Review of Current Wildlife Species Genetic Research: Identification of a Priority List of Wildlife Species in Trade, Where DNA Research Would Assist Law Enforcement
A Review of Current Wildlife Species Genetic Research: Identification of a priority list of wildlife species in trade, where DNA research would assist law enforcement
Revised Final Report
February 22, 2002 (Revised Mar 2004) Report No 3 LGC/LS/2004/001 A Review of Current Wildlife Species Genetic Research: Identification of a priority list of wildlife species in trade, where DNA research would assist law enforcement
Revised Final Report
Report No 3
Contact Point: Carole Foy Tel: 020 8943 7335.
Prepared by: LGC: Carole Foy Lydia Ballam
TRAFFIC: Crawford Allan Angela Barden
Approved by: Alison Woolford ______
Date: 22nd February 2002 (Revised Mar 2004)
______
The work described in this report was supported under contract with DEFRA
LGC/LS/2004/001 © LGC (Teddington) Limited 2004 Contents
1. Executive Summary 1
2. Project Aims 2
3. Background 2
4. Approach 5 4.1 Development of Priority Species Selection Criteria 5 4.1.1 The Primary Filter Process and Selection Criteria 5 4.1.2 Development of a DNA search strategy 8 4.2 Development of Analytical Database System 11 4.3 The Ranking, Scoring and Weighting Systems 11 4.3.1 DNA Ranking Strategy 11
5. Output 17
6. Recommendations 20
7. Conclusion 21
8. Acknowledgements 22
9. Appendices 24 9.1 Appendix 1 : Alternative animal ranking and prioritisation strategy 24 9.2 Appendix 2 : Species Database Construction and Use 26 9.3 Appendix 3 : Individuals/organisations contacted 37 9.4 Appendix 4 : Individuals/organisations offering assistance 37 9.5 Appendix 5 : DNA References 37 9.6 Appendix 6 : Summary of animal DNA information 65 9.7 Appendix 7 : Summary of plant DNA information 73 9.8 Appendix 8 : Wildlife trade regulation in the european union 75 9.9 Appendix 9 : Definitons for the Red List categories 77
Review of Current Wildlife Species Genetic Research - i - Final Report 1. Executive Summary DNA testing is becoming a standard tool to assist law enforcement through provision of robust evidence, and it is being applied more widely for wildlife trade law enforcement cases. There are limitations on its use for cases involving particular species, when DNA tests are not developed for that target species. Extensive research is ongoing to develop species-specific tests but often this may be duplicating the effort of others or may be misplaced. A need was recognised to develop a system to focus research where it was most needed, to support enforcement cases. Usually the need for a test arises from an enforcment case but development takes time, which is often too long for the requirements of a particular case. Development of a system to prioritise where research on DNA should be focussed, to meet the needs before they arise was an obvious step.
Enforcement resources are highly restricted and it was determined that efforts should focus on those species most threatened with extinction and protected in law, as these would most likely be the species for which resources could be allocated. DNA tests are able to provide assistance in enforcement cases in many instances and there is a need to prioritise those species where such tests would have the greatest impact. Once prioritised, there is a further need to determine the current availability, or otherwise, of DNA markers such that future research to develop markers can be focussed effectively.
Under support from the Department for the Environment, Food and Rural Affairs (DEFRA), LGC and TRAFFIC International have identified a priority list of endangered species in trade where DNA information is currently lacking but, if available, could help in wildlife trade law enforcement cases.
In producing this list two additional resources have been developed: • an analytical system that can be revised or adapted to generate priority lists in future if conditions change or different scenarios are applied; • a catalogue of details of the main papers, researchers and laboratories involved in genetic studies on endangered wildlife
The development and implementation of the system and the results are outlined and discussed in this report. The work focussed on developing a filter and ranking mechanism within a database structure, which scored species based on a variety of criteria such as extent of illegal trade, DNA research undertaken, breeding capacity, legal controls and degree of threat. From a first cut of over 5000 species in the database, the system was filtered down to a working data set of nearly 350 species, from which a priority list of 100 species has been produced.
Whilst the system has been developed to take the most significant factors into consideration and has incorporated a great deal of research and analysis, its value is as the best guide available and it should not be seen as providing a definitive answer.
Review of Current Wildlife Species Genetic Research - 1 - Final Report 2. Project Aims
The overall aims of the project were directed by DEFRA in their original tender document, as follows:
• Identify a priority list of 75-100 endangered species in trade where DNA-based research to support enforcement activity is likely to deliver the most significant benefits; • Assess the current availability, or otherwise, of DNA markers for these species by reviewing current literature and research effort; • Identify individuals and institutions with expertise in the development and/or utilisation of these DNA techniques; Although these were the main aims, the project did expand somewhat with the need identified by the project executants to ensure that an analytical system be developed, which would allow for future updating with changes in DNA research, legislation and enforcement needs. The additional aim of the project was therefore:
• To develop an analytical process that lends itself to future revisions, should the need arise to produce a new priority list as a result of changes that would significantly impact the existing list.
3. Background
There is no doubt that the existence of many species is being threatened by illegal trade in them, either as living animals or plants or their parts and derivatives. National and international laws have been established to regulate and prohibit trade in wildlife in an attempt to ensure that trade in some species is sustainable and in others is banned to limit further risk of extinction. Enforcing these laws can be complicated and many fraudulent methods have been developed to avoid detection by those who would wish to contravene the laws. Increasingly sophisticated criminal methods are employed in illegal wildlife trade and enforcers have responded by relying on advanced technologies to counter the trade, particularly DNA testing.
Research to develop DNA tests, which can assist in efforts to protect endangered species by supporting enforcement activities, is increasingly being carried out in many centres around the world. DNA can assist enforcement bodies in determining whether shipments being inspected or cases investigated involve infraction of wildlife trade laws and can provide evidence for prosecution in a variety of ways. It can provide a means of species identification to establish whether a plant or animal (including parts and derivatives) is an endangered species that is protected in law. This is useful, as many species will not be traded as a more easily recognisable whole animal or plant. For example, a plant could be traded as a seed or powdered leaves in medicines, while animals could be traded as lumps of bush meat, pelts or ground up bones to be used in herbal medicines and remedies. Alternatively, DNA testing provides a means to discriminate between individuals, where population and/or familial-specific markers can identify whether an animal has been bred in captivity or taken from the wild. DNA markers can also be used to link an individual specimen to a suspected criminal believed to be involved in the poaching or smuggling of that specimen. DNA can also provide geographical and population information as markers can discriminate at the sub species / geographical population level e.g. South China Tiger or a Sumatran Tiger.
Review of Current Wildlife Species Genetic Research - 2 - Final Report DNA is the analyte of choice for species identification for a variety of reasons. It is a very robust molecule, DNA can be highly degraded e.g. cooked (as in the case of bushmeat) or very old (as in the case of ivory) and a positive identification can still be obtained. The DNA tests developed are also extremely sensitive with only minute quantities of DNA needed to gain a positive result. Sensitivity and assay robustness is further enhanced through the use of markers derived from mitochondrial DNA, as this molecule is present in many copies within each cell. This is especially useful in mixed herbal medicines where the sample may only make up a small percentage of the overall mixture. DNA analysis will also have few collection issues because DNA is in all biological cells and can therefore be obtained from the smallest of samples from any part of the animal or plant. As DNA research is at the cutting edge of molecular biology, research is on going with new and improved techniques constantly being developed to aid detection.
DNA markers available include:
Microsatellite markers • Microsatellites are short polymorphic repeat sequences. Microsatellite markers can identify specific species, familial relationships, whether an animal is captive bred or wild and what geographical location or population it came from. Microsatellite markers have been developed across taxonomically similar species so sets of primers for one species may amplify a related species or closely related taxa.
Mitochondrial markers • Mitochondrial or chloroplast markers are increasingly being used to identify species and sub species. Mitochondrial DNA is chosen over nuclear DNA for the development of DNA markers, as it is more prone to genetic drift, meaning that a greater proportion of variation is distributed between populations. These markers can also identify phylogenetic splits and so provide unique insights into population history and can suggest hypotheses about boundaries of genetically divergent groups. However this type of DNA marker can rarely differentiate between individuals and so is less sensitive than the microsatellite marker.
Although there is a wealth of DNA research developing new markers, there are still thousands of species that have been recognised as being under threat, where no such markers have been developed. It is accepted that resources are not available to develop DNA methodology to underpin enforcement activities for every such species. DNA researchers and enforcers need to allocate resources only where there is the most significant need. Determining the most significant species is a highly complex task in itself and to date has arisen on an ad hoc basis, often only as specific enforcement cases have demanded. To determine the priority species for future development of DNA research a number of focus areas were recognised that were the basis for the selection process: • Clearly, for a species to be subject to law enforcement interest in it must be included under legislation that restricts or regulates its trade. The species that are legally protected are those which are in trade and are at risk from it unless trade is controlled. • To ensure that the species are of the greatest priority they must be recognised as being threatened with extinction. Scarce resources are far more likely to be allocated for those species of greatest concern. • Enforcement needs to target the species that are actually in illegal trade, so it was essential to determine the extent to which the species are illegally traded.
Review of Current Wildlife Species Genetic Research - 3 - Final Report • The breeding of wildlife can offset demand from the wild and legitimate, widespread and regular breeding reduces the likelihood of illegal trade. The influence of breeding needed to be factored into the selection process. • The ease of identification of specimens to species level or to prove familial or geographic origins was significant, as law enforcement is more likely to require DNA tests for the species that are more difficult to identify. The ease with which a species can be identified was also a factor that required measurement. • Existence of a DNA test was obviously a critical factor in determining the need for future DNA research. Where tests were available there was a lower likelihood of DNA research being required.
Therefore, it was the aim of this project to develop a strategy to select a priority list of species where DNA marker information could be sought. This initial list was then prioritised further to identify 75-100 endangered species that were illegally traded, difficult to breed in captivity and where DNA markers were lacking, therefore identifying potential priority areas for future funding and research.
As DNA research is on going, information for many new markers will have not have been published and so will not be publicly available. For this reason individual experts or appropriate organisations that may have been aware of unpublished markers or ongoing research, or were able to assist in the development of new markers were identified and contacted. This may also allow collaborations to evolve to aid speedier development of new markers, due to the sharing of expertise and ideas. Initially it was expected that potential areas of contact would be zoos, botanical gardens, forensics laboratories, wildlife genetic research centres, websites and key authors researching on a particular species of plant or animal.
The key challenges in carrying out this project were:
• Development of appropriate criteria and scoring mechanisms to enable selection of the species suitable for inclusion on the priority list; • Determination of the incidences of illegal trade in species information, which is often difficult to obtain due to its confidential nature; • Consistent evaluation of the ease of breeding and breeding capacity across a vast range of species; • Identification of relevant DNA research activities relating to these, or closely related, species and identification of active research groups; • Interpretation and assessment of current research activities for these species; • Compilation, interpretation and linking of the selected species list with current research activities to produce the final priority list; • Development of an analytical system that could be easily updated in future and adjusted according to changes in the criteria.
Review of Current Wildlife Species Genetic Research - 4 - Final Report 4. Approach
4.1 Development of Priority Species Selection Criteria
Wildlife trade law enforcement has to continually adapt to changes in legislation, altering the species that are protected in law on a regular basis. Trade trends are also in constant flux and enforcement needs to keep up with the smugglers and illegal traders and the latest species that are subject to their criminal activity. DNA tools are essential to assist law enforcement in proving illegal activity or otherwise. The development of DNA tools and technology are also constantly evolving. However, enforcers must have the tools they need to hand and waiting for development of a test, that may take years of research, can often be too late. A trade trend can evolve quickly and have lasting damage on the future viability of a species in the wild. The work on this project recognised from the outset that a priority ranking mechanism for research was vital to help ensure that the most appropriate tools were provided in a timely manner. However, it was also recognised that the changes in legislation, trends in trade and DNA research meant that very soon after a priority list was produced it would be obsolete. The development of an automated ranking system based around a database, with flexibility for revision when key changes take place in future, was clearly the most appropriate way forward.
4.1.1 The Primary Filter Process and Selection Criteria
To allow the prioritisation of species, two main methods were applied, firstly a filter system, followed by a scoring system for species and subspecies. The filter system took all species globally as a starting point for the data set, to which two coarse filters were applied.
The Legislative Controls Filter The first filter applied was to select all species that are regulated in international trade or are likely to be so in the near future. Obviously enforcement is focused solely on laws and the prime selection criteria had to relate to species that are subject to legislation. There are currently many mechanisms worldwide that create lists of priority species that are both of conservation concern and are in trade, or are likely to be in trade if regulation did not prevent it. Governments from many countries use their experts to regularly provide input into these processes and keep a close watch on species that potentially should be regulated. Therefore, there was no need as a first cut to research the conservation or trade threats of all species, as this has already been done by treaties and regulations such as CITES and the European Union Regulation (338/97 on protection of species of wild fauna and flora in trade). CITES alone lists over 30,000 species that are in trade and potentially at risk if not regulated. However, the most appropriate list of species to use as a starting point, was the EU Regulation, as it includes all CITES species as a basis and then adds more species which are deemed to be in need of extra regulation in the European Union. There are other species, not yet included in the EU Annexes, which are only under domestic protection in their countries of origin but are subject to illegal collection and trade. It was beyond the remit of this project to undertake research in those areas, as the mechanisms for inclusion of such species in the processes of CITES and the EU Regulations should be relied upon. This filter left a first cut data set of over 30,000 taxa, which were then subject to the next filter.
Review of Current Wildlife Species Genetic Research - 5 - Final Report The Threatened Species Filter It is generally recognised that species are categorised in conservation terms according to their level of threat and their likelihood of extinction in future. Much research is undertaken to determine the threat status of taxa internationally, nationally and locally. The remit of this project was to focus on taxa of greatest conservation concern internationally because these species are the ones of priority for protection. It is also important to note that for enforcers the application of DNA tests is relatively expensive, when there are many competing priorities. Therefore, it is often the case that enforcement will only wish to apply such resources for the species of greatest concern. The second filter applied was therefore to select from the first cut data set only those taxa that were thought to be threatened with extinction. IUCN produces global lists of threatened species ranked according to their degree of threat using their internationally recognised threat assessment methodology. These lists are entitled the IUCN Red Lists of Animals and Plants. The IUCN Red List of Threatened Species, 2000 is the most up-to-date work establishing the degree of threat to animal species. It uses the latest assessment methodology. Animals categorised as “Critically Endangered”, “Endangered” and “Vulnerable” are of the greatest conservation concern. The IUCN Red List of Threatened Plants, 1997 is the more appropriate work for selection of plant species than the 2000 plant list, as it is more extensive and categorises a greater number of species that are in trade. The 2000 list applies the new methodology but has been only applied to a limited number of taxa. Plants categorised as “Endangered”, “Vulnerable” and “Rare” are of the greatest conservation concern. However, those species potentially threatened but for which no data is available were considered after consultation with IUCN where new but unpublished data arose. Once this filter was applied the working dataset was refined to approximately 5,000 taxa (1,584 animals and 3,472 plants). The next steps were to apply ranking systems to the working data set by allocating scores under two selection criteria of the level of illegal trade and the ease of breeding/propagation.
The Illegal Trade Selection Criteria The next method to contribute towards a priority ranking involved compiling and scoring data relating to illegal trade in the species and the need for identification methods for law enforcement. For enforcement purposes there is only a need to develop DNA tests to assist in combating illegal trade for species that are subject to illegal trade. For each species researched scores were applied to three sub-criteria as follows:
• Seizures Records and Evidence of Poaching: where there are known enforcement seizures of illegal specimens of the species or where there is known to be records or evidence of poaching from the wild. This is solid evidence that illegal trade has taken place;
• Intelligence on Illegal Trade: this refers to a range of information that contributes towards a picture of the scale and nature of the illegal trade in the species. This information is compiled from sources such as comments by traders, market survey results, enforcement intelligence information, expert comments and price lists and advertisements. Some of this information is from confidential sources that cannot be referenced for the purposes of this project; and
• Ease of Identification of the Species for Law Enforcement: the degree of ease of identification of a species in the forms that it is in illegal trade (e.g. live, bones, seeds, meat, skins, carvings, medicines). This emphasises the need for DNA testing where identification is difficult and includes data on determining sub-population origins, familial relationships etc. One species may be scored higher than another if for example, it is traded in a
Review of Current Wildlife Species Genetic Research - 6 - Final Report derivative form that is hard to distinguish, is easily smuggled and is in greater demand as a derivative rather than a live specimen.
TRAFFIC used its Network's resources and expertise in monitoring the illegal trade and analysed in particular its records of global seizures and prosecutions of wild species. A large variety of research material on illegal trade was directly available to TRAFFIC, including international intelligence networks, research studies, unpublished materials and TRAFFIC’s own investigations and ongoing monitoring of trade at all levels and regions. The poaching or illegal removal of species from the wild was researched from these files and reports also. The ease of identification was an assessment based upon data of the forms in which the specimens are traded and knowledge of the likely need to prove both familial relationships and sub population origins.
The Breeding Selection Criteria Where species are commonly bred in captivity or artificially propagated this offsets the need for illegal collection from the wild and illegal trade. Where it is known that species are readily available from legally bred or propagated sources this reduces the priority for DNA testing in that species. Research was undertaken to score each species based upon the following sub- criteria:
• Ease of Breeding / Propagation: this refers to the level of ease when captive breeding / artificially propagating a species. This is compiled from sources including expert comments, reports of breeding / propagation programmes, and conservation action plans;
• Capacity of Breeding / Propagation: this refers to the degree to which a species is currently being bred in captivity / artificially propagated. This is compiled from sources including expert comments, nursery catalogues, species studbooks and zoo records, registers of facilities breeding / propagating CITES-listed species.
This research was based upon assessment of the claimed breeding of species from zoo and breeder records and the availability of captive bred/artificially propagated specimens on the global market. The species that are commonly captive bred/artificially propagated, without the need for collection from wild stocks to replenish captive/propagated gene pools, were given the lowest scores as being of less significance for the priority listing. However, it was determined that some species even though more commonly captive bred/artificially propagated, still have a degree of illegal trade, for example for specialist collectors, and therefore, the demand for wild specimens versus reared specimens was also accounted for in the analysis.
Criteria Testing and Data Set Refinement An assessment of the level of effort required to research, assess and rank the data for the two sub-criteria of illegal trade and breeding and the DNA data was undertaken. This provided an indication of the degree to which the dataset of circa 5,000 taxa should be reduced for effective research. The assessments of the possible ranking systems indicated that emphasis should focus on the most critically endangered and endangered animals and plants, with some sample species grouped under other threat categories as controls. In addition the focus should be aimed at the most strictly regulated species, those on Annex A of the EU Regulation, again with some sample species from Annex B. The highly endangered and strictly regulated species would be ranked at the highest levels as they were of greatest concern for conservation and law enforcement. Enforcement effort was more likely to utilise resources for DNA testing for such species over species in the lower divisions of threat and regulation. The effort required to
Review of Current Wildlife Species Genetic Research - 7 - Final Report research these lower divisions was likely to be irrelevant as they were highly likely to be excluded from the priority list as the scoring for these species would be much lower. The working data subset of species was refined to a total of 342 taxa (255 animals and 87 plants), including test control species. This was a far more workable number of species for the detailed research and assessment in the time allocated, which was required to produce a priority list with a high degree of confidence in its accuracy.
4.1.2 Development of a DNA search strategy The 342 taxa (255 animals and 87 plants) outlined above were investigated for available DNA information. After extensive discussions with information professionals a tiered search strategy was developed to identify relevant DNA markers for the species under investigation:
1. National Centre for Biotechnology Information (NCBI) database searching 2. Dialog searching 3. Internet searching 4. Discussions with experts
The strategy was devised to allow the maximum amount of information to be retrieved in a consistent, efficient and cost-effective manner. Initial searches were performed on publicly available databases of published literature and repositories of DNA sequence information using a series of key words (outlined below). Those species for which large amounts of relevant information could be identified using the initial approach did not proceed to the second, more comprehensive, search process. The remaining species were then subjected to a second investigation using a different package of databases, searching of which was charged on a “pay- per-go” basis. After the second round of searching the remaining species were investigated using more general internet search strategies. Finally, experts were identified and contacted to request assistance on identifying the availability of markers for the small remaining sub-set of species for which no DNA information could be identified using the above three approaches. The strategy used is outlined in more detail below:
1. NCBI searching
The first stage of the search for DNA information was to use the National Centre for Biotechnology Information (NCBI) website (www.ncbi.nlm.nih.gov). This was established in 1988 as a national resource for molecular biology information and contains many different databases containing DNA information. The Entrez section was used as this acts as a search and retrieval system that integrates information from all the different databases at NCBI.
Within Entrez, two databases were searched: • GenBank (nucleotide sequence database) and • MEDLINE (through PubMed).
These provided a simple method to retrieve available DNA sequence data and published literature citations.
For both database searches the Latin name for each species was entered. Once the Latin name had been entered and a search initiated, GenBank or PubMed generated a list of “hits” for further analysis.
Review of Current Wildlife Species Genetic Research - 8 - Final Report If the full Latin name failed to produce a list of hits the search was repeated using the genus part of the species only. This allowed the identification of “possible hits” which may consist of markers that differentiate other members of the genus and may prove useful in the species under investigation. With the animal subset in most cases this broader search provided a positive result, however less information was retrieved for the plants and the animal sub-species.
GenBank Searching
Hits from the GenBank search were examined and accession numbers recorded in the following order of priority: • Entire mitochondrial /chloroplast sequence • Entire cytochrome b gene • Partial mitochondrial/chloroplast sequences
With some species microsatellite and other markers where also identified through GenBank. Many of the hits were direct submissions to NCBI only and had not been published in the literature.
PubMed Searching
Depending on the number of entries (>100 for species specific entries), searches were refined to identify records containing reference to DNA markers using the following identifiers:
• Genetic • DNA • Character* • Marker* • Profil* • Fingerprint
Abstracts were viewed and relevant references obtained from the British Library Document Supply Centre.
If several reports describing the use of DNA markers for either species identification or familial analysis were identified the species was not investigated further.
2. DIALOG searching Species for which no DNA related information could be identified in the above resources, or had possible markers to a genus level only were then searched in specialised databases available through the DIALOG database host. These databases are available on a pay as you go basis and were used for the data-deficient species. Using a search strategy devised by an in-house information professional the remaining animals were searched for in Zoological Abstracts and Biosis, while plants were searched for within the agricultural database CAB abstracts. Zoological Abstracts provides extensive coverage of the worlds zoological literature with particular emphasis on the systematic/taxonomic information, while CAB abstracts is a comprehensive file of agricultural information, containing records from the abstract journals published by CAB International (CABI) recognised as a leading scientific information service in agriculture and related sciences. These databases were selected by the information professional after the results of trial searches for animals and plants within the subject indexes on the DIALOG host.
Review of Current Wildlife Species Genetic Research - 9 - Final Report Searching was performed using a similar strategy to the PubMed searching e.g. species Latin name in combination with key DNA-related words. If no information could be found for a species, articles describing the use of DNA markers in other members of the genus were identified. Once the entire reference details had been obtained a hard copy of the reference was obtained from the British Library and fully evaluated. If several reports describing the use of DNA markers for either species identification or familial analysis were identified the species was not investigated further. Very few references were identified through DIALOG that had not already been identified by PubMed and many of those found were only to genus level.
3. Internet searching Remaining species for which no DNA related information could be identified were investigated further using general Internet search engines such as www.google.com. The common and latin names were used as search terms. The web sites and related-links from world-renowned organisations were also searched. For example, a useful web site was identified: (http://snook.bio.indiana.edu/MENotes/easy_search.html) where species or family names were inputted into the database and all available primers developed for that species were shown. For the data-deficient species no further markers could be identified through internet searching, although useful contact details were obtained (see next section).
4. Discussion with experts The final stage of the DNA information search was to identify and contact relevant experts in the fields of wildlife genetics, conservation and DNA-based analysis to seek assistance.
Likely individuals and institutions were identified through a combination of: • discussions with experts already known to LGC; • discussions with individuals identified in stages 1 and 2 as actively publishing in the fields of wildlife genetics or with a particular interest in species on the list; • internet searching performed in stage 3.
Experts were contacted primarily by e-mail and asked if they were aware of any existing, new or unpublished markers for the DNA deficient species provided. Details regarding current research interests, expertise in identifying, developing and using DNA markers and willingness to assist in future potential studies were also requested. Experts were also asked to provide information on other individuals who may be able to offer assistance.
General DNA information After completing the search strategy a sub-set of species was identified as having no DNA information available. These were primarily birds, plants at the species level and animals at the sub species level. However, several general papers were identified that may prove useful in the development of DNA markers. Regarding the lack of plant species DNA information a paper was identified which outlined an easy protocol for developing universally useful primer sets to detect low copy number genes. Wider application of this approach should be effective at greatly increasing the amount of genetic information available for a diversity of plant nuclear genomes (Strand et al 1997). Two general papers regarding DNA research on birds were also identified: one of these papers describes a PCR based approach to sequencing complete avian mitochondrial genomes. The authors used a set of 86 degenerate primers spaced at 500 base pair intervals along both stands of the avian genome such that complete mitochondrial sequence amplification could be achieved (Sorenson et al 1999). The third paper described a way of sequencing several key genes within the avian genome and then using phylogenetic and jacknife
Review of Current Wildlife Species Genetic Research - 10 - Final Report analyses. This could aid the development of an avian phylogenetic tree that could in turn assist in the understanding of which primers would work on which species (van Tuinen 2000).
4.2 Development of Analytical Database System All data was compiled into an MS Access database. The database was designed and developed by LGC’s database specialist. Database construction and instructions for use are described in appendix 2.
4.3 The Ranking, Scoring and Weighting Systems
Once the working list had been honed down to a more workable size, based on the activities above, the selection and prioritisation system was developed to refine and focus attention on particular species to assess whether they are viable candidates for inclusion in the priority list. The system developed ranks species into priority order through a scoring and weighting system applied to the filters, criteria and sub-criteria and DNA data outlined above. The sub-criteria scores are totalled to produce criteria scores and the criteria scores, DNA scores and filter scores are totalled to produce a final rank value. Various weightings are applied to the different scores at different stages to ensure balance between the influence of certain sub-criteria and DNA data. The system was regularly reviewed and revised to ensure the scoring and weighting of the selection criteria was sensitive enough. The system is explained below.
4.3.1 DNA Ranking Strategy Once all the searches had been completed and the DNA information had been collected the data was ranked according to the level of DNA information available for each species. The ranking system chosen had a three-tier system:
Rank 1: markers available at the species/familial level Rank 2: “potential” markers available Rank 3: No DNA information identified
Rank 1 A species was ranked 1 if reports of markers (either microsatellite or mitochondrial/chloroplast markers) had been identified to distinguish the species from closely related taxa. A species was also ranked 1 if reports of markers (predominantly microsatellite) to examine the genetic variation within a species were identified (e.g. at the population, breeding group or individual level). For almost all species ranked 1 cytochrome b gene sequence information was available.
Example of rank 1 species
Javan Rhinoceros Rhinoceros sondaicus
The entire cytochrome b gene had been sequenced for this species and was identified on the NCBI website (GenBank Reference AJ245725). Several relevant published markers were identified using PubMed e.g. Tougard et al (2001) identified DNA markers capable of distinguishing the Javan rhino from other rhino species.
Review of Current Wildlife Species Genetic Research - 11 - Final Report Rank 2 A species was ranked as 2 if “potential or unconfirmed” markers were identified or sources of DNA information were available which may assist in the future identification and development of markers. Sources of information resulting in a rank of 2 included: • Mitochondrial sequence on GenBank. Although no specific markers may have been identified mitochondrial sequences from related sequences could be aligned and potential markers developed. • Genus level markers. Markers identified for other species within a genus may have the potential for application in the species under investigation. • Other potential/unconfirmed DNA markers. This included “in press” publications and other reports of DNA information which may be useful for the development of markers.
Example of rank 2 species
Black-faced Lion Tamarin Leontopithecus caissara
GenBank Reference AF320581
Using the search strategy outlined no specific markers were identified. However, microsatellites markers were identified at the genus level for Leontopithecus which may be able to identify the species under investigation e.g. Mundy et al (2000), Horovitz et al (1995 and 1998), Pastroni et al (1998) and Nagamachi et al (1999).
Rank 3 A species was ranked 3 if no DNA information could be identified.
Example of rank 3 species
Red and Blue Lory Eos Histrio
After using all searches no DNA information or leads could be identified.
Weighting Application It was determined early in development that the illegal trade criterion was one third more significant than the captive breeding criterion and proportionate weighting was in-built as explained below. If this was to be disproven later, other weightings could be applied to alter the balance between the criteria. Similarly the scores for the EU Annexes and IUCN Red List categories had in-built weightings. All weightings are fixed solely on the importance of the criteria compared to each other, generically for all species. The weightings were not assessed for each species with different weightings allocated. In addition to these fixed weightings, there was a need to apply an additional adaptable weighting to certain criteria, dependant upon different scenarios determining their significance to each other in how they influence the final priority list. This weighting was determined during the refinement stage. It applies to the weighting between the significance of the illegal trade and breeding criteria totals combined together with the total scores for the DNA data. It was agreed that the DNA data was of less significance that the illegal trade data and should be weighted accordingly. The extent to which
Review of Current Wildlife Species Genetic Research - 12 - Final Report it should weighted was tested to determine its impact on the final priority list. The weighting adjusts the DNA criteria totals, affecting the total score for each species. The combined totals of the illegal trade and breeding scores potentially range from 0 to 22.5. The weighting applied for the DNA information was to multiply the DNA score by a range of factors that would make the balance more appropriate with the illegal trade and breeding totals. Ultimately it was determined that the DNA scores should range from 0 to 10. This meant that DNA data was deemed to be of lesser significance to the illegal trade and breeding data scores combined.
EU Regulation Annex Ranking Strategy The significance of listing species under different levels of protection in the EU Annexes was scored to influence priority ranking. The Annexes were scored from zero to five according to their category or Annex, as follows: EU Annex Score A5 B3 C2 D0
Annex A was deemed to be of greater significance because the level of protection and importance attributed to these species is measurably greater than those in the lower Annexes. Annex A tends to be more aimed at preventing commercial trade in wild specimens of these species whereas the other Annexes aims to ensure that commercial trade is monitored. This has in-built weighting in the way the scoring is designed.
IUCN Threat Category Ranking Strategy The significance of listing species under different categories of threat in the IUCN Red Lists was scored to influence priority ranking. The threat categories were scored from zero to five according to their category, as follows:
Animals (2000 Red List categories) Score Extinct in the Wild (EW) 5 Critically Endangered (CR) 5 Endangered (EN) 4 Vulnerable (VU) 3 Lower Risk Near Threatened (LR:nt) 2 Lower Risk Conservation Dependant (LR:cd) 2 Data Deficient (DD) 1 Not Evaluated (NE) 1 Extinct (EX) 0 Lower Risk Least Concern (LR:lc) 0
Plants (1997 Red List categories) Extinct/Endangered (EX/EN) 5 Endangered (EN) 4 Vulnerable (VU) 3 Rare (R) 2 Indeterminate (I) 1 Insufficiently Known (K) 1 Extinct (EX) 0 Not Threatened (nt) 0
Review of Current Wildlife Species Genetic Research - 13 - Final Report Because different listings were used for animals and plants due to data completeness, scores had to be developed for the different criteria. It was determined that those species in greatest danger of extinction should be attributed the highest scores. The influence of whether or not these species occur in trade etc. is resolved with the addition of the data on illegal trade etc. This has in-built weighting in the way the scoring is designed.
An alternative ranking strategy to increase the weighting of those species classified as Data Deficient from 1 to 2 in order to reflect the potential threat of endangerment of those species was also used to generate an alternative priority animal list (appendix 1).
Illegal Trade Criteria Ranking Strategy The illegal trade criteria is comprised of three sub-criteria (seizures/poaching, intelligence, ease of identification). Each sub-criteria is totalled and added to the other sub-criteria to produce a criteria total for illegal trade. Each sub-criteria is evaluated for each species through research and a significance score is attributed to it. This significance score ranges from zero to three. The significance scores are attributed under the following rules:
0 No data available, unknown score, highly unlikely to be of significance 1 Little data available, one or two records found 2 Some data available between two and five records found 3 A good deal of data available more than five records founds
Each significance score is also attributed an error margin that is basically an evaluation of the accuracy and reliability of the information and sources from which it came from. The error score ranges from 0 to 1.5. The error scores are attributed under the following rules:
0 No error assessment possible, unknown score 0.5 Highest likelihood of error, source has unknown or poor reputation, data reliability is low, little correlating data to support it 1 Medium likelihood of error, source has good reputation, data reliability is medium, some correlating data to support it 1.5 Lowest likelihood or error, an official source or the most respected reputation, data reliability is high, a good deal of correlating data to support it
The error scores are totalled with the significance scores to produce a sub-criteria total potentially ranging from 0 – 4.5 for each species. All of the sub-totals for each sub-criteria are then totalled to produce the total score for the criteria of illegal trade for each species. This total score can potentially range from 0 to 13.5. For example:
Species Record Sub-criteria Significance Score Error Score Sub-Total Seizure / Poaching Records 3 1.5 4.5 Intelligence Information 1 0.5 1.5 Ease of Identification 2 1 3
Illegal Trade Criteria Total 9
Breeding Criteria Ranking Strategy
Review of Current Wildlife Species Genetic Research - 14 - Final Report The breeding / propagation criteria are comprised of two sub-criteria (ease of breeding / propagation and breeding / propagation capacity). The scoring mechanism is the same as outlined for the illegal trade criteria above, with exactly the same significance score ranges, error margin ranges and system of producing a total score. The significance scores are attributed under the following rules:
0 No data available, unknown score, highly unlikely to be of significance 1 High breeding / propagative capacity or easy to breed /propagate 2 ‘Average’ breeding / propagative capacity or ‘average’ to breed /propagate 3 Low breeding / propagative capacity or difficult to breed / propagate
However, as there are only two sub-criteria the total score for the criteria can only potentially range between 0-9, rather than 0-13.5 as with illegal trade. This is because illegal trade information is deemed to be of greater significance than breeding information. This brings in a natural weighting to the system that accommodates the difference in significance by a factor of 33 percent in favour of the illegal trade criteria. An example of scoring for this criterion is provided here:
Species Record Sub-criteria Significance Score Error Score Sub-Total Ease of Breeding 2 1 3 Breeding Capacity 1 0.5 1.5
Breeding Criteria Total 4.5
DNA Information Weighting Strategy DNA Significance Score DNA rank 3 10 DNA rank 2 5 DNA rank 1 0
Summary of Weighting Criteria CATEGORY SCORE Annexes Annexe A 5 Annexe B 3 Annexe C 2 Annexe D 0
IUCN Animals (1994 categories) Extinct in the Wild (EW), Critically Endangered (CR) 5 Endangered (EN) 4 Vulnerable (VU) 3 Lower Risk Near Threatened (LR:nt), Lower Risk Conservation 2 Dependant (LR:cd) Data Deficient (DD), Not Evaluated (NE) 1 Extinct (EX), Lower Risk Least Concern (LR:lc) 0
IUCN Plants (pre 1994 categories) Extinct/Endangered (EX/EN) 5 Endangered (EN) 4
Review of Current Wildlife Species Genetic Research - 15 - Final Report Vulnerable (VU) 3 Rare (R) 2 Indeterminate (I), Insufficiently Known (K) 1 Extinct (EX), Not Threatened (nt) 0
Illegal trade Total of three categories 0-13.5
Captive breeding Total of two categories 0-9
DNA DNA rank 3 10 DNA rank 2 5 DNA rank 1 0
Calculation of Overall Priority Rankings The combination of values for sub-criteria (producing criteria scores) and criteria scores combined with the influence of weightings, produce a final rank score for the taxa that allows sorting into a priority list. The total scoring and ranking system is outlined here (showing maximum potential scores):
EU Annex Score + Red List Score + (Illegal Trade + Breeding ) + (DNA Score x Weighting) = Rank Score
EU Annex Score 5 Red List Score 5 Illegal Trade 13.5 Breeding 9 DNA Score 10 Rank Score 42.5
The potential total range of scores for each species is 0 to 42.5. It was determined that this would provide the degree of resolution required to produce a priority list of 75-100 taxa.
Review of Current Wildlife Species Genetic Research - 16 - Final Report 5. Output
Availability of DNA markers The availability of DNA markers for all species investigated are described in appendixes 6 and 7 for animals and plants repectively. A summary of the overall DNA ranking is shown below:
Rank Animals Plants 1 126 6 2 105 77 3254 Total 256 87
Generation of “Top 100” priority list of plants and animals The overall priority ranking for each species was generated automatically by the MS Access database using the ranking calculation described previously. The individual rank components of the potential priority species were examined manually and those species scoring zero for DNA rank (which indicates that DNA markers are available) were excluded from the priority list. The following tables show the priority rankings for the top 75 animals and 75 plants:
Priority Animal List Full_Latin_Name Priority DNA Annex IUCN Breed Trade Data Rank Rank Rank Rank Data total total Batagur baska 38 10 5 5 6.5 11.5 Pithecophaga jefferyi 38 10 5 5 9 9 Ognorhynchus icterotis 36.5 10 5 5 8.5 8 Rhodonessa caryophyllacea 36 10 5 5 9 7 Pitta gurneyi 35 10 5 5 9 6 Odontophorus strophium 34 10 5 5 8 6 Pseudibis gigantea 34 10 5 5 8.5 5.5 Dicerorhinus sumatrensis sumatrensis 34 5 5 5 9 10 Ceratotherium simum cottoni 34 5 5 5 9 10 Rheobatrachus silus 33.5 10 5 5 8.5 5 Ophrysia superciliosa 33.5 10 5 5 8.5 5 Aspideretes nigricans 33.5 10 5 5 8.5 5 Moschus moschiferus 33.5 5 3 3 9 13.5 Dicerorhinus sumatrensis harrissoni 33.5 5 5 5 8.5 10 Capra falconeri heptneri 33 5 5 5 8 10 Diceros bicornis longipes 33 5 5 5 9 9 Procolobus pennantii bouvieri 32.5 10 5 5 8 4.5 Moschus chrysogaster 32.5 5 3 2 9 13.5 Anodorhynchus leari 32.5 5 5 5 6 11.5 Cyclura carinata carinata 32.5 5 5 5 7.5 10 Rhinoceros sondaicus annamiticus 32.5 5 5 5 8.5 9 Acinonyx jubatus venaticus 32.5 5 5 5 9 8.5 Mitu mitu 32 10 5 5 8 4 Pteropus phaeocephalus 32 5 5 5 7 10 Amazona imperialis 32 5 5 4 8.5 9.5
Review of Current Wildlife Species Genetic Research - 17 - Final Report Rhinoceros sondaicus sondaicus 32 5 5 5 8.5 8.5 Ovis ammon nigrimontana 32 5 5 5 8.5 8.5 Brachylophus fasciatus 31.5 5 5 4 7.5 10 Testudo graeca nikolskii 31.5 5 5 5 8 8.5 Malacochersus tornieri 30.5 10 5 3 12.5 Amazona brasiliensis 30.5 5 5 4 6 10.5 Saimiri oerstedii citrinellus 30.5 5 5 5 8 7.5 Propithecus diadema perrieri 30.5 5 5 5 8.5 7 Propithecus diadema candidus 30.5 5 5 5 8.5 7 Pteropus molossinus 30 5 5 5 7 8 Equus africanus 30 5 5 5 7 8 Cyclura carinata bartschi 30 5 5 5 7.5 7.5 Cercocebus galeritus galeritus 30 5 5 5 8.5 6.5 Anodorhynchus glaucus 30 5 5 5 8.5 6.5 Monachus monachus 30 5 5 5 9 6 Bufo periglenes 30 5 5 5 9 6 Pteropus voeltzkowi 29.5 5 5 5 7 7.5 Sus salvanius 29.5 5 5 5 7.5 7 Aythya innotata 29.5 5 5 5 7.5 7 Leontopithecus caissara 29.5 5 5 5 8.5 6 Tadorna cristata 29.5 5 5 5 9 5.5 Acrantophis dumerili 29 5 5 3 5.5 10.5 Ara glaucogularis 29 5 5 5 5.5 8.5 Panthera tigris amoyensis 29 5 5 5 6.5 7.5 Pteropus insularis 29 5 5 5 7 7 Numenius borealis 29 5 5 5 8 6 Eos histrio 28.5 10 5 4 9.5 Cervus duvaucelii ranjitsinhi 28.5 5 5 5 6 7.5 Cyclura rileyi rileyi 28.5 5 5 5 7.5 6 Numenius tenuirostris 28.5 5 5 5 8 5.5 Papasula abbotti 28.5 5 5 5 8.5 5 Zosterops albogularis 28 5 5 5 8 5 Penelope albipennis 27.5 5 5 5 7 5.5 Pteropus livingstonei 27.5 5 5 5 7.5 5 Cervus eldii eldii 27.5 5 5 5 7.5 5 Aceros nipalensis 27 10 5 3 3 6 Chinchilla brevicaudata 27 5 5 5 5 7 Bubo bubo 26.5 5 5 0 6 10.5 Equus africanus somalicus 26.5 5 5 5 5 6.5 Testudo kleinmanni 26 5 5 4 12 Athene blewitti 26 5 5 5 6 5 Antilocapra americana peninsularis 26 5 5 5 7.5 3.5 Dromus dromas 25.5 10 5 5 5.5 Villosa trabalis 25.5 10 5 5 1 4.5 Toxolasma cylindrellus 25.5 10 5 5 1 4.5 Plethobasus cooperianus 25.5 10 5 5 1 4.5 Plethobasus cicatricosus 25.5 10 5 5 1 4.5 Leptotila wellsi 25.5 10 5 5 1 4.5 Lampsilis virescens 25.5 10 5 5 1 4.5 Varanus melinus 25.5 5 3 1 5.5 11
Review of Current Wildlife Species Genetic Research - 18 - Final Report Priority Plant List Full_Latin_Name Priority DNA Annex IUCN Art Prop Trade Total Rank Rank Rank Rank Total Protea odorata 33.5 10 5 4 9 5.5 Discocactus horstii 33 10 5 4 6 8 Saussurea costus 33 5 5 4 5.5 13.5 Ariocarpus bravoanus 33 5 5 4 8.5 10.5 Discocactus subviridigriseus 32.5 10 5 4 6 7.5 Ariocarpus agavoides 32 5 5 4 7.5 10.5 Paphiopedilum armeniacum 32 5 5 4 5.5 12.5 Uebelmannia buiningii 31 5 5 4 6.5 10.5 Turbinicarpus schmiedickeanus 31 5 5 4 6.5 10.5 flaviflorus Paphiopedilum tonsum 31 5 5 4 7.5 9.5 Paphiopedilum victoria-regina 31 5 5 4 7.5 9.5 chamberlainianum Paphiopedilum fairrieanum 31 5 5 4 5.5 11.5 Paphiopedilum dayanum 30.5 5 5 4 6.5 10 Pediocactus bradyi 30.5 5 5 4 5.5 11 Paphiopedilum micranthum 30.5 5 5 4 5.5 11 Paphiopedilum rothschildianum 30.5 5 5 4 5.5 11 Encephalartos munchii 30.5 5 5 4 6.5 10 Echinocereus schmollii 30.5 5 5 4 5.5 11 Ceratozamia microstrobila 30.5 5 5 4 6.5 10 Paphiopedilum javanicum virens 30 5 5 4 6.5 9.5 Pediocactus winkleri 30 5 5 4 6.5 9.5 Paphiopedilum sanderianum 30 5 5 4 5.5 10.5 Aloe helenae 30 5 5 4 7.5 8.5 Sclerocactus wrightiae 30 5 5 4 6.5 9.5 Pachypodium ambongense 30 5 5 4 8 8 Ceratozamia euryphyllidia 30 5 5 4 6.5 9.5 Pachypodium decaryi 30 5 5 4 6.5 9.5 Melocactus conoideus 30 10 5 4 4 7 Pediocactus knowltonii 30 5 5 4 5.5 10.5 Euphorbia handiensis 30 5 5 4 7.5 8.5 Paphiopedilum malipoense 30 5 5 4 5.5 10.5 Paphiopedilum druryi 30 5 5 4 6.5 9.5 Paphiopedilum glaucophyllum 30 5 5 4 6.5 9.5 Paphiopedilum exul 30 5 5 4 6.5 9.5 Aloe polyphylla 29.5 5 5 4 6.5 9 Encephalartos aemulans 29.5 5 5 4 7 8.5 Aloe suzannae 29.5 5 5 4 5.5 10 Echinocereus ferreirianus lindsayi 29.5 5 5 4 5.5 10 Ceratozamia zaragozae 29.5 5 5 4 6.5 9 Cycas beddomei 29.5 5 5 4 6.5 9 Encephalartos concinnus 29 5 5 4 6.5 8.5 Orchis scopulorum 29 5 5 4 8 7 Paphiopedilum stonei 29 5 5 4 6.5 8.5 Encephalartos whitelockii 29 5 5 4 6.5 8.5 Aloe albiflora 29 5 5 4 7 8 Encephalartos pterogonus 29 5 5 4 6.5 8.5 Phragmipedium exstaminodium 29 5 5 4 6.5 8.5 Ceratozamia hildae 28.5 5 5 4 4.5 10 Aloe fragilis 28.5 5 5 4 5.5 9
Review of Current Wildlife Species Genetic Research - 19 - Final Report Aloe pillansii 28.5 5 5 4 5.5 9 Encephalartos cerinus 28.5 5 5 4 6.5 8 Encephalartos brevifoliolatus 28.5 5 5 4 6.5 8 Encephalartos venetus 28 5 5 4 6.5 7.5 Encephalartos nubimontanus 28 5 5 4 6.5 7.5 Encephalartos middelburgensis 28 5 5 4 6.5 7.5 Euphorbia ambovombensis 28 5 5 4 6.5 7.5 Encephalartos msinganus 28 5 5 4 6.5 7.5 Encephalartos heenanii 28 5 5 4 6.5 7.5 Encephalartos dyerianus 28 5 5 4 6.5 7.5 Encephalartos dolomiticus 28 5 5 4 6.5 7.5 Encephalartos laevifolius 28 5 5 4 6.5 7.5 Aloe parvula 28 5 5 4 5.5 8.5 Encephalartos inopinus 28 5 5 4 6.5 7.5 Agave arizonica 28 5 5 4 6.5 7.5 Encephalartos cupidus 28 5 5 4 6.5 7.5 Dudleya traskiae 28 5 5 4 8 6 Dudleya stolonifera 28 5 5 4 8 6 Goodyera macrophylla 27.5 5 5 4 7.5 6 Encephalartos schmitzii 27.5 5 5 4 6.5 7 Escobaria minima 27.5 5 5 4 5.5 8 Encephalartos chimanimaniensis 27 5 5 4 6.5 6.5 Aloe calcairophylla 26.5 5 5 4 6.5 6 Aloe compressa compressa 26.5 5 5 4 6.5 6 Aloe bellatula 26 5 5 4 4.5 7.5 Coryphantha werdermannii 26 5 5 4 5.5 6.5 Aloe descoingsii 25.5 5 5 4 5.5 6
6. Recommendations
1. Further research to make data holdings more extensive and the priority list more accurate: The priority list could be more conclusive if further research were undertaken to complete the data for a wider range of species. It would be of particular value to collate data for more species listed in the IUCN threat categories other than critically endangered and endangered.
2. The dataset should be revised biennially Ideally revision should follow each amendment to the CITES Appendices at the CITES Conference of the Parties that impacts on the EU Regulation Annexes, and each revision of the IUCN Redlists. Revising the DNA research data should take place for particular species that are added to the database or altered that are very likely to be included in the top 100 list
3. Testing the system further Further testing of the system should be performed where funding allows to look at the influence of a variety of weighting and scoring scenarios as well as assessing whether new or additional criteria would add refinement to the prioritising mechanism
5. Future updates for DNA information should focus on searching the NCBI site:
Review of Current Wildlife Species Genetic Research - 20 - Final Report The majority of the DNA information retrieved was through the NCBI site only. Very few new sources of DNA information were located through the other search engines, which were in some cases very costly due to high access time charges.
6. Dissemination of findings: The development of the system and the findings should be promoted where relevant, including publishing papers in appropriate journals and presentations at conferences. 7. Conclusion The project has successful created an analytical filtering and ranking system that has generated a priority list of endangered species for genetic research, to benefit wildlife trade law enforcement. The project has developed a database and applied filter and ranking systems to select and refine subsets of species for potential selection. Extensive research has documented and developed scores for a range of criteria that contribute to the total rank score for each species. Extensive studies into the illegal trade, ease of identification, breeding and DNA research for the species have been completed within the time and resources allocated. This study has documented the current availability of DNA markers for over 300 high priority species. A ranking strategy has been devised to highlight those species where development of DNA markers would have the most impact. The priority lists generated during this study will provide a valuable resource, both for researchers developing DNA markers for endangered species and also for those directing the focus of future research programmes. The current availability of DNA markers and lists of researchers with expertise in the area, who would be willing to assist in marker development and in enforcement cases, will be of use to those currently involved in enforcing the laws.
The financial constraints of the project have meant that only a time restrictive range of species could be selected for research. The main emphasis for species selection was on those species that were therefore most threatened with extinction and the most strictly protected by wildlife trade law. Further resources would be needed to examine species in lower priority groups. Selected examples from species in lower threat categories have been examined during the course of the project. Those species in lower categories which scored highly for trade, breeding and DNA criteria achieved relatively high overall priority rankings, indicating that the allocation of further resources to investigate the availability of DNA information for species in lower threat categories should be considered. As a result of the development of DNA Markers being ongoing, the database will quickly become out-dated if the records are not updated and the database maintained. We have endeavoured to be as comprehensive as possible with the searching but there may be markers available that were not identified during the course of the investigation.
The priority lists may contain some species that are in reality not priorities to assist law enforcement because they are unlikely to occur in illegal trade or they are not priorities for DNA research because there has already been extensive DNA research undertaken. The combined influence of other factors may outweigh the influence of the illegal trade or DNA information in some cases. This is unnavoidable in a formulaic system such as this where the DNA and illegal trade scoring ranges are roughly equal. They have to be roughly equal as they are the two most critical elements and a list should not bias too much in favour of one or the other. There is no point in a list that includes species that are subject to illegal trade but that have DNA tests developed for them. Equally, the list should not include species that are not subject to illegal trade but that have no DNA research evident. An example of this would be some of the Achatinella snails, which are now very rare terrestrial snails from Hawaii, known only in very few isolated sites in certain valleys. These are no longer in trade due to their rarity, but in the
Review of Current Wildlife Species Genetic Research - 21 - Final Report past they were traded for their ornate shells by collectors and for museum specimens. Very little DNA research could be identified and they are not bred in captivity on any significant scale.
Another factor to consider is the rapid changes over time that mean a species that was a priority only a few years ago may not be a priority today. The collation of the illegal trade and breeding data focussed on the period 1991-2001 for each species. However, records of illegal trade ten years ago may have been during a time when the species was far more abundant or when it was in demand in trade. The rapid decline of some species has meant that in the present day they are no longer in trade because they have become so scarce or trade trends have changed. It is highly unlikely in some cases that there will be illegal trade in some of these species in future (but if there were, no DNA test would be available to support an enforcement case). In these cases, a final filter should be applied to remove those species that have very low scores for either DNA research or illegal trade information to provide a necessary ‘reality check’ to ensure that the results of this theoretical system are applicable in reality.
Of greatest significance is the development of a system that can be updated in future as a result of changes in the regulation of species in trade, breeding advances, threat classification or DNA research. This project has created the mechanism by which this can be achieved. This task in itself was far more involved and difficult than could have been envisaged from the original proposal. There was far more analysis and research required than was expected. The system is by no means flawless but is a vehicle for the future upon which the prioritisation for species research can be based. Whilst the system has been developed taking the most significant factors into consideration, incorporating a great deal of research and analysis, its value is in providing guidance not in providing a definitive answer. The accuracy of the system is only as reliable as the data it utilises. The research was time restricted and therefore research effort was critical in determining the results. While we are confident in our methods and results, the latter should be taken as the best guide available not the definitive answer to deciding research priorities. The priority list produced is adaptable, depending upon the significance placed by the operator of the system on the criteria and the relationships between them. To a certain extent the weightings and scoring could be seen as subjective but they are based upon sound research and scientific judgement and all potential influences of error are accounted for in the analysis. Other users of the system in future may decide to change the emphasis on certain criteria, for example the weightings for the threat category of a species may be reduced if the user deems this to be of less significance and more species from lower IUCN threat categories may rise up the priority list. There is much potential for fine tuning the system according to user need.
A great deal has been learnt about the process of prioritising species to meet the aims set out in the project. Efforts should be made to ensure that this expertise and information is applied and that the system is continually revised. The only limitation is the time and resources required to gather, analyse and enter the data into the system.
8. Acknowledgements The MS Access database and guideline for use was designed and created by Allen Brown. Simon Cowen assisted with the database design and advised on ranking strategies and Sarah Morris (information professional) assisted with compiling the DIALOG database search strategy and provided general advice on information retrieval. Bruce Keeble assisted with the database searching and data retrieval. Helen Parkes, Jason Sawyer and Ric Treble developed the original project for LGC.
Review of Current Wildlife Species Genetic Research - 22 - Final Report Stephanie Pendry assisted in project development for TRAFFIC International. UNEP-WCMC provided the basic dataset of threatened species listed on the EU Annexes. Craig Hilton-Taylor of the IUCN/SSC Red List Proramme advised on Red List issues. Dr. Wolfgang Stuppy, Royal Botanic Gardens, Kew, Dr. Onnie Byers and Dr. Ulysses S. Seal of the IUCN/SSC Conservation Breeding Specialist Group, advised on the development of the propagation / breeding criterion. We also gratefully acknowledge the many experts who advised on appropriate scores for individual taxa.
Prof. Mike Bruford of Cardiff University, Nick P. Williams and Jane Withey of DEFRA, provided invaluable guidance in the Steering Group and review of the reports.
Review of Current Wildlife Species Genetic Research - 23 - Final Report 9. Appendices
9.1 Appendix 1 : Alternative animal ranking and prioritisation strategy An alternative scoring/ranking strategy was devised to produce an alternative prioritisation list for the animal species. The data deficient/insufficiently known score was changed from 1 to 2 to reflect the fact that species for which there was insufficient data available may be at a higher risk than indicated by a score of 1. In addition, all animal sub-speies for which there are DNA markers available for the species as a whole (or other sub-species within that taxa) were removed from the list on the assumption that those markers available for the species as a whole may be informative in all sub-species within the taxa. Those sub-species for which there are no DNA markers available for any members of the species remain in the list. The alternative revised priority list is shown below:
Alternative Priority Animal List Full_Latin_Name Priority DNA Rank Annex IUCN Breed Trade Rank Rank Rank Data total Data total Pithecophaga jefferyi 38 10 5 5 9 9 Batagur baska 38 10 5 5 6.5 11.5 Ognorhynchus icterotis 36.5 10 5 5 8.5 8 Rhodonessa caryophyllacea 36 10 5 5 9 7 Pitta gurneyi 35 10 5 5 9 6 Odontophorus strophium 35 10 5 5 9 6 Pseudibis gigantea 34.5 10 5 5 9 5.5 Malacochersus tornieri 34.5 10 5 3 4 12.5 Rheobatrachus silus 34 10 5 5 9 5 Aspideretes nigricans 34 10 5 5 9 5 Moschus moschiferus 33.5 5 3 3 9 13.5 Moschus chrysogaster 32.5 5 3 2 9 13.5 Anodorhynchus leari 32.5 5 5 5 6 11.5 Toxolasma cylindrellus 32 10 5 5 7.5 4.5 Amazona imperialis 32 5 5 4 8.5 9.5 Rhinoceros unicornis 31.5 0 5 4 9 13.5 Dicerorhinus sumatrensis 31.5 0 5 5 9 12.5 Brachylophus fasciatus 31.5 5 5 4 7.5 10 Acipenser sturio 31.5 0 5 5 8 13.5 Amazona brasiliensis 30.5 5 5 4 6 10.5 Uncia uncia 30 0 5 4 8 13 Pteropus molossinus 30 5 5 5 7 8 Equus africanus 30 5 5 5 7 8 Bufo periglenes 30 5 5 5 9 6 Tadorna cristata 29.5 5 5 5 9 5.5 Sus salvanius 29.5 5 5 5 7.5 7 Aythya innotata 29.5 5 5 5 7.5 7 Numenius borealis 29 5 5 5 8 6 Leontopithecus rosalia 29 0 5 5 7 12 Diceros bicornis 29 0 5 5 7.5 11.5 Ara glaucogularis 29 5 5 5 5.5 8.5 Acrantophis dumerili 29 5 5 3 5.5 10.5 Papasula abbotti 28.5 5 5 5 8.5 5 Pantholops hodgsonii 28.5 0 5 4 6 13.5 Panthera tigris 28.5 0 5 4 6 13.5
Review of Current Wildlife Species Genetic Research - 24 - Final Report Numenius tenuirostris 28.5 5 5 5 8 5.5 Eos histrio 28.5 10 5 4 9.5 Cacatua haematuropygia 28.5 0 5 5 8.5 10 Zosterops albogularis 28 5 5 5 8 5 Rhinoceros sondaicus 28 0 5 5 8.5 9.5 Crocodylus siamensis 28 0 5 5 5 13 Saiga tatarica 27.5 0 3 2 9 13.5 Pyxis planicauda 27.5 5 4 9 9.5 Cyclura cornuta 27.5 0 5 3 7.5 12 Cyclura carinata 27.5 0 5 5 7.5 10 Vicugna vicugna 27 0 5 2 6.5 13.5 Tremarctos ornatus 27 0 5 3 7.5 11.5 Chinchilla brevicaudata 27 5 5 5 5 7 Aceros nipalensis 27 10 5 3 3 6 Scleropages formosus 26.5 0 5 4 5 12.5 Cyclura collei 26.5 0 5 5 7.5 9 Bubo bubo 26.5 5 5 0 6 10.5 Ursus thibetanus 26 0 5 3 5.5 12.5 Testudo kleinmanni 26 5 5 4 12 Mergus octosetaceus 26 0 5 5 9 7 Cyclura pinguis 26 0 5 5 7.5 8.5 Canis simensis 26 0 5 5 9 7 Athene blewitti 26 5 5 5 6 5 Varanus melinus 25.5 5 3 1 5.5 11 Leucopsar rothschildi 25.5 0 5 5 6 9.5 Dromus dromas 25.5 10 5 5 5.5 Zyzomys pedunculatus 25 10 5 5 5 Pteropus phaeocephalus 25 5 5 5 10 Pseudemydura umbrina 25 0 5 5 7 8 Pardofelis marmorata 25 5 1 8.5 10.5 Ophrysia superciliosa 25 10 5 5 5 Haliaeetus pelagicus 25 5 5 3 12 Grus leucogeranus 25 0 5 5 7 8 Falco rusticolus 25 0 5 0 6.5 13.5 Eutriorchis astur 25 10 5 5 5 Conraua goliath 25 10 3 3 9 Brachylophus vitiensis 25 0 5 5 7.5 7.5 Achatinella vulpina 25 5 5 5 6 4 Achatinella viridans 25 5 5 5 6 4 Achatinella turgida 25 5 5 5 6 4 Achatinella taeniolata 25 5 5 5 6 4 Achatinella swiftii 25 5 5 5 6 4 Achatinella stewartii 25 5 5 5 6 4 Achatinella pupukanioe 25 5 5 5 6 4 Achatinella pulcherrima 25 5 5 5 6 4 Achatinella phaeozona 25 5 5 5 6 4 Achatinella lorata 25 5 5 5 6 4 Achatinella curta 25 5 5 5 6 4 Achatinella concavospira 25 5 5 5 6 4 Achatinella cestus 25 5 5 5 6 4 Achatinella bulimoides 25 5 5 5 6 4 Achatinella bellula 25 5 5 5 6 4 Villosa trabalis 24.5 10 5 5 4.5 Procolobus pennantii 24.5 10 5 5 4.5
Review of Current Wildlife Species Genetic Research - 25 - Final Report bouvieri Plethobasus cooperianus 24.5 10 5 5 4.5 Plethobasus cicatricosus 24.5 10 5 5 4.5 Panthera pardus 24.5 0 5 0 6 13.5 Milvus milvus 24.5 0 5 0 7 12.5 Leptotila wellsi 24.5 10 5 5 4.5 Lampsilis virescens 24.5 10 5 5 4.5 Geochelone platynota 24.5 5 3 5 11.5 Fregata andrewsi 24.5 5 5 5 5.5 4 Crocodylus intermedius 24.5 0 5 5 7 7.5
9.2 Appendix 2 : Species Database Construction and Use The Species Database has been developed to collect data relating to endangered species of plants and animals. The data is used to put the species in order of rank according to the level of risk that exists.
General Description of Database
The database has been structured to store data relating to animals and plants in separate parts. The criteria that are used to put the species of animals and plants in a final rank order of endangerment are somewhat different.
Both the animals and the plants parts of the application are constructed using main tables that have unique information relating to each record. These have been labelled the Master Species tables. These master tables are linked to a number of information tables that contain data about each entry on the master table. Each record in the master tables contains the unique Latin name for each record.
When viewing or editing data in the various information tables, the master table record for that species remains visible at all times.
Operating Instructions Main Menu
Choose which part of the database to use by clicking the ‘Animals’ or the ‘Plants’ part of the ‘Species’ option. Whichever option is chosen, all the other options on the Main Menu will open parts of the database relating to the choice of Species.
Review of Current Wildlife Species Genetic Research - 26 - Final Report Records When the ‘Records’ button is clicked, the application opens a form showing information in the master table.
The illustration shows the form that is opened when the Animals Records are chosen. At the top of this form are five buttons that open sub forms relating to the master record, namely ‘Captive Breeding, Breeding Data, Illegal Trade, Illegal Trade Data and DNA:
Captive Breeding Captive Breeding Data
Illegal Trade Illegal Trade Data
Review of Current Wildlife Species Genetic Research - 27 - Final Report At the bottom of the four windows shown above, there is an option to open another form where references relating to the data can be recorded. To activate this reference form, click the ‘Yes’ box to reveal the references form. A button labelled ‘Get information’ appears to open the reference form.
Note that when this form is opened, the Latin name of the species is automatically filled into the first box. Move to the ‘Reference’ box and then to the ‘Notes’ box to enter information. For each reference and note, a new line should be used and the Latin name will appear in the ‘Full Latin Name’ box.
DNA When the ‘DNA’ button is clicked, the following message appears :
“Availability of DNA markers investigated?” Where the answer to this question is ‘Yes’, then the DNA information form is opened:
The DNA Priority Rank value appears in the box and a series of forms that contain information about markers and other relevant factors are viewed where the option settings are set to ‘Yes’. Where the option is ‘Yes’, click the ‘Get Information’ button to access the relevant data.
The brief descriptions of the forms given above are taken from the animals part of the application but the same procedures and formats have been used for the plants part.
Review of Current Wildlife Species Genetic Research - 28 - Final Report Searches At the top right hand side of the main form is a button labelled ‘Search’. When this is clicked it opens a menu where a choice of searches can be made.
Choose ‘Composite Search’ for searching records where the search criteria are entered as a mathematical logic statement.
Choose ‘General Search’ for searching where the search criteria are entered into boxes assigned to each field.
Composite Search
To activate a search, a statement is typed in the ‘Search for’ box. When the ‘Search’ button is clicked the application searches the tables and matches records with the criteria. The contents of the ‘Search for’ box is written in a code that can be understood by the application and the following notes are designed to be of assistance.
Review of Current Wildlife Species Genetic Research - 29 - Final Report The search statement has three basic parts; it begins with a field name, the middle part is a condition and the end part is a value.
Example To search the animals and find records where the Genus is Abeillia, we type in the following statement in the ‘Search for’ box:
Genus = "Abeillia" Genus is the field name = is the condition Abeillia is the value
Note that the value is surrounded by speech marks and each part of the statement is separated by a space.
To activate the search, click the ‘Search’ button.
If any records are found they are shown on a form very similar to the main form. This form has the same five buttons at the top allowing the user to view the various related tables and values for the found animal or plant. To view other found records use the navigation buttons at the bottom left hand corner of the form or use the Page Up and Page Down buttons. Click the ‘Close’ button to return to the Search Station.
We can search for more than one field or value at any one time. For example, to find animals that have a Latin name ‘Accipiter butleri’ or ‘Achatinella bulimoides rosea’, we would type the following statement:
Full_Latin_Name = "Abeillia abeillei" or Full_Latin_Name = "Accipiter gundlachi " To assist typing in field names accurately, the field names can be inserted by double clicking the name listed under ‘Searchable Fields’. A list of IUCN categories is also given and can be inserted by double clicking.
Sometimes it might be necessary to search for a value that is part of a longer value in a field. For example, to search for a red parrot where the Latin name is not known.
Review of Current Wildlife Species Genetic Research - 30 - Final Report We could type the following in the ‘Search for’ box:
Common_Name = "Parrot" The chances are, however, that this is not what has been entered as the common name although ‘red parrot’ is probably part of the name. To overcome this dilemma we use a wild card that indicates that red parrot is only part of the name.
The wild card character is a star (*).
Our revised search statement is now
Common_Name like "*Parrot" Notice that the value is still enclosed in speech marks and that the star is typed before the value. Also, when we use wild card characters, we use the like condition – not the equals condition.
When we type the wild card character at the beginning of the value we wish to test then only records where the value is at the end of the field will be found. In the given example the results included Puerto Rican Parrot and Night Parrot.
If we type the wild card after the value then the value will be searched for where it occurs at the beginning of the name.
Common_Name like "Red*" This statement will look for records where the common name begins with the word ‘Red’.
If we wish to search for records where the value can be any part of the field then we use two wild card characters:
Common_Name like "*Red Parrot*" We place one star at the beginning of our value and one at the end. Now as long as the common name contains the words RED PARROT, they will be found.
Other buttons on the Search form:
View Tags When viewing or editing data, it is possible to mark records by ticking the ‘Tag’ box. A tick in the box indicates ‘Yes’ whereas a blank in the box indicates ‘No’. To view all the records that have been marked with a Tag click the ‘View Tags’ button.
Clear Tags Click to set all the marked tagged records to ‘No’.
Tag Records Once a set of records has been found, clicking this button can mark them all. This is a useful way of creating a set of records to view.
Search Type This is used where it is required to search only the records found in the previous search setup.
Example of using Search Type Enter the following statement into the ‘Search for’ box:
Review of Current Wildlife Species Genetic Research - 31 - Final Report DNA_Priority_Rank = 2 Click the ‘Search’ button to find the records.
When the records have been viewed, return to the Search Station and click the ‘Clear Search for’ button. Also click the ‘Search Type’ to indicate ‘found records’.
Now type the following in the ‘Search for’ box:
EU_Annex Like "*b" Click the ‘Search’ button. The found records will be those in the set of records where the DNA Priority Rank was 2. Note the number of records found.
Click the ‘Search Type’ to read ‘all records’ and then perform the search again by clicking the ‘Search’ button. Note that the number of records has probably changed although the search criteria are the same.
View Found Records When this button is clicked, the results of the last search can be viewed.
Clear Search For Clears the ‘Search for’ box of input so that a new search statement can be written.
Reset This button clears the ‘Search for’ box and finds all the records in the database (animals or plants – depending which part is open).
General Search This is the alternative button on the ‘Search Menu’.
On this form the search criteria are entered into the boxes. One or more boxes may be used for a search.
Review of Current Wildlife Species Genetic Research - 32 - Final Report Example of a general search If we are looking for all the animals that have a common name that includes the word ‘fox’, we type ‘fox’ in the Common Name box. Click the ‘Records’ button under the ‘Search’ heading. A message appears advising what the search criteria are. Click ‘OK’ and the search starts. The found records are displayed on a form similar to the master form. Use the navigation buttons or the ‘Page Up[ and ‘Page Down’ buttons to move from record to record. To clear the criteria in the search box click the ‘Search Criteria’ under the ‘Clear’ heading.
To search for more than one criterion type the criteria in the boxes that you wish to investigate. For example, to find the animals that belong to the ‘TROCHILIDAE’ family and those that have an EU Annex value of ‘A’, type ‘TROCHILIDAE’ in the ‘family’ box And ‘A’ in the ‘EU Annex’ box. Click ‘Records’ under the ‘Search’ heading to commence the search.
Instead of combing the search criteria boxes together with the ‘And’ command we could use the ‘Or’ command by clicking ‘Or’ under ‘Search type’. In the last example the search would look for animals that were in the ‘TROCHILIDAE’ family Or have an EU Annex value of ‘A’.
Sometimes it might be necessary to find more than one value in a particular field. Say we wanted to find animals that had a common name of ‘lion’ or ‘tiger’. First clear the search criteria boxes. Type ‘lion’ in the ‘common name’ box. Click the ‘Records’ button under ‘Search’. After viewing the records, click the ‘Found Records’ button under the ‘Save’ heading. This will mark all the found records so that we can see them later.
Now type ‘tiger’ in the ‘common name’ box and click the ‘Records’ button under the ‘Search’ heading. After viewing the found records, click the ‘Add to Saved’ button under the ‘Save’ heading. This will mark all the ‘tigers’ and remember to mark the lions as well. Click the ‘Saved Records’ button under ‘View’ to look at the lion and tiger records.
To view all the records, click the ‘Records’ button under the ‘Search’ heading.
In order to search for a particular criterion that applies only to the set of marked or saved records we use the ‘Saved records’ button under the ‘Search’ heading.
Example To find lions or tigers with an EU Annex value of ‘A’. We have already found the lions and tigers as described above. Click the ‘Search Criteria’ under the ‘Clear’ heading. Now type ‘A’ in the ‘EU Annex’ box. Instead of searching all the records, we only wish to search the saved records and so we click the ‘Saved Record’ button under the ‘Search’ heading.
Sets of records can be gradually built up by using the techniques described above but more complex and powerful searches can be performed under the ‘Composite Searches’ section. (see above).
These are the values that are used to generate the Priority Ranks for Animals and Plants. The Priority Rank for each is the sum of the values allocated to each set of tables.
Review of Current Wildlife Species Genetic Research - 33 - Final Report Summary of Weighting Criteria CATEGORY SCORE Annexes Annexe A 50 Annexe B 30 Annexe C 20 Annexe D 0
IUCN Animals (1994 categories) Extinct in the Wild (EW), Critically Endangered (CR) 50 Endangered (EN) 40 Vulnerable (VU) 30 Lower Risk Near Threatened (LR:nt), Lower Risk 20 Conservation Dependant (LR:cd) Data Deficient (DD), Not Evaluated (NE) 10 Extinct (EX), Lower Risk Least Concern (LR:lc) 0
IUCN Plants (pre 1994 categories) Extinct/Endangered (EX/EN) 50 Endangered (EN) 40 Vulnerable (VU) 30 Rare (R) 20 Indeterminate (I), Insufficiently Known (K) 10 Extinct (EX), Not Threatened (nt) 0
Illegal trade Total of three categories 0-13.5
Captive breeding Total of two categories 0-9
DNA DNA rank 3 10 DNA rank 2 5 DNA rank 1 0
EU Annex and IUCN values are recorded in the Species_Animals_Master and the Species_Plants_Master tables. Illegal Trade values are in the Illegal Trade tables. DNA values are in the DNA list tables.
Review of Current Wildlife Species Genetic Research - 34 - Final Report Relationships between Animal Species tables
This diagram shows the main relationships between the various animal tables. The ‘Species_Animals_Master’ table contains a list of all the animals in the database. The other tables are connected directly, or indirectly, to the ‘Species_Animals_Master’ table and supply information displayed in the relevant forms that can be viewed within the application.
Review of Current Wildlife Species Genetic Research - 35 - Final Report Relationships between Plant Species tables
This diagram shows the main relationships between the various plant tables. The ‘Species_Plants_Master’ table contains a list of all the plants in the database. The other tables are connected directly, or indirectly, to the ‘Species_Plants_Master’ table and supply information displayed in the relevant forms that can be viewed within the application.
Review of Current Wildlife Species Genetic Research - 36 - Final Report 9.3 Appendix 3 : Individuals/organisations contacted Information held by DEFRA
9.4 Appendix 4 : Individuals/organisations offering assistance Information held by DEFRA
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Review of Current Wildlife Species Genetic Research - 47 - Final Report 9.6 Appendix 6 : Summary of animal DNA information
Genus Species Sub Common name Genbank DNA Population Genus References Species Referenc Species Accession Rank References Number Aceros nipalensis Rufous-necked Hornbill N/I 3 N/I N/I N/I Achatinella apexfulva Achatinella snail AF159469 1 N/I N/I Thacker (2000) Achatinella bellula Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella bulimoides Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella byronii Achatinella snail AF159470 1 N/I N/I Thacker (2000) Achatinella cestus Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella concavosira Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella curta Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella decipiens Achatinella snail AF159471 1 N/I N/I Thacker (2000) Achatinella fulgens Achatinella snail AF159474 1 N/I N/I Thacker (2000) Achatinella fuscobasis Achatinella snail AF159481 1 N/I N/I Thacker (2000) Achatinella lila Achatinella snail AF159473 1 N/I N/I Thacker (2000) Achatinella lorata Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella mustelina Achatinella snail AF159475 1 N/I N/I Thacker (2000) Achatinella phaezona Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella pulcherrima Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella pupukanioe Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella sowerbyana Achatinella snail AF159468 1 N/I N/I Thacker (2000) Achatinella stewartii Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella swiftii Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella taeniolata Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella turgida Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella viridans Achatinella snail AF159469 2 N/I Thacker (2000) N/I Achatinella vulpina Achatinella snail AF159469 2 N/I Thacker (2000) N/I Acinonyx jubatus venaticus Asiatic Cheetah AF348641 2 Freeman (2001) N/I Freeman (2001) H Harley (2000) (1997) Johnson (1 Acipenser sturio Baltic Sturgeon AJ245839 1 Ludwig (1998) N/I Birstein (1998) Lu (1998) Acrantophis dumeili Dumeril's Boa U69735 2 N/I N/I N/I Acrantophis madagascarie Madagascar Boa AF296730 1 N/I N/I Matson (2001) nsis Addax nasomaculatu Addax AJ235310 1 N/I Gatsey (1997) Ha s Hassanin (1998) Alligator sinensis Chinese Alligator AF237577 1 Glenn (1998) Hedges (1994) Forstner Glenn (1998) Glen (1995) Roman (2000) Kumazawa (1995) Mindell (1997) Alouatta coibensis trabeata AF289989 2 N/I Bonvicino (2001) Mundy N/I (2000) Horovitz (1995) Horovitz(1998) Amazona brasiliensis Red-Tailed Amazon AF338279 2 N/I Wright (2001) Mattos N/I (1998) Russello x 2 (2001) Miyaki (1998) Brock (1992) Quinn (1992) Eberhard (2001) Amazona guildingii Saint Vincent Amazon AF339762 1 Russello/Amato Wright (2001) Mattos Russello x2 (2001 (2001) (1998) Miyaki (1998) Brock (1992) Quinn (1992) Eberhard (2001) Amazona imperialis Imperial Amazon AF338279 2 N/I Wright (2001) Mattos N/I (1998) Russello x 2 (2001) Miyaki (1998) Brock (1992) Quinn (1992) Eberhard (2001) Amazona leucocephala Cuban Amazon AF338279 2 N/I Wright (2001) Mattos N/I (1998) Russello x 2 (2001) Miyaki (1998) Brock (1992) Quinn (1992) Eberhard (2001) Amazona vittata Red-fronted Amazon AF338279 1 Brock (1992) Wright (2001) Mattos Brock (1992) Quin (1998) Russello x 2 (2001) Miyaki (1998) Eberhard (2001) Anodorhynchu glaucus Glaucous Macaw U70763 2 N/I Miyaki (1998) N/I s Anodorhynchu hyacinthinus Hyacinthine macaw U70763 1 Miyaki (1998) Miyaki (1998) N/I s
Review of Current Wildlife Species Genetic Research - 65 - Final Report Anodorhynchu leari Lear's Macaw U70763 2 N/I Miyaki (1998) N/I s Antilocapra americana peninsularis Baja California Pronghorn AJ235314 2 N/I N/I Murray (1995) De Apalone ater Cuatro Cienegas Softshell N/I 2 N/I Roman (2000) Weisrock N/I (2000) Aquila chrysaetos Golden eagle Z73462 1 Nesje x2 (2000) Wink (1996) Nesje x2 (2000) S Seibold (1995) (1998) Ara glaucogularis Blue-throated Macaw U88001 2 N/I Miyaki (1998) Nader N/I (1999) Cooper (1997) Aspideretes nigricans Black Softshell Turtle N/I 3 N/I N/I N/I Aspidites ramsayi Woma U69741 2 N/I N/I N/I Athene blewitti Forest Spotted Owlet N/I 2 N/I Muller (2001) N/I Aythya innotata Madagascar Pochard AF090337 2 N/I Johnson (1998) Mindell N/I (1998) Batagur baska Common Batagur N/I 3 N/I N/I N/I Boa constrictor occidentalis Argentin Boa U69747 1 Kumazawa (1995) Forstner (1995) Kumazawa (1995 Bos sauveli Kouprey AF281090 1 N/I Gatsey (1997) Forstner Hassanin (1998) (1995) Tougard (2001) Brachylophus fasciatus Fiji Banded Iguana U48834 2 N/I N/I N/I Brachylophus vitiensis Fiji Crested Iguana U48841 1 N/I N/I Colgan (1997) Brachyteles arachnoides Muriqui AF216253 1 N/I N/I Horovitz (1995) H Bonvicino(2001) Bubalus mindorensis Tamarou D82895 1 N/I N/I Tanaka (1996) Bubo bubo Eurasian Eagel owl AF172386 2 N/I Mindell (1997) N/I Bufo periglenes Monte Verde Toad AY037823 2 N/I Rowe (1999) Leblois N/I (2000) Tikel(2000) Lamb (2000) Zeisset (1998) Vences (2000) Buteo bueto Common buzzard X86741 1 Seibold (1995) Wink (1996) Seibold (1995) Mi Cacatua haematuropygia Red-vented Cockatoo AF313637 1 N/I N/I Madsen (1992) Cacatua sulphurea Yellow-crested Cockatoo AF313750 2 N/I Madsen (1992) N/I Callithrix aurita White-eared Marmoset U89001 1 N/I N/I Nagamachi (1999 Campephilus imperialis Imperial Woodpecker N/I 2 N/I N/I Mindell (1997) Canis simensis Abyssinian Wolf AF028168 1 Gottelli (1994) Lehman (1991) Gottelli (1994) Wa Lehman(1991) Capra falconeri heptneri Tadjik Markhor D84202 2 N/I N/I Luikart (2001) Cephalophus jentinki Jentikx Duiker AF153888 1 N/I N/I van Vuuren (2001 Ceratotherium simum cottoni Northern Square-lipped NC_001808 2 N/I N/I Tougard (2001) X Rhinoceros Cercocebus galeritus galeritus Tana River Mangabey AF177898 2 N/I N/I Disotell (1992) va Cercopithecus diana roloway Roloway Monkey L35193 1 N/I Disotell (1992) Ruvolo N/I (1991) Zischler (1998) Wickings (1992) Cercopithecus solatus Sun-Tailed Monkey AF212100 1 N/I Disotell (1992) Ruvolo Wickings (1992) (1991) Zischler (1998)van der Kuyl (1995) Cervus duvaucelii ranjitsinhi U37507 2 N/I Randi (2001) Polziehn Cronin (1996) (2000) Polziehn (1998) Okada(2000) Tamate(1995) Cervus eldii eldii Manipur Brow-antlered AF423202 2 N/I Randi (2001) Polziehn N/I Deer (2000) Polziehn (1998) Okada (2000) Tamate (1995) Cronin (1996) Chasmistes cujus Cui-ui AF314751 1 Britten (1996) Tranah (2001) Britten (1996) Chelonia mydas Green Turtle AF366263 1 Roman (2000) N/I Dutton (1996) Rom Karl (1992) Bowen (1999) FitzSimmo (1993) Encalada (1995) Karl (1992 (1996) (1993) Encalada ( Chinchilla brevicaudata Short-tailed Chinchilla AF283978 2 N/I N/I N/I Conraua goliath Goliath Frog N/I 3 N/I N/I N/I Crax alberti Blue-billed Curassow AF106498 2 N/I N/I N/I Crocodylus intermedius Orinoco Crocodile AF237578 1 Lang (1993) Lang (1993) Kumazawa Glenn (1996) (1995) Glenn (1998) Crocodylus siamensis Siamese Crocodile AF306453 1 Glenn (1996) Lang Lang (1993) Kumazawa Glenn (1998) (1993) (1995) Glenn (1996) Cyanopsitta spixii Spix's Macaw U70764 1 N/I N/I Miyaki (1998) Cyclura carinata bartschi Booby Cay Ground AF217779 2 N/I Forstner (1995) Malone (2000) Iguana Rassmann (1997) Sites (1996) Cyclura carinata carinata Turks and Caicos Ground AF217779 2 N/I Forstner (1995) N/I Iguana Rassmann (1997) Sites (1996) Cyclura carinata Bahamas Rock Iguana AF217779 1 Forstner (1995) Malone (2000) Rassmann (1997) Sites (1996)
Review of Current Wildlife Species Genetic Research - 66 - Final Report Cyclura collei Jamaica Ground Iguana AF217773 1 N/I Forstner (1995) Malone (2000) Rassmann (1997) Sites (1996) Cyclura cornuta Rhinoceros Iguana U88955 1 N/I Forstner (1995) Sites Malone (2000) Ra (1996) Cyclura nubila caymanensi Cayman Island Ground AF217762 1 N/I Forstner (1995) N/I s Iguana Rassmann (1997) Sites (1996) Cyclura nubila lewisi Cayman Island Ground AF217763 1 N/I Forstner (1995) N/I Iguana Rassmann (1997) Sites (1996) Cyclura pinguis Anegada Ground Iguana AF217772 1 N/I Forstner (1995) Malone (2000) Rassmann (1997) Sites (1996) Cyclura ricordi Ricord's Ground Iguana AF217768 1 N/I Forstner (1995) Malone (2000) Sit Rassmann (1997) Cyclura rileyi cristata San Salvador Rock AF020255 1 N/I Forstner (1995) N/I Iguana Rassmann (1997) Sites (1996) Cyclura rileyi rileyi San Salvador Rock AF020255 2 N/I Forstner (1995) Malone (2000) Iguana Rassmann (1997) Sites (1996) Dermochelys coriacea Trunkback turtle AF121964 1 N/I N/I Dutton (1996) Dicerorhinus sumatrensis harrissoni AJ245723 2 Morales (1997) N/I Morales (1997) Br (2001) Dicerorhinus sumatrensis sumatrensis AJ245723 2 Morales (1997) N/I Morales (1997) Br (2001) Dicerorhinus sumatrensis Sumatran Rhinoceros AJ245723 1 Morales (1997) N/I Morales (1997) Br (2001) Diceros bicornis longpipes AJ245721 2 Brown (1999) N/I Jama (1993) Brow (2001) Ali (1999) C Swart (1994) Diceros bicornis michaeli AJ245721 1 N/I N/I Tougard (2001) A (1999) Swart (199 Diceros bicornis minor AF129734 1 Brown (1999) N/I Tougard (2001) A (1999) Swart (199 Diceros bicornis Hook-lipped Rhinoceros AJ245721 1 Brown (1999) N/I Jama (1993) Brow (2001) Ali (1999) C Swart (1994) Dromus dromas Dromedary Naiad N/I 3 N/I N/I N/I Dyscophus antongilii Tomato Frog AF124122 2 N/I Vences (2000) N/I Elephas maximus Asian Elephant AJ303056 1 Fernando x 2 N/I Greenwood, (1999 (2000) Fernando x 2 (200 Eos histrio Red and Blue Lory N/I 3 N/I N/I N/I Epioblasma florentina curtisi Curtis' Naiad AF156528 2 N/I N/I N/I Epioblasma florentina walkeri AF156528 2 N/I N/I N/I Equus africanus africanus Nubian Wild Ass NC_001788 2 N/I Xu (1996) Tozaki (2001) N/I Tougard (2001) Oakenfull (1998) Equus africanus somalicus Somalia Wild Ass NC_001788 2 N/I Xu (1996) Tozaki (2001) N/I Tougard (2001) Oakenfull (1998) Equus africanus African Wild Ass NC-001788 2 N/I Xu (1996) Tozaki (2001) N/I Tougard (2001) Oakenfull (1998) Equus asinus Wild Ass NC_001788 1 N/I Tozaki (2001) Tougard Xu (1996) (2001) Oakenfull (1998) Equus prezewalskii Przewalski's Wild Horse AF055879 1 N/I Xu (1996) Tozaki (2001) Oakenfull (1998) Tougard (2001) Eretmochelys imbricata Hawksbill Turtle U73561 1 Bass (1996) N/I Dutton (1996) Bas FitzSimmons (1995) Bowen (19 (1995) Eulemur fulvus albocollaris White-collared Brown AF224558 1 N/I Fausser (2000) Yoder (1996) Lemur Eulemur macaco flavifrons Sclater's Lemur AF224531 1 N/I N/I Yoder (1996)
Eutriorchis astur Madagascar Serpent- N/I 3 N/I N/I N/I Eagle Falco naumanni Lesser kestral AF090338 1 Negro (1996) Quinn (1992) Wetton Nichols (2001) Ne (1997) Nesje x 2 (2000) Seibold (1995) Longmire (1988) Mindell (1997) Mindell (1998) Falco peregrinus Peregrine Falcon AF090338 1 Nesje x2 (2000) Quinn (1992) Seibold Nesje x2 (2000) L Longmire (1988) (1995) Negro (1996) (1997) Mindall (19 Wetton (1997) Nichols (2001)
Review of Current Wildlife Species Genetic Research - 67 - Final Report Falco rusticolus Gyr Falcon AF200206 1 Nesje x2 (2000) Quinn (1992) Mindall Nesje x2 (2000) (1997) Mindall (1998) Wetton (1997) Seibold (1995) Negro (1996) Nichols (2001) Longmire (1988) Fregata andrewsi Andrews' Frigatebird N/I 2 N/I van Tuinen (2000) N/I Cooper(1997) Hedges (1994) Fusconaia cuneolus Fine-rayed Pigtoe AF232797 2 N/I Hoeh (1996) Lydeard N/I (2000) Gallotia simonyi Hierro Giant Lizard Z79498 1 Richard (2000) N/I Rando (1997) Car (2000) Geochelone nigra abingdoni Abingdon Island Tortoise AF192932 1 N/I N/I N/I
Geochelone nigra ephippium Duncan Island Tortoise AF192930 1 N/I N/I N/I
Geochelone nigra hoodensis Hood Island Tortoise AF192933 1 N/I N/I N/I
Geochelone platynota Burmese Starred Tortoise AF175337 2 N/I Caccone/Amato (1999) N/I Geochelone radiata Radiated Tortoise AF020897 1 N/I N/I Caccone/Amato ( Geochelone yniphora Angonoka AF020896 1 N/I N/I Caccone/Amato ( Geopsittacus occidentalis Night Parrot AH005658 1 N/I N/I Leeton (1994) Miy Geronticus eremita Hermit Ibis AF172372 1 Signer (1994) N/I Signer (1994) Gorilla gorilla diehli NC_001645 2 Morin (1993) Morin Bonthorn (1999) Gerloff Garner (1996) Ru (1994) Goossens (1999) Arnason (1996) Xu Kuyl (1995) Wicki (2000) (1996) (1986) ) Foran (19 Horai (1992) ) Ada (1995) Nachman (2001) Gagneux (1999) Morin (199 Goossens (1996) Gorilla gorilla Gorilla D38114 1 Morin (1993) Morin Gerloff (1999) Bonthorn Ruvolo (1991) Va (1994) Goossens (1999) Arnason (1996) (1993) Morin (199 (2000) Horovitz (1995) N (1996) Foran (198 (1995) Horai, (199 (1996) Gagneux ( (1999) Wickings(1 (2001) Clifford (19 Grus japonensis Japanese Crane U11063 1 Quinn (1992) van N/I Krajewski (1999) H Tuinen (2000) Mindell (1997) Grus leucogeranus Snow Crane U27549 1 Quinn (1992) van N/I Krajewski (1999) Tuinen (2000) Mindell (1997) Hasegawa (2000) Gymnogyps californianus California Condor AF173574 1 N/I N/I Hedges (1994) va (1994) Haliaeetus albicilla White-Tailed eagle X86753 1 N/I N/I Wink (1996) Seibo Haliaeetus pelagicus Steller's Sea-eagle Z73470 2 N/I Wink (1996) Seibold N/I (1995) Haliaeetus vociferoides Madagascar Fish-eagle AF132843 1 N/I Seibold (1995) Wink (1996) Hapalemur aureus Golden Lemur AY043333 2 N/I Wyner (2000) Montagon N/I (1993) Yoder (1996) Hapalemur griseus alaotrensis Alaotran Gentle Lemur U53574 2 N/I Wyner (2000) Montagon (1993) Hapalemur simus Greater Bamboo Lemur AF175890 1 N/I Yoder (1996) Montagnon Wyner (2000) (11993) Hippotragus niger variani Giant Sable Antelope AF0493832 1 N/I N/I Gatesy (1997) Hylobates concolour Black Gibbon AB049471 1 N/I Ruvolo (1991) Andayani Zischler (1998) (2001) Aranson x2 (1996) Oka (2001) Hall (1998) Horovitz (1995) Hylobates lar yunnanensis NC_002082 2 N/I Ruvolo (1991) Andayani Aranson x2 (1996 (2001) (1998) Zischler (1 Hylobates moloch moloch AJ010580 2 N/I Ruvolo (1991) Aranson x2 Zischler (1998) A (1996) Oka (2001) Hall (1998) Horovitz (1995) Hylobates moloch pongoalsoni AJ010580 2 N/I Ruvolo (1991) Aranson x2 Zischler (1998) A (1996) Oka (2001) Hall (1998) Horovitz (1995) Hylobates moloch Silvery Gibbon AJ010580 1 N/I Ruvolo (1991) Aranson x2 Zischler (1998) A (1996) Oka (2001) Hall (1998) Horovitz (1995) Lagorchestes hirsutus nova Mala AF187544 2 N/I N/I N/I Lampsilis virescens Alabama Lamp Naiad N/I 3 N/I N/I N/I Lasiorhinus krefftii Queensland Hairy-nosed AH008995 1 Taylor (1994) N/I Taylor (1994) Wombat Latimeria chalumnae Coelacanth U82228 1 N/I N/I Holder (1999) Zar Latimeria menadoensis Menado Coelacanth AF176901 1 N/I Zardoya (1997) Holder (1999)
Review of Current Wildlife Species Genetic Research - 68 - Final Report Leontopithecus caissara Black-faced Lion Tamarin AF320581 2 N/I Pastorini (1998) Mundy N/I (2000) Horovitz (1995) Horovitz (1998) Nagamachi (1999) Canavez(1999) Leontopithecus chrysopygus Black Lion Tamarin AF362381 2 N/I Pastorini (1998) Mundy N/I (2000) Horovitz (1995) Horovitz (1998) Nagamachi (1999) Canavez(1999) Leontopithecus rosalia Golden Lion Tamarin AF320581 1 N/I Canavez(1999) Pastorini (1998) M (1995) Horovitz (1 Lepidochelys kempi Mexican Ridley AF051777 1 Bowen (1998) N/I Dutton (1996) Bow Bowen (1991) (1991) Leptotila wellsi Grenada Dove N/I 3 N/I N/I N/I Leucopsar rothschildi Rothschild's Starling AF151397 1 Ashworth (1992) N/I Ashworth (1992) Lipotes vexillifer Chinese Lake Dolphin AF248731 1 N/I N/I Nikaido (2001) Loxodonta africana African Elephant AF298857 1 N/I N/I Greenwood (1999 Nyakaana (1998) Comstock (2000) Fernando (2000) E Lutra lutra European River Otter AJ276627 1 N/I N/I Pertoldi (2001) Da (2000) Malacochersus tornieri Pancake Tortoise N/I 3 N/I N/I N/I Mandrillus leucophaeus Drill AF020588 1 N/I Zischler (1998) Disotell (1992) Zh (1999) Mandrillus sphinx Mandrill AF020423 1 N/I Disotell (1992) Harris (1999) Zisc (1998) Mantella aurantiaca Golden Mantella X86311 2 N/I Vences (2000) N/I Mergus octosetaceus Brazilian Merganser M35143 1 N/I McHugh (1990) Livezey (1989) Milvus milvus Red kite X86755 1 N/I Wink (1996) Seibold (1995) Mitu mitu Razor-billed Curassow N/I 3 N/I N/I N/I Monachus monachus Mediterranean Monk Seal U12847 2 N/I Lento (1995) N/I Moschus chrysogaster Himalayan Musk Deer AF026887 2 N/I N/I N/I Moschus moschiferus Siberian Musk Deer AF026883 2 N/I N/I N/I Mustela nigripes Black-footed Ferret AF068543 2 Hosoda (2000) Hosoda (2000) Davison N/I (2001) Masuda (1994) Neophema chrysogaster Orange-bellied Parakeet N/I 1 Robertson (2000) Leeton (1994) Robertson (2000) Numenius borealis Eskimo Curlew N/I 2 N/I Mindell (1997) N/I Numenius tenuirostris Slender-billed Curlew N/I 2 N/I Mindell (1997) N/I Odontophorus strophium Gorgeted Wood-Quail N/I 3 N/I N/I N/I Ognorhynchus icterotis Yellow-eared Conure N/I 3 N/I N/I N/I Ophrysia superciliosa Himalayan Quail N/I 3 N/I N/I N/I Ornithoptera alexandrae Queen Alexandra's AB044652 2 N/I N/I N/I Birdwing Oryx dammah Scimitar-horned Oryx/ AJ222685 2 N/I N/I N/I Sahara Oryx Osteolaemus tetraspis African Dwarf Crocodile N/I 1 Glenn (1996) Glenn (1998) Glenn (1996) Ovis ammon nigrimontan Kara Tau Argali AJ251327 2 N/I Hassanin (2001) Hassanin (1998) P a (1997) Pan paniscus Bonobo NC_001644 1 N/I Vigilant (2001) Bonthorn Reinartz (2000) K (1999) Gagneux (2001) Horovitz (1995) Va Goossens (2000) Morin Ruvolo (1991) For (1993) Morin (1994) (1986) Horai (199 Nachman (1996) Arnason (1996) Gerloff (19 (1996) Xu (1996)Wickings (1992) Pan troglodytes Chimpanzee NC_001643 1 Morin (1993) Morin Gerloff (1999) Bonthorn Morin (1993) Goo (1994) Goossens (1999) Arnason (1996) Kuyl (1995) Horov (2000) (1996) Foran (198 (1995) Horai (199 (1996) Gagneux ( (1999) Ruvolo (19 Morin (1994) Vigil (2000) Panthera leo persica Indian Lion AF088864 1 Gilbert (1991) Chelomina (1999) Gilbert (1991) Lop Cracraft (1998) Miththapala (1996) (1997) Masuda (1 Wentzel (1998) Tougard (2001) Spong (2000) Panthera pardus nimr South Arabian Leopard AY005809 1 Miththapala (1996) Masuda (1996) Cracraft Spong (2000) Lop (1998) Wentzel (1998) (1997) Chelomina Tougard (2001) Shankaranarayanan (1997) Gilbert (1991) Panthera pardus orientalis Amur Leopard AY005809 1 Miththapala (1996) Masuda (1996) Cracraft Spong (2000)Lope (1998) Wentzel (1998) (1997) Miththapa Tougard (2001) Shankaranarayanan (1997) Gilbert (1991)
Review of Current Wildlife Species Genetic Research - 69 - Final Report Panthera pardus panthera North African Leopard AY005809 1 Miththapala (1996) Masuda (1996) Cracraft Spong (2000)Lope (1998) Wentzel (1998) (1997) Chelomina Tougard (2001) Shankaranarayanan (1997) Gilbert (1991) Panthera pardus tulliana Anatolian Leopard AY005809 1 Miththapala (1996) Masuda (1996) Cracraft Spong (2000)Lope (1998) Wentzel (1998) (1997) Chelomina Tougard (2001) Shankaranarayanan (1997) Gilbert (1991) Panthera tigris altaica Amur Tiger AF088866 1 Cracraft (1998) Masuda (1996) Johnson (1997) T Miththapala (1996) Gilbert (1997) Shankaran (1991) Chelomina (1999) Wentzel (1998) Spong (2000) Panthera tigris amoyensis South China Tiger AF088866 2 Cracraft (1998) Masuda (1996) Johnson (1997) T Miththapala (1996) Gilbert (1997) Shankaran (1991) Chelomina (1999) Wentzel (1998) C Spong (2000) Panthera tigris sumatrae Sumatran Tiger AF296751 1 Cracraft (1998) Masuda (1996) Johnson (1997) T Miththapala (1996) Gilbert (1997) Shankaran (1991) Chelomina (1999) Wentzel (1998) Spong (2000)
Panthera pardus leopard AY005809 1 Miththapala (1996) Masuda (1996) Cracraft Johnson (1997) M (1998) Wentzel (1998) Lopez (1997) Che Tougard (2001) (2000) Shankaranarayanan (1997) Gilbert (1991) Panthera tigris Tiger AF053018 1 Cracraft (1998) Masuda (1996) Johnson (1997) T Miththapala (1996) Gilbert (1997) Shankaran (1991) Chelomina (1999) Wentzel (1998) C Spong (2000) Panthera tigris tigris IndianTiger AF088865 1 Cracraft (1998) Masuda (1996) Johnson (1997) T Miththapala (1996) Gilbert (1997)Wentzel (19 (1991) Chelomina (1999) Spong (2000) Pantholops hodgsonii Chiru AF034724 1 N/I N/I Gatesy (1997) Ha Papasula abbotti Abbott's Booby U90000 2 N/I N/I N/I Parnassius apollo Apollo AJ224055 1 Yagi (2001) N/I Aubert (1999) Penelope albipennis White-winged Guan N/I 2 N/I N/I N/I
Phocoena sinus Gulf of California Harbour AF084051 1 N/I N/I Rosel (1995) LeD Porpoise Pipile pipile Trinidad White-headed N/I 2 Pereira (1996) Pereira (1996) N/I Piping Guan
Pithecophaga jefferyi Monkey-eating Eagle N/I 3 N/I N/I N/I Pitta gurneyi Gurney's Pitta N/I 3 N/I N/I N/I Plethobasus cicatricosus White Warty-back Pearly N/I 3 N/I N/I N/I Mussel Plethobasus cooperianus Orange-footed N/I 3 N/I N/I N/I Pimpleback Mussel Pleurobema plenum Rough Pigtoe Pearly N/I 2 N/I Kandl (2001) N/I Mussel Pongo pygmaeus Orang-utan NC_001646 1 Bonthorn (1999) N/I Warren (2000) Ka Mundy (2000) (1986) Horai (199 (1996) Potamilus capax Fat Pocketbook Pearly AF049513 1 N/I N/I Roe (1998) Mussel Procolobus pennantii bouvieri Bouvier's Red Colobus N/I 3 N/I N/I N/I Propithecus diadema candidus Silky Sifaka AY043341 2 Yoder (1996) N/I Pastorini (2001) Wyner (2000) Propithecus diadema diadema Diademed Sifaka AY043341 2 Yoder (1996) N/I Pastorini (2001) Wyner (2000) Propithecus diadema perrieri Perrier's Sifaka AY043341 2 Yoder (1996) N/I Pastorini (2001) Wyner (2000) Propithecus tattersalli Tattersall's Sifaka AF081027 2 Wyner (2000) N/I Pastorini (2001) Y Propithecus verreauxi coronatus Crowned Sifaka AF285451 1 Yoder (1996) N/I N/I Wyner (2000) Pseudemydura umbrina Western Short-necked AF113644 1 N/I N/I Seddon (1997) Turtle Pseudibis gigantea Giant Ibis N/I 3 N/I N/I N/I Pteronura brasiliensis Giant Otter AF057126 1 N/I N/I Pertoldi (2001) Da (2000) Pteropus insularis Chuuk Flying-fox AF044655 2 N/I Lin/Penny (2001) Juste N/I (1999) Bastian (2001)
Review of Current Wildlife Species Genetic Research - 70 - Final Report Nikaido (2000)
Pteropus livingstonei Comoro Black Flying-fox AF044655 2 N/I Lin/Penny (2001) Juste N/I (1999) Bastian (2001) Nikaido (2000) Pteropus molossinus Pohnpei Flying-fox AF044655 2 N/I Lin/Penny (2001) Juste N/I (1999) Bastian (2001) Nikaido (2000) Pteropus phaeocensis Mortlock Flying-fox AF044655 2 N/I Lin/Penny (2001) Juste N/I (1999) Bastian (2001) Nikaido (2000) Pteropus rodricensis Rodrigues Flying-fox AF044655 1 N/I Lin/Penny (2001) Bastian Juste (1999) (2001) Nikaido (2000) Pteropus voeltzkowi Pemba Flying-fox AF044655 2 N/I Lin/Penny (2001) Juste N/I (1999) Bastian (2001) Nikaido (2000) Puma concolor coryi Florida Panther AF340006 1 Culver (2000) N/I Culver (2001) Ma Culver (2001) (1997) Wentzel (1 Puma concolor couguar Eastern Panther AF340006 1 Culver (2000) N/I Culver (2001) Ma Culver (2001) (1997) Wentzel (1 Pygathrix nemaeus Douc langur AJ243282 2 N/I Bonthorn (1999) N/I Python molurus Indian Python U69855 2 N/I N/I N/I Pyxis planicauda Flat-shelled Spider AF020895 1 N/I N/I Caccone (1999) Tortoise Quadrula intermedia Cumberland Monkey-face N/I 2 N/I Johnson x2 (1998) Berg N/I Pearly Mussel (1998) Quadrula sparsa Appalachian Monkey-face N/I 2 N/I Johnson x2 (1998) Berg N/I Pearly Mussel (1998) Rheobatrachus silus Conondale Gastric- N/I 3 N/I N/I N/I brooding Frog Rhinoceros sondaicus annamiticus AJ245725 2 N/I Xu (1997) Ali (1999) Tougard (2001) Rhinoceros sondaicus sondaicus AJ245725 2 N/I Xu (1997) Ali (1999) Tougard (2001) Rhinoceros sondaicus Javan Rhinoceros AJ245725 1 N/I Xu (1997) Ali (1999) Tougard (2001) Rhinoceros unicornis Great Indian Rhinoceros NC_001779 1 N/I N/I Xu (1997) Ali (199 Rhodonessa caryophyllace Pink-headed Duck N/I 3 N/I N/I N/I a Saguinus oedipus Cotton-top Tamarin AF069973 1 N/I Pastorini (1998) Canavez (1999) H (2000) Saiga tatarica Saiga AF064487 1 N/I N/I Milner-Gulland (19 Saimiri oerstedii citrinellus AF245094 2 N/I Alverez (2000) Yoder Mundy (2000) (1996) Horovitz (1995) Horovitz (1998) Sanzinia madagascariensis Madagascar Tree Boa AF296732 1 N/I N/I Matson (2001) Scleropages formosus Asian Bonytongue AB035234 1 Yue (2000) N/I Kumazawa (2000 Sphenodon guntheri Brother Islands Tuatara AH004861 2 N/I Quinn (1996) Gorr (1998) N/I Strigops habroptilus Owl Parrot AF296719 1 N/I Robertson (2000) Leeton (1994) Ro Sus salvanius Pygmy Hog AB053629 1 N/I Tougard (2001) N/I Tadorna cristata Crested Shelduck U46473 2 N/I Sorenson (1999) Johnson N/I (1998) Testudo graeca nikolskii AF067510 2 Alverez (2000) N/I Alverez (2000) Testudo kleinmanni Kleinmann's Tortoise AF175332 2 N/I Alverez (2000) N/I Toxolasma cylindrellus Pale Lilliput Naiad N/I 3 N/I N/I N/I Tremarctos ornatus Spectacled Bear U23554 1 N/I N/I Talbot (1996) Zha Uncia uncia Snow Leopard AF006450 1 N/I N/I Watanabe (2000) Ursus actos Brown Bear U12855 1 Cronin (1991) Kitahara (2000) Zhang (1993) Talb Kohn (1995) Waits (1995) Taberlet (1 (2000) Masuda Taberlet(1994) Ko (1998) Matsuhashi Masuda (1998) Cr (1999) Taberlet (1999) (1994) Taberlet (1997) Ursus thibetanus gedrosianus Baluchistan Bear AB040113 1 Kitahara (2000) Lento (1995) Taberlet Zhang (1993) Talb (1997) Taberlet (1995) Taberlet(1994) Kohn (1995) Waits (2000) Masuda (1998) Cronin (1991) Matsuhashi (1999) Ursus thibetanus Asiatic Black Bear U23558 1 Kitahara (2000) Lento (1995) Cronin Talbot x 2(1996) Z (1991) Kohn (1995) Waits (2000) (2000) Taberlet (1994) Taberlet (1997) Taberlet (1995) Masuda (1998) Matsuhashi, (1999) Varanus komodoensis Komodo Dragon AF005437 1 N/I N/I Ciofi (1999) Varanus melinus Quince Monitor AF407511 2 N/I Ciofi (1999) Forstner N/I (1995) Fuller (1998) Varecia variegata rubra Red Ruffed Lemur AF175850 1 N/I N/I N/I Vicugna vicugna Vicuña AB042969 1 N/I N/I Lin/Nomura (2001 Villosa trabalis Cumberland Bean Pearly N/I 3 N/I N/I N/I
Review of Current Wildlife Species Genetic Research - 71 - Final Report Mussel Vipera ursinii moldavica AF182552 2 N/I N/I N/I Zosterops albogularis White-breasted Silvereye N/I 2 N/I Degnan (1993) Degnan (1993)
Zyzomys pedunculatus Macdonnell Range Rock- N/I 3 N/I N/I N/I rat
Key: N/I = no references identified, / = not relevant
Review of Current Wildlife Species Genetic Research - 72 - Final Report 9.7 Appendix 7 : Summary of plant DNA information
Genus Species Sub Species Common name Genbank DNA Population Genus References Accession Rank References Number Agave arizonica Arizona agave AF209521 2 N/I Bogler (1995) Vega (2001) Aloe albiflora LO5029 2 N/I Van der Bank (1996) Aloe bellatula LO5029 2 N/I Van der Bank (1996) Aloe calcairophylla LO5029 2 N/I Van der Bank (1996) Aloe compressa compressa LO5029 2 N/I Van der Bank (1996) Aloe descoingsii LO5029 2 N/I Van der Bank (1996) Aloe fragilis LO5029 2 N/I Van der Bank (1996) Aloe helenae LO5029 2 N/I Van der Bank (1996) Aloe parvula LO5029 2 N/I Van der Bank (1996) Aloe pillansii Bastard quiver tree (E), basterkokerboom LO5029 2 N/I Van der Bank (1996) Aloe polyphylla spiral aloe (E) LO5029 2 N/I Van der Bank (1996) Aloe suzannae LO5029 2 N/I Van der Bank (1996) Ariocarpus agavoides Tamaulipas living-rock cactus AF267918 2 N/I N/I Ariocarpus bravoanus AF267918 2 N/I N/I Astrophytum asterias star cactus AY015288 1 N/I N/I Ceratozamia euryphyllidia AF410172 2 N/I Caputo (1991) Ceratozamia hildae AF410172 2 N/I Caputo (1991) Ceratozamia microstrobila AF410172 2 N/I Caputo (1991) Ceratozamia zaragozae AF410172 2 N/I Caputo (1991) Chigua bernalii N/I 2 N/I Caputo (1991) Chigua restrepoi N/I 1 N/I N/I
Coryphantha werdermannii jabali pincushion cactus AF267926 2 N/I N/I Cycas beddomei AF410165 2 N/I Caputo (1991) Discocactus horstii N/I 3 N/I N/I Discocactus subviridigriseus N/I 3 N/I N/I Dudleya stolonifera Laguna Beach Liveforever, Laguna Beach AF274614 2 N/I N/I Dudleya Dudleya traskiae Santa Barbara Island Liveforever, Santa AF274614 2 N/I N/I Barbara Island Dudleya Echinocereus ferreirianus lindsayi Lindsay's cactus, Lindsay's hedgehog cacti AY015307 2 N/I N/I Echinocereus schmollii lamb's-tail cactus AY015307 2 N/I N/I Encephalartos aemulans L12676 2 N/I Savard (1994) van der Bank ( Encephalartos arenarius L12676 1 N/I Savard (1994)
Encephalartos brevifoliolatus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos cerinus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos chimanimaniensi L12676 2 N/I Savard (1994) van der Bank ( s Encephalartos concinnus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos cupidus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos dolomiticus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos dyerianus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos heenanii L12676 2 N/I Savard (1994) van der Bank ( Encephalartos inopinus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos laevifolius L12676 2 N/I Savard (1994) van der Bank ( Encephalartos latifrons L12676 1 N/I Savard (1994)
Encephalartos marunguensis L12676 2 N/I Savard (1994) van der Bank ( Encephalartos middelburgensis L12676 2 N/I Savard (1994) van der Bank ( Encephalartos msinganus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos munchii L12676 2 N/I Savard (1994) van der Bank ( Encephalartos nubimontanus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos pterogonus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos schmitzii L12676 2 N/I Savard (1994) van der Bank ( Encephalartos turneri L12676 2 N/I Savard (1994) van der Bank ( Encephalartos venetus L12676 2 N/I Savard (1994) van der Bank ( Encephalartos whitelockii L12676 2 N/I Savard (1994) van der Bank ( Encephalartos sp. L12676 2 N/I Savard (1994) van der Bank ( Escobaria minima Nellie's cory cactus AF267932 2 N/I N/I Euphorbia ambovombensis AF417576 2 N/I Ling (1997) Rowe (1997) Sta (1999) Euphorbia handiensis AF417576 2 N/I Ling (1997) Rowe (1997) Sta (1999) Goodyera macrophylla AF314838 2 N/I N/I Laelia lobata lelia-da-g vea (Portuguese) AY008675 1 N/I N/I
Mammillaria pectinifera Conchilinque AY015289 1 N/I N/I Mammillaria solisioides Pitayita AY015289 2 N/I Das (1999) Melocactus conoideus Conelike Turl's-cap cactus N/I 3 N/I N/I
Review of Current Wildlife Species Genetic Research - 73 - Final Report Orchis scopulorum AY014587 2 N/I Soliva (2001) Qamaruz-Zame (1998)
Pachypodium ambongense AJ002887 2 N/I N/I Pachypodium decaryi AJ002887 2 N/I N/I Paphiopedilum armeniacum Z78496 2 N/I N/I Paphiopedilum dayanum Z784459 2 N/I N/I Paphiopedilum druryi Drury's slipper orchid (E) Z78489 2 N/I N/I Paphiopedilum exul Z78489 2 N/I N/I Paphiopedilum fairrieanum Z78490 2 N/I N/I Paphiopedilum glaucophyllum Z78476 2 N/I N/I Paphiopedilum javanicum virens Z78455 2 N/I N/I Paphiopedilum malipoense Z78498 2 N/I N/I Paphiopedilum micranthum Z78499 2 N/I N/I Paphiopedilum rothschildianum Z78499 2 N/I N/I Paphiopedilum sanderianum Z78473 2 N/I N/I Paphiopedilum stonei Z78467 2 N/I N/I Paphiopedilum tonsum Z78456 2 N/I N/I Paphiopedilum victoria-regina chamberlain Z78478 2 N/I N/I ianum Pediocactus bradyi Brady Pincushion Cactus AF267962 2 N/I N/I Pediocactus knowltonii Knowlton's minature cactus (E), Knowlton AF267962 2 N/I N/I cactus, Knowlton's pincushion cactus Pediocactus winkleri Winkler's Pincushion-cactus AF267962 2 N/I N/I Phragmipediu exstaminodium Z78511 2 N/I N/I m Protea odorata Ground-rose N/I 3 N/I N/I Saussurea costus kostus, kuth, costus root (E) AF257788 2 N/I N/I Sclerocactus wrightiae Wright's fishhook cactus AF267966 2 N/I N/I Turbinicarpus schmiedickeanus flaviflorus AF267972 2 N/I N/I Uebelmannia buiningii AY015319 2 N/I N/I Key: N/I = No references identified, / = not relevant
Review of Current Wildlife Species Genetic Research - 74 - Final Report 9.8 Appendix 8 : Wildlife trade regulation in the european union The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) has been implemented in the European Union since 1984 through a number of Regulations. In 1997, after 15 years, the old legislation was replaced by two new Regulations, which since that date are the core of the Community’s wildlife trade legislation.
1) Council Regulation (EC) No. 338/97 which deals with the protection of species of wild fauna and flora by regulating the trade in these species. The full text is published in the Official Journal of the European Communities, L 61, Volume 40, 3 March 1997 (ISSN 0378-6978).
2) Commission Regulation (EC) No. 939/37 came into effect on 1 June 1997. It lays down detailed rules for Member States on the implementation of Council Regulation (EC) No 338/97, as described above. This Regulation is published in the Official Journal of the European Communities, L 140, Volume 40, 30 May 1997 (ISSN 0378-6978).
Commission Regulation (EC) No. 939/97 has recently been replaced by Commission Regulation (EC) No.1808/2001. The Regulation is published in the Official Journal L 250, 19 September 2001.
Protected Species Commission Regulation (EC) No. 338/37 covers species listed in its four Annexes:
Annex A • All CITES Appendix I species • Some CITES Appendix II and III species, for which the EU has adopted stricter domestic measures. • Some non-CITES species
Annex B • All other CITES Appendix II species • Some CITES Appendix III species • Some non-CITES species
Annex C • All other CITES Appendix III species
Annex D • Some CITES Appendix III species for which the EU holds a reservation • Some non-CITES species
Species Listed in the Annexes A list of species included in the Annexes is given in the full text of the Regulation.
Reference Guide The text of the regulations is necessarily written in legalistic language. In order to facilitate better understanding of the provisions of the laws, a simply written, but nonetheless detailed Reference Guide has been written which is available at http://europa.eu.int/comm/environment/cites/legislation_en.htm.
Anon. Reference Guide: European Community Wildlife Trade Regulations. European Commission / TRAFFIC Europe / WWF, Brussels (1998).
Review of Current Wildlife Species Genetic Research - 75 - Final Report Amendments to Existing Regulations and other Relevant Regulations Whenever the list of species listed in the Annexes to Council Regulation 338/97 changes, this is done through a new Commission Regulation.
The latest issued Regulation is Commission Regulation (EC) No 2476/2001 of 17 December 2001 amending Council Regulation (EC) No 338/97 on the protection of species of wild fauna and flora by regulating trade therein (Official Journal L 334 of 18 December 2001). This is available at http://europa.eu.int/eur-lex/en/lif/reg/en_register_15103020.html.
Council Regulation (EC) No 338/97 provides the Commission with the possibility to restrict the introduction of species into the European Union. This is done after consultation of the countries of origin concerned and taking into account any opinion of the Scientific Review Group. The list of such restrictions, if any, is published on a quarterly basis in the Official Journal of the European Communities.
The most recent Suspensions Regulation is Commission Regulation (EC) No 2087/2001 of 24 October 2001 suspending the introduction into the Community of specimens of certain species of wild fauna and flora (Official Journal L 282 of 26 October 2001). This is available at http://europa.eu.int/comm/environment/cites/legislation_en.htm.
Sources: Http://europa.eu.int/comm/environment/cites/legislation_en.htm Http://europa.eu.int/eur-lex/en/lif/reg/en_register_15103020.html
Review of Current Wildlife Species Genetic Research - 76 - Final Report 9.9 Appendix 9 : Definitons for the Red List categories
Plant Categories Definitions for the plant categories were taken from: http://www.unep- wcmc.org/index.html?http://www.unep-wcmc.org/species/plants/overview.htm~main
Walter, K.S. and Gillet, H.J. (Eds). 1997 IUCN Red List of Threatened Plants.. Compiled by the World Conservation Monitoring Centre. IUCN, Gland, Switzerland and Cambridge, UK (1998).
Animal Categories The full definitions for the animal categories were taken from: http://www.redlist.org/info/categories_criteria.html
Hilton-Talyor, C. (Comp). 2000 IUCN Red List of Threatened Species. IUCN, Gland, Switzerland and Cambridge, UK (2000).
Review of Current Wildlife Species Genetic Research - 77 - Final Report