infochembio.ethz.ch/links/en/zool_voegel_spechte.html>;
y Natural History image collections on the Web
<http://www.ucmp.berkeley.edu/collections/otherother.html>;
y Digital Orthoptera Specimen Access (DORSA) <http://www.dorsa.de/>;
y Australasian Bird Image Database <http://www.aviceda.org/abid/>;
y Imagens da Biodiversidade Brasileira <http://imagem.cria.org.br/>;
y Digital Florilegium – part of the New Endeavour project
<http://www.invisible-consulting.com/endeavour/flora.php>;
y Google Images <http://www.google.com>;
Public Participation Programs
Public participation conservation programs are becoming popular events. These can involve
assistance in managing a river catchment area for conservation, water use and production;
community planting of degraded areas; or conducting community-based conservation assessment.
Examples:
y The Calabash Program in Africa is a program to improve public participation in
environmental assessments in Southern Africa
<http://www.sarpn.org.za/documents/d0000772/index.php>;
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y The Inter-American Environment Program of the Environment Law Institute is supporting
and encouraging public participation in protecting landscapes in Argentina and in
Conserving Community Lands in Mexico
<http://www2.eli.org/research/interamerican2.htm>
y In Australia, the Federal Government funds community organizations to plant up areas of
land degradation, high erosion, develop wildlife corridors, etc. Primary biodiversity data
are used to identify suitable plant species and areas for planting
<http://www.landcareaustralia.com.au/>;
y Again in Australia, Integrated Catchment Management Plans, sees community groups
work closely with State and Federal Governments to plan and implement management
plans for managing the resources, including water and biodiversity, and to balance that
with agricultural production <http://www.dlwc.nsw.gov.au/community/index.html>;
y In Connecticut, in the United States, in the BioBlitz, program scientists work with
community groups to carry out a rapid biodiversity assessment of local areas over intensive
weekend programs (Lundmark 2003) <http://www.mnh.uconn.edu/BioBlitz/>;
y In the UK, the Natural History Museum the Walking with Woodlice project uses schools,
local clubs, and individuals to survey UK woodlice
<http://www.nhm.ac.uk/interactive/woodlice/biodiversity.html>;
y The Alcoa Frogwatch Program aims to involve a large number of people of all ages in
actively helping to increase the quality of large-scale frog habitat
<http://frogs.org.au/frogwatch/>;
y Total Catchment Management – public participation
<http://www.dlwc.nsw.gov.au/community/index.html>;
y National Biodiversity Network’s Local Records Centers
<http://www.nbn-nfbr.org.uk/nfbr.php>.
Tree of Life
The Tree of Life Web Project and similar collaborative projects provide information about the
diversity of organisms on Earth, their history, and characteristics.
Examples:
y Tree of Life <http://tolweb.org/tree/phylogeny.html>;
y Diptera species pages <http://www.diptera.org>.
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Ecotourism
Ecotourism is rapidly becoming one of the largest sources of income for many biodiversity-rich
countries. UNEP recognises ecotourism as of special interest because of the role it can play in
conservation, sustainability and maintenance of biological diversity
(http://www.uneptie.org/pc/tourism/ecotourism/home.htm). Primary species-occurrence data are
important in the development of good ecotourism programs – in the development of guidebooks,
pamphlets, and information products and in helping countries determine suitable areas for use as
ecotourism sites.
Valuing Ecotourism
One of the pressures against ecotourism is being able to put a value on biodiversity, conservation
and ecotourism as an alternative to consumption and more intensive uses. But in many ecotourism
projects, ecotourism and production can work side by side.
Examples:
y Valuing a tree for ecotourism
<http://www.nuevomundotravel.com/nuevomundo.php?c=129>;
y Valuing ecotourism in the Sierra Tarahumara region in Mexico
<http://www.srs.fs.usda.gov/econ/research/std43_8.htm>;
y Valuing Ecotourism as an Ecosystem Service (The Nature Conservancy)
<http://nature.org/event/wpc/files/drumm_presentation.pdf>;
y The Economics of “Eco Tourism”: A Galapagos Island Economy-wide Perspective (Taylor
et al. 2002) <http://www.reap.ucdavis.edu/working_papers/jet-galapagos.pdf>.
Training Guides and Operators
The training of tour guides and tourism operators in understanding biodiversity is an area where
primary species-occurrence data play a key role. Quite often, reference collections are made and
kept at ranger stations, and carried by guides, and these require primary species data for
identifications and training.
Examples:
y Eco-certified ecotourism in Australia
<http://www.ecotourism.org.au/eco_certification.asp>;
y Ecotourism certification workshops
<http://www.planeta.com/ecotravel/tour/certification.html>;
y Ecotourism Training Manual for Protected Area Managers (Strasdas 2002);
y Training Manual for Community-based Tourism (Inwent Zschortau, Leipzig, Germany)
(Hausler and Strasdas 2003).
Guide Books
Guidebooks, pamphlets and other publications are an essential part of ecotourism and like
guidebooks mentioned elsewhere are dependant upon species-occurrence data for their preparation.
Examples:
y Examples can be found in any bookshop or on the web of tour guidebooks, and most have
an ecotourism section;
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y A Guide to the Birds of Panama (Ridgely and Gwynne 1989);
y Costa Rica’s National Parks and Preserves: a visitor’s guide (Franke 1999).
Gardens, Zoos, Aquariums, Museums and Wildlife Parks
Botanical gardens, zoos, aquariums, wildlife parks and museums all play a part in ecotourism.
Many new aquaria, for example include an underwater viewing area with access to the open sea.
Most botanic gardens, zoos and wildlife parks maintain displays of the fauna and flora of the local
regions and museums usually have extensive natural history displays. Most of these also have an
education component. The labelling and information attached to these exhibits requires good data
and information to prepare and maintain, including the names of the organisms involved and their
distributions.
Examples:
y Monterey Bay Aquarium <http://www.mbayaq.org/>;
y Kirstenbosch National Botanical Garden <http://www.nbi.ac.za/frames/kirstfram.htm>;
y Jurong Bird Park, Singapore <http://www.birdpark.com.sg/Main/>;
y Jersey Zoo and Durrell Wildlife Conservation Trust <http://www.durrellwildlife.org/>;
y Smithsonian National Museum of Natural History <http://www.mnh.si.edu/>;
y Virtual Library: Museums around the world <http://vlmp.museophile.org/world.html>.
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Art and History
Art has played an integral role in understanding and conservation of biodiversity. Most early
scientific expeditions included an artist amongst their entourage to record the biodiversity. Today,
artists continue to paint nature, and seek information on the names and locations of the subjects they
paint. History is also a user of primary species-occurrence data. Early explorers were also natural
historians and collected biodiversity specimens. With many centenaries and bicentenaries of these
explorations coming up, many researchers are attempting to trace the steps of these early explorers
and species-occurrence data are a major source of information for them.
History of Science —Tracking Explorers and Collectors
Early and modern explorers and scientists have deposited voucher specimens in natural history
collections. “These specimens document the paths and objectives of the explorers and scientists
over the centuries and provide a unique and irreplaceable source of historical data” (Page et al.
2004). As collections have aged, the year in which they were collected has become increasingly
important (Winker 2004).
Examples:
y Nature's Investigator: The Diary of Robert Brown in Australia 1801-1805 (Vallance et al.
2001);
y Identifying collection patterns using Mexican bird specimens (Peterson et al. 1998);
y The New Endeavour is a project to revisit the landfalls of Captain James Cook's voyage in
HMS Endeavour (1768-1771) http://www.invisible-consulting.com/endeavour/
y History of systematic botany in Australasia (Short 1990);
y Plant collectors in Brazil (Koch 2003) <http://splink.cria.org.br/collectors_db>;
y Lewis and Clarke Expedition in America
<http://www.cr.nps.gov/nr/travel/lewisandclark/encounters.htm>;
y Australian Plant Collectors and Illustrators 1780s-1980s
<http://www.anbg.gov.au/bot-biog/index.html>.
Art and Science
As mentioned above, art played an important part in early scientific discoveries. There were no
cameras around and paintings were the only representation available of many plants and animals.
Some early artist’s interpretations of plants and animals was so detailed that many regard them as
superior to many modern photographs.
y Sydney Parkinson was the artist on Cook’s voyage of discovery to the South Seas in 1768-
1771. He painted many animals (<http://pages.quicksilver.net.nz/jcr/~parkinson.html>),
insects (<http://www.nhm.ac.uk/services/ibd/gfx/te/vod/17.jpg>) and plants
(<http://internt.nhm.ac.uk/cgi-bin/perth/cook/>) and made the first sketch of a kangaroo
<http://www.nhm.ac.uk/library/art/drawingconclusions/more/hibiscus_more_info.htm#collection>;
y Ferdinand Bauer (1760-1826) is regarded as one of the most remarkable botanical artists of
all time (Bauer et al. 1976) <http://nokomis.com.au/html/biography.html>;
y John Gould’s Birds of Asia
<http://www.jadestonegallery.com/printgallery/gould/birdsofasia.htm>;
y Birds of the World – McClung Museum Special Exhibition 1997
<http://mcclungmuseum.utk.edu/specex/birds/birds.htm>;
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y The World of Insects in Chinese Art: A Special Exhibition of Plant-and-Insect Paintings
was an exhibition held at the National Palace Museum in Taiwan in 2001
<http://www.taiwanheadlines.gov.tw/20010816/20010814f2.html>.
Indigenous Art
Indigenous art and artefacts are a major source of income for indigenous peoples. Increasingly,
artists want to supply information about the subjects of their art or the materials that make up the
artefacts and products.
Examples:
y Untapped potential for cooperation between science and technology for mountain
conservation in the Andes and Himalayas (Camino 2002)
<http://www.mtnforum.org/resources/library/camia02a.htm>;
y Canna indica is commonly used in jewellery and for other purposes
<http://waynesword.palomar.edu/pljune98.htm>;
y Nickernuts (Caesalpinia bonduc) are used for necklaces in Ecuador
<http://waynesword.palomar.edu/nicker.htm>;
y Feathers have been a traditional adornment in many societies, The use of Birds-of-Paradise
in Papua New Guinea is a good example (Frith and Beehler 1998)
y Yams are used for masks in Papua New Guinea <http://www.art-
pacific.com/artifacts/nuguinea/yamwoodo.htm>;
y Shells, feathers, grass twine and other materials are commonly used in indigenous art
<http://www.lostworldarts.com/new_page_2.htm>;
y Wool is used in the Andes and Himalayas <www.andeansoftware.com>;
y Fibres are used in basket making <http://www.aotearoa.co.nz/flaxworks/>;
y Bamboo and other woods are used in making musical instruments
<http://www.canne-et-bambou.com/eng/bamboo_flutes.htm>;
y Bark is used for paintings by indigenous Australians
<http://www.aboriginalartonline.com/art/bark.html>.
Stamps
Most modern societies around the world use biodiversity on their stamps. These stamps often
include scientific as well as common names, and stamp producers rely on primary species data for
these identifications.
Examples:
y Australian Stamps: Bush Tucker
<http://www.auspost.com.au/philatelic/stamps/index.asp?link_id=2.608>;
y Birds on stamps <http://www.birdtheme.org/regions/region.html>;
y Kyrgyzstan animal stamps <http://ecopage.freenet.kg/biodiversity/animals.html>;
y Fijian stamps often include plants, insects and other animals
<http://www.stampsfiji.com/stamps/peregrine_falcon/index.html>.
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Society and Politics
Many of the uses of species data in society and politics are covered under other topics; however,
several uses do not seem to fit easily elsewhere.
Social Uses of Biodiversity
Biodiversity sits within the social context of human population – the competition between
conservation and the need for food and shelter for survival is a never ending conflict. Many new
studies are looking at the interaction between biodiversity and the social culture of humans.
Examples:
y Areas of high avian endemism also hold dense human populations and rapid rates of
habitat loss, thus human population density and growth rates must be factored into
conservation priority setting (Brooks 2001);
y Other important-and “often sensitive and contentious-parameters include the distributions
of military conflict, refugee movements, timber and mining concessions, commodity
production, bushmeat hunting, and the narcotics trade” (Brooks 2001);
y Several projects of the Biota/FAPESP Program in São Paulo, Brazil are examining social
aspects of biodiversity
o One study is looking at an environmental atlas to help in planning a balance between
human activities and biodiversity
<http://www.biota.org.br/projeto/index?show+192>;
o Another study is examining the use of natural resources for fishing, artefacts and for
spiritual purposes by coastal inhabitants. The study is examining uses and local
nomenclature as well as examining how the communities live and fish, and what
effects their activities may have on the environment
<http://www.biota.org.br/projeto/index?show+226>;
y Mobilising European social research potential in support of biodiversity ecosystem
management (SoBio) (European Centre for Nature Conservation)
<http://www.ecnc.nl/doc/ecnc/press/070404.html>;
y Unit for Social and Environmental Research – Chiang Mai University
<http://www.sea-user.org/>;
Anthropology and Language
Anthropological studies, and even some biological studies (Basset et al. 2000) have been attempting
to link indigenous nomenclatural systems for species to the Linnaeus system.
Examples:
y In Papua New Guinea, studies are attempting to link local forest species nomenclature to
species names as part of a project to train local people as parataxonomists and collectors of
insects (Basset et al. 2000);
y Primary species data have been used to compare primate proteins
<http://www.bioquest.org/bioinformatics/module/tutorials/Anthropology/>;
y Plant species data are used to identify species used in diets to track migration patterns
(Newton-Fisher 1999)
<http://www.budongo.org/nen1000/reprints/NewtonFisher_1999_diet.pdf>.
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Ethnobiology
Local knowledge about useful plants and animals, extending back more than 300,000 years, is an
important subject of research by ethnobotanists (Gómez-Pompa 2004) and ethnozoologists. The
integration of this knowledge with distributional studies from primary species-occurrence data is an
important area of research.
Examples:
y Some anthropology studies look at the use of plant and animal species in healing,
medicine, and for food
<http://www.library.adelaide.edu.au/guide/soc/anthro/subj/med.html>;
y Laboratory of Ethnobotany houses thousands of records of species used for food and
medicine <http://www.umma.lsa.umich.edu/ethnobotany/ethnobotany.html>;
y Nuaulu Ethnozoology – A Systematic Inventory by Roy Allen from the University of Kent
at Canterbury <http://lucy.ukc.ac.uk/csacpub/ellen_ch1.html>;
y Acacia in Australia: Ethnobotany and Potential Food Crop (Lister et al. 1996)
<http://www.hort.purdue.edu/newcrop/proceedings1996/v3-228.html>;
y Ethonzoology of the Tsou People: Fishing with poison
<http://tk.agron.ntu.edu.tw/Segawa1/fishing_poison.htm>
y Native Peoples, Plants and Animals <http://www2.sfu.ca/halk-ethnobiology/>;
y Ethnozoological Research on Reptiles on Mt. Kilimanjaro
<http://www.uni-bayreuth.de/departments/toek2/claudia/fEthnozoology.htm>;
y Ethnobotany: Plants and People Interacting
<http://maya.ucr.edu/pril/ethnobotany/Start.html>.
Data Repatriation
The Convention on Biological Diversity (CBD) calls for repatriation of information to countries of
origin. More recently, the idea of one to one data repatriation of museum and herbarium collections
has moved more toward the idea of data sharing, and especially through use of on-line data
availability using portals such as the .
Examples:
y Report on study on data sharing with countries of origin (GBIF)
<http://www.gbif.org/Stories/STORY1079623109>;
y Only 0.8% of the world’s beetle researchers reside in Africa and few of the type specimens
(Miller and Rogo 2001);
y The Natural History Museum in London is working in Chile on Access to Genetic
Resources, Benefit Sharing and Traditional Knowledge
<http://www.darwin.gov.uk/news/projects/access_gen.html>;
y The Natural History Museum is also working on the repatriation of herbarium data for the
flora of Bahia, Brazil <http://www.darwin.gov.uk/projects/details/7108.html>
y Using Virtual museums to increase information repatriation and sharing Whole Earth 2000
<http://www.findarticles.com/p/articles/mi_m0GER/is_2000_Fall/ai_66240384>;
y A Mexican case study on a centralised database from World Natural History Collections
(Navarro et al. 2003)
<http://journals.eecs.qub.ac.uk/codata/Journal/Contents/1_1/1_1pdf/DS105.Pdf>.
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Biodiversity collecting
In many countries the development and expansion of protected areas is in some cases making it
more difficult for scientists to collect and study biodiversity in these areas. Because of this, existing
species-occurrence data will need to be relied on even more heavily in those areas where access for
new collections may be restricted.
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Recreational Activities
Recreational activities form another use for species-occurrence data. Many recreational activities
involve biodiversity in one way or another – fishing, hunting, bird and whale watching, gardening,
bushwalking, horse-riding, etc.
Recreational fishing
Recreational fishing is a large industry, and fishermen want to know what the fish is that they have
caught – where certain species of fish occur and when, etc. All of this information is based on
primary species-occurrence data.
Examples:
y Recreational fishers in Western Australia want habitat protected to improve recreational
fishing <http://www.recfishwest.org.au/PolicyFishHab.htm>;
y In planning for zoning on the Great Barrier Reef, 36% of all submissions were from
recreational fishers
<http://www.gbrmpa.gov.au/corp_site/management/zoning/rap/rap/overview/intro/recfish.
html>;
y Recreational fishing in Belarus is a major cause of biodiversity decline
<http://www.iucn-ce.org.pl/documents/belarus.pdf>;
y Recreational fishing is being considered in management of fishing resources in the Upper
Paraná River Basin in Brazil
<http://www.unep.org/bpsp/Fisheries/Fisheries%20Case%20Studies/AGOSTINHO.pdf>.
Hunting
Like recreational fishers, hunters want to know what species they are hunting and where and when
they occur. Conservations are also involved in knowing what species hunters are taking so that they
can be taken into account in species management.
Examples:
y Hunting and Biodiversity in Atlantic Forest Fragments, São Paulo, Brazil
<http://www.wildlifetrust.org/huntipe.htm>;
y Extinction caused by hunting
<http://www.virtualglobe.org/en/info/env/04/diversity07.html>;
y Impacts of hunting on native species in New Zealand
<http://www.biodiversity.govt.nz/picture/biodiversity/state/hunting.html>;
y The North American Hunting Heritage Accord plans for sustainable hunting
<http://centralflyway.org/Hunting_Accord_Draft.html>.
Photography and Film-making
Photography of wildlife is another major recreational activity that relies on primary species-
occurrence data for identification, and for determining where to find certain species to photograph,
etc. Photographers are responsible for books, calendars, stamps, documentaries, etc. as well as on-
line collections.
Examples:
y North American Nature Photography Association <http://www.nanpa.org/index.html>;
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y The Finnish Nature Photographers Association <http://www.luontokuva.org/>;
y The Discovery Channel <http://dsc.discovery.com/>;
y Nature and Wildlife Movies
<http://www.dropbears.com/b/broughsbooks/movies/nature_wildlife.htm>;
y David Attenborough Films
<http://www.bbc.co.uk/nature/programmes/who/david_attenborough.shtml>.
Gardening
Gardening is a passion among many, and the need to know what the plants are, essential to most
gardeners. Books and magazines on gardening are constantly being marketed and all rely on
species-occurrence data for their information. A number of people are also starting to get into
organic gardening and are searching for species for growing.
Examples:
y Royal Horticultural Society <http://www.rhs.org.uk/research/biodiversity/index.asp>;
y Gardening for Biodiversity <http://www.english-nature.org.uk/news/story.asp?ID=257>;
y Organic gardening books <http://supak.com/organic_gardening/organic.htm>;
y Australian Plants online – Society for Growing Australian Plants
<http://farrer.riv.csu.edu.au/ASGAP/apoline.html>.
Bushwalking, Hiking and Trekking
Bushwalking, hiking or trekking in natural areas is a common pastime that often involves people
wanting to know what the species are that they pass.
Examples:
y Bushwalking in New South Wales
<http://www.npansw.org.au/web/activities/bushwalking.htm>;
y Hiking in Guatemala <http://www.guatemalaventures.com/hiking_tours.htm>;
y Hiking in Southeastern Arizona
<http://www.geo.arizona.edu/geophysics/students/tinker/SEhiking.html>;
y Trekking in Ecuador
<http://www.surtrek.com/ecuador/adventuretours/trek_podocarpus.htm>;
y Tramping in New Zealand <http://www.enzed.com/tramp.html>.
Bird Observing
Bird observing is a major recreational activity around the world, with many bird-observers clubs
and bird activities. All rely on being able to identify the bird they have seen and thus rely on guide
books and field guides created from primary species-occurrence data.
Examples:
y Birding.com <http://www.birding.com/>;
y National Audibon Society <http://www.audubon.org/>;
y Birding in Canada <http://www.web-nat.com/bic/>;
y Birds Australia <http://www.birdsaustralia.com.au/>;
y Birding Africa <http://www.birding-africa.com/>.
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Human Infrastructure Planning
Planning of human infrastructure – roads, powerlines, subdivisions, etc. – requires species-
occurrence data for finding the best place to build, and to do the least harm to the environment.
Risk Assessment
The building of roads and services requires risk assessment involving the most cost effective
placement from both financial and ecological points of view. The management of weeds and
hazardous vegetation on public lands, and the decision as to what species should be planted along
roads and streets also involves risk assessment and species identifications.
Examples:
y Rights-of-Way Environmental Issues in Siting, Development and Management (Electric
Power Research Institute) <http://www.epri.com/destinations/descriptions/57_row.pdf>;
y Management of noxious weeds and hazardous vegetation on public lands – risk assessment
for humans and non-target species
<http://www.fs.fed.us/r3/projects/ro/ea-noxiousweeds/ea-weedsappa.html>;
y Land use impact costs of transportation (Litman 1995)
<http://www.agenda21.ee/english/transport/landuse_costs_extern.pdf>;
y Significant costs in road maintenance can result from use of comprehensive biological
survey <http://www.bionet-intl.org/case_studies/case19.htm>.
Landscaping
Tree roots of certain species can cause great damage to houses, sewage lines, etc. Street trees are
often planted under powerlines and have to be trimmed at great cost as they get too tall, other
species crack pavements and roads. Some species are more susceptible to damage in cyclones and
tornadoes, etc. The selection of species that save energy and use less water can be important in
some areas of the world. The identification of trees for planting in sensitive locations and the
identification of plants from their roots, etc. can require information from primary species-
occurrence data.
Examples:
y Using dune vegetation to stop coastal dune erosion
<http://www.epa.qld.gov.au/environmental_management/coast_and_oceans/beaches_and_
dunes/coastal_dunes/>;
y A Benefit-cost analysis of planting street tree species in Modesto, California (McPherson
2003) <http://www.treelink.org/joa/2003/jan/01McPherson.pdf>;
y Landscaping to save energy <http://www.pioneerthinking.com/landscape.html>;
y Tree roots a growing problem (South East Water Ltd, Melbourne, Australia)
<http://www.sewl.com.au/sewl/upload/document/treeroots.pdf>;
y Windbreak trees for economic biodiversity (Stace 1995)
<http://www.newcrops.uq.edu.au/acotanc/papers/stace.htm>;
y Planning tree windbreaks in Missouri
<http://muextension.missouri.edu/xplor/agguides/forestry/g05900.htm>;
y Different species have differing abilities to ride out cyclones
<http://www.plant.id.au/home/guide_view.aspx?id=15>.
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Wild Animals and Infrastructure
Wild animals and human infrastructure always leads to clashes. Animals are killed on highways and
roads, birds get sucked into aircraft engines, and wind turbines, dams stop species migrating up
stream to spawn, etc. Primary species data are important in understanding species behaviour,
locations etc.
Examples:
y Environment Canada is reducing wildlife roadkill
<http://www.pc.gc.ca/pn-np/ab/banff/docs/routes/chap3/sec4/routes3d_e.asp>;
y The U.S Critter crossings reduce roadkills
<http://www.fhwa.dot.gov/environment/wildlifecrossings/index.htm>;
y Avian interactions with utility structures, wind turbines and communication towers
(EPRI’s Destinations 2005) <http://www.epri.com/destinations/product.aspx?id=309>;
y Dams are being removed to save salmon
<http://www.wildsalmon.org/library/lib-detail.cfm?docID=300>.
Building timbers
The selection of plant species for use in buildings for termite resistance, railway sleepers, bridges,
fences, and power poles requires research into suitable species.
Examples:
y Termites and houses
<http://www.ces.ncsu.edu/depts/ent/notes/Urban/termites/termites.htm>;
y Species of eucalypt are used in Australia for furniture, railway sleepers, bridge
construction, flooring, etc. <http://www.tpcvic.org.au/page_timber_info.htm>;
y Acceptable species for use as power poles in Australia
<http://www.daleandmeyers.com.au/species.html>;
y Incorrect identififcation of termites can be costly <http://www.bionet-
intl.org/case_studies/case20.htm>.
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Aquatic and Marine Biodiversity
Aquatic and marine biodiversity is largely covered under other topics above; however, they are
covered separately here as there are some specific marine and aquatic biodiversity systems that
require specific species-occurrence data.
Examples:
y Ocean Biogeographic Information System (OBIS)
<http://www.coml.org/descrip/obis.htm>;
y Gulf of Maine Biogeographic Information System Atlas (GMBIS)
<http://gmbis.marinebiodiversity.ca/aconw95/aconscripts/gmbis.html>;
y Riverine aquatic protected areas: protecting species, communities or ecosystem processes?
(Koehn 2003);
y Census of Marine Life – “is a growing global network of researchers in more than 70
nations engaged in a ten-year initiative to assess and explain the diversity, distribution, and
abundance of marine life in the oceans -- past, present, and future”
<http://www.coml.org/coml.htm>.
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Conclusion
As seen throughout this document, uses for primary species-occurrence data are endless and touch
just about every aspect of human endeavour, along with every part of the globe. They extend from
uses for day to day survival such as food and shelter, through to education and learning, to pleasure
and recreation. Most of us rely on these data without even thinking about them or even knowing
they exist. But without them, whether held in museums or herbaria, in bird-observers databases or
in survey databases held by Universities, individuals and corporations, we would not have the
understanding of biodiversity that we have today, and our survival would be even further
jeopardised than it already is.
We need to make maximum use of these data to better understand our biodiversity and our planet –
to mitigate and monitor changes to our environment, to improve, conserve and sustainably use the
resources we rely on and to educate and train future generations to appreciate and understand the
biodiversity on which the data are based.
There are sure to be many uses that this document has missed, and it has been impossible to
reference every example. It is hoped that the document may be made “live” in some format so that
it can be kept updated and so that new uses can be added, possible by the on-line users of the data
themselves.
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Acknowledgements
Many people have been instrumental in helping with this paper. First and foremost, I would like to
thank the Global Biodiversity Information Facility (GBIF) for funding the project. Staff at GBIF,
and especially Larry Speers, Meredith Lane and Jim Edwards have been helpful in making
suggestion of uses and providing valuable contacts. Many other people have unhesitatingly supplied
references, publications, information and suggestions. They include: Lee Belbin (Australian
Antarctic Data Center, Hobart, Tasmania), Daniel R. Brooks (University of Toronto, Canada),
Vanderlei Perez Canhos and Dora A.L. Canhos and staff (CRIA, Campinas, Brazil), Barry Chernoff
(Wesleyan University, Connecticut, USA), Robert Colwell (University of Connecticut, USA),
Trevor James (National Biodiversity Network, UK), Carlos Joly (University of Campinas, Brazil),
Ingrid Koch (CRIA, Campinas, Brazil), Scott Miller (Smithsonian Institution, Washington, USA),
Robert Morris (University of Massachusets, Boston, USA), A. Town Peterson (University of
Kansas, USA), Daniel Roseau and Cameron Slatyer (Department of the Environment and Heritage,
Canberra, Australia), Peter Shalk (ETI, Amsterdam, Holland), Jorge Soberón Mainero (Conabio,
Mexico), Jim Staley (University of Washington, Seatle, USA), Bob Bloomfield and Honor Gay
(The Natural History Museum, London), Antonio López Almirall (Museo Nacional de Historia
Natural, Cuba), Johann Breytenbach (Ezemvelo Nature Reserve, South Africa), Judy West and
Greg Whibread (Centre for Plant Biodiversity Research, Canberra, Australia), Patricia Mergen
(Belgian GBIF, Belgium), Anton Güntsch (Botanischer Garten und Botanisches Museum Berlin-
Dahlem, Germany), Marc Stadler (Bayer HealthCare AG, Wuppertal, Germany), Barbara Gemmel
(Herren) (FAU, Rome, Italy) and Anna Weitzman (Smithsonian Institution, Washington, DC,
USA). Lastly, I would like to thank the staff at the Library of the University of Southern
Queensland, Toowoomba, Australia for their help in obtaining some of the more obscure
publications.
Paper by Athur Chapman Page 84 Release date:
commissioned by GBIF July 2005
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