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Trends in wildlife crime continue to rise and contribute to the ongoing decline of our planet’s biodiversity. We applied a genetic approach to ascertain the geographic origin of a suspected Seychelles Magpie-robin confiscated in Singapore during international transit, and to confirm illegal trade of this species. However, mitochondrial analyses revealed this individual to be a subspecies of Oriental Magpie-robin, endemic to the island of Borneo, and bearing similar morphology to the Seychelles species. We thus consider the implications of correct species identification on captive care and repatriation in cases of wildlife confiscation, and emphasise the value of using genetics in wildlife crime investigation.

1. Genetic diversity is one of the three main levels of biodiversity recognised in the Convention on Biological Diversity (CBD). Fundamental for species adaptation to environmental change, genetic diversity is nonetheless under-reported within global and national indicators. When it is reported, the focus is often narrow and confined to domesticated or other commercial species. 2. Several approaches have recently been developed to address this shortfall in reporting on genetic diversity of wild species. While multiplicity of approaches is helpful in any development process, it can also lead to confusion among policy makers and heighten a perception that conservation genetics is too abstract to be of use to organisations and governments. 3. As the developers of five of the different approaches, we have come together to explain how various approaches relate to each other and propose a scorecard, as a unifying reporting mechanism for genetic diversity. 4. Policy implications. We believe the proposed combined approach captures the strengths of its components and is practical for all nations and subnational governments. It is scalable and can be used to evaluate species conservation projects as well as genetic conservation projects., Journal of Applied Ecology, 59 (9), ISSN:0021-8901, ISSN:1365-2664

Aim: The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species. It is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations, but also poses a potential disease risk to other species, including humans and livestock. Despite the imminent threat to the species’ survival and its prevalence in the wildlife trade, the phylogeography and evolution of the Sunda pangolin is not well understood. We aimed to investigate the species’ phylogeography across its distribution to improve our understanding of the species’ evolutionary history, elucidate any taxonomic uncertainties and enhance the species’ conservation genetic management and wildlife forensics applications. Location: Southeast Asia and southern China. Methods: We sequenced mtDNA genomes from 23 wild Sunda pangolins from Borneo and Peninsular Malaysia. We used these data in conjunction with previous generated mtDNA and nuclear datasets from across the species’ range to perform various phylogenetic and population genetic analyses. Results: We identified an evolutionarily distinct mtDNA lineage in north Borneo, which was estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time of the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. Main conclusions: These findings are consistent with the ‘out of Borneo hypothesis’, whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex, and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic species identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators. ispartof: CONSERVATION GENETICS vol:24 issue:2 pages:181-191 ispartof: location:Netherlands status: published

The Japanese golden eagle (Aquila chrysaetos japonica) is an endangered subspecies with declining reproductive success. Previous research on this subspecies reported genetic diversity in northern Japan and in captivity using neutral genetic markers, but the situation in other areas of Japan and diversity at functional genetic loci are understudied. Here, we increased wild samples from western Japan and captive samples from zoos, and analyzed genetic diversity of mitochondrial DNA, nuclear microsatellite loci, and the major histocompatibility complex (MHC) DRB exon 2 region. In addition, wild Scottish samples were analyzed and literature from European subspecies and other raptor species was surveyed to compare with the Japanese golden eagle. Overall, levels of mtDNA haplotype and microsatellite diversity observed in western Japan were similar to previously studied northern regions. However, microsallite allelic diversity was lower compared to other golden eagle subspecies. MHC diversity indices, especially in captive Japanese golden eagles, were also low relative to raptors classified as Least Concern by the IUCN. This pattern could be explained by the loss of rare alleles due to genetic drift – a consequence of a declining population – suggesting the possibility of an early population bottleneck. Moreover, genetic structure analyses suggested that the Japanese population likely consists of one gene pool, so the bottleneck may affect the entire population. From these results, we suggest maintaining gene flow between local populations to prevent inbreeding and further loss of alleles, increasing the number of breeding pairs in captivity, and releasing captive individuals to reinforce the wild population.

The past decade has seen a rapid expansion of non-human forensic genetics coinciding with the development of 2nd and 3rd generation DNA sequencing technologies. Nanopore sequencing is one such technology that offers massively parallel sequencing at a fraction of the capital cost of other sequencing platforms. The application of nanopore sequencing to species identification has already been widely demonstrated in biomonitoring studies and has significant potential for non-human forensic casework, particularly in the area of wildlife forensics. This review examines nanopore sequencing technology and assesses its potential applications, advantages and drawbacks for use in non-human forensics, alongside other next-generation sequencing platforms and as a possible replacement to Sanger sequencing. We assess the specific challenges of sequence error rate and the standardisation of consensus sequence production, before discussing recent progress in the validation of nanopore sequencing for use in forensic casework. We conclude that nanopore sequencing may be able to play a considerable role in the future of non-human forensic genetics, especially for applications to wildlife law enforcement within emerging forensic laboratories.

A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9

Fisheries enforcement relies on visual catch identification and quantification at sea or when landed. Silage (fish dissolved in acid) and fish blocks (block frozen fish) are promising methods for on-board processing and storage of low-value catches. We examined the use of non-destructive sampling and two DNA-based methods, quantitative PCR (qPCR) and metabarcoding, to assess species composition and relative abundance in industrial grade experimental silage and fish blocks. We demonstrate the ability to identify and quantify DNA from fish species in both products. qPCR analysis of small silage samples collected over 21 days detected all target control species. DNA from one species (Atlantic wolffish) was consistently overrepresented while, for three species of gadoids (Atlantic cod, haddock and whiting), the DNA content matched input tissue proportions with high accuracy. qPCR and metabarcoding of fish blocks, sampled as run-off water and exterior swabs, provided consistent species detection, with the highest variance observed in quantification from swab samples. Our analysis shows that DNA-based methods have significant potential as a tool for species identification and quantification of complex on-board-processed seafood products and are readily applicable to taxonomically and morphologically similar fish. There is, however, a need for establishing DNA/weight calibration factors for primary fisheries species.

The application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.

Advances in sequencing technologies have revolutionized wildlife conservation genetics. Analysis of genomic data sets can provide high-resolution estimates of genetic structure, genetic diversity, gene flow, and evolutionary history. These data can be used to characterize conservation units and to effectively manage the genetic health of species in a broad evolutionary context. Here we utilize thousands of genome-wide single-nucleotide polymorphisms (SNPs) and mitochondrial DNA to provide the first genetic assessment of the Australian red-tailed black-cockatoo (Calyptorhynchus banksii), a widespread bird species comprising populations of varying conservation concern. We identified five evolutionarily significant units, which are estimated to have diverged during the Pleistocene. These units are only partially congruent with the existing morphology-based subspecies taxonomy. Genetic clusters inferred from mitochondrial DNA differed from those based on SNPs and were less resolved. Our study has a range of conservation and taxonomic implications for this species. In particular, we provide advice on the potential genetic rescue of the Endangered and restricted-range subspecies C. b. graptogyne, and propose that the western C. b. samueli population is diagnosable as a separate subspecies. The results of our study highlight the utility of considering the phylogeographic relationships inferred from genome-wide SNPs when characterizing conservation units and management priorities, which is particularly relevant as genomic data sets become increasingly accessible.

イヌワシの一亜種であるニホンイヌワシ（Aquila chrysaetos japonica）は，個体数と繁殖状況の現状調査に基づいて，環境省版レッドリストの絶滅危惧種に指定されている。現在，国による保全活動が行われているものの，個体数減少の原因とその改善方法に関する知見は，十分とはいえない。この数十年の間に，日本を含む世界各地において，イヌワシの種の回復に関する多分野にわたる科学的な研究が行われ，本種の保全計画に必要な情報が集められつつある。しかしながら，これらの研究は個別に進められており，学際的なアプローチが充分になされていない。本稿では，生態学，遺伝学，獣医学的健康管理，生息地管理などの，ニホンイヌワシの保全に関する諸研究を総合して概観した。野生および飼育下個体群の現状と傾向を分析し，現在および将来の保全管理の活動を報告し，ニホンイヌワシの生息域内保全および生息域外保全に向けた対策について，統合的な見地から議論した。この総説では，イヌワシの生物学や健康科学に関する国内および海外の専門家グループが，学術的な情報と実用的な解決策の両方を提示した。本稿によって，ニホンイヌワシの数の減少をくいとめるのに必要な情報と技術を提供し，日本における長期的な本種の保全に応用するための枠組みを示すことを目指す。, According to current trends in census size and reproduction, the Japanese golden eagle (Aquila chrysaetos japonica) is at risk of extinction this century, leading the Japanese government to recognize the subspecies as endangered. It is now the focus of national conservation efforts, yet gaps remain in our knowledge regarding the reasons for the observed population decline and how best to improve the situation. Over recent decades, scientific research concerning golden eagle conservation in Japan, and in other parts of the world, has established a multi-disciplinary body of evidence that should support plans for species restoration. However, until now, these strands of research have been largely separate, limiting the potential benefits offered by an inter-disciplinary approach. In this paper, we provide an integrated review of Japanese golden eagle conservation science, including studies of ecology, genetics, veterinary health and habitat management. We assess the status and trends in the wild and captive populations; identify current and future conservation management interventions and discuss the opportunities for taking an integrated approach to Japanese golden eagle conservation science through in-situ and ex-situ viewpoint. This review, prepared by national and international experts in golden eagle biology and health, describes outstanding scientific questions alongside potential practical solutions. It sets out a framework for applied research that will provide the information and techniques required to successfully reverse the decline in golden eagle numbers, and hopefully secure the long-term future of the species in Japan.

Effective wildlife management requires information on population status and distribution. Survey methods that provide estimates of these population parameters can vary greatly in effort required, area covered, precision of estimates, and cost. Trade-offs are required, because increasing precision and area coverage generally requires increasing field effort and incurs a higher cost. We compare DNA- and camera trap based-spatial capture-recapture approaches (DNA-SCR and CT-SCR) to the widely-used, dung-based line transect distance sampling (LTDS) method to assess their performance when applied to three relatively large populations of forest elephant Loxodonta cyclotis (>500 individuals), in order to evaluate their feasibility for future use at national and regional scales. Six of the nine surveys had a coefficient of variation below 20%; area coverage via DNA-SCR and LTDS was comparable and greatly exceeded that of the CT-SCR as applied; overall cost was highest for the LTDS surveys compared to the other two methods. We designed a new metric with which to compare survey methods: an integrated feasibility index (IFI). This combines three typical survey components: total area covered, level of precision achieved, and cost. The IFI suggests that DNA-SCR and LTDS are equally acceptable in terms of the combination of the three survey components, and that either survey method is suitable for large (national or regional) spatial scales for forest elephant density estimation. CT-SCR provides more precise estimates, but has double the IFI, due to the high cost per km2. DNA-SCR in particular, given the improvements highlighted in this study, is now being used at a national scale in Gabon. In conclusion, we recommend that the use of these spatial capture-recapture (SCR) methods, and their development, continue. Future findings and improvements should be compiled across studies to ensure their robust evolution as an option for monitoring the African forest elephant across its range and inform strategies and action for its conservation.

We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.

ispartof: CONSERVATION GENETICS vol:22 issue:4 pages:533-536 status: published

Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterised. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black-cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site associated DNA marker approach (DArTseqTM). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5-123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species; instead the geographic sampling, missing data, and bioinformatic methods had larger impact. We did identify a bias towards low diversity SNPs in older samples, that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.

In recent years lion bones have been legally traded internationally to Asian markets from captive-bred sources in South Africa. There are also indications of increasing instances of illegal international trade in wild lion bones. The existence of parallel captive and wild supplies of lion bone are a cause of law enforcement concern regarding the potential for the laundering of illegally sourced bones through legal trade, and present a problem for the assessment of the conservation impact of wild lion bone trade due to the difficulty of determining what market-share wild and captive-bred lion bones account for. Captive-bred and wild lion bone are visually indistinguishable and no reliable method currently exists for distinguishing them. We present a preliminary study that explores the use of DART mass spectrometry as a method to differentiate between captive-bred and wild lion bones. We find that DART is able to differentiate between a batch of captive-bred South African lion bone and a batch of wild lion bone and suggest that DART mass spectrometry shows strong potential as a tool for the regulation and investigation of lion bone trade. Further testing is needed to prove the suitability of this technique. Therefore, we suggest that further research focuses on testing the capability of DART to differentiate between contemporary wild and captive-bred lion bone originating from South Africa, and attempts to identify chemical markers in bone that can be used as indicators of captive-bred origin.

The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.\ud\ud Previous article in issue

In many parts of the world, human-mediated environmental change is depleting biodiversity faster than it can be characterized, while invasive species cause agricultural damage, threaten human health, and disrupt native habitats. Consequently, the application of effective approaches for rapid surveillance and identification of biological specimens is increasingly important to inform conservation and biosurveillance efforts. Taxonomic assignments have been greatly advanced using sequence-based applications, such as DNA barcoding, a diagnostic technique that utilizes polymerase chain reaction (PCR) and DNA sequence analysis of standardized genetic regions. However, in many biodiversity hotspots, endeavors are often hindered by a lack of laboratory infrastructure, funding for biodiversity research, and restrictions on the transport of biological samples. A promising development is the advent of low-cost, miniaturized scientific equipment. Such tools can be assembled into functional laboratories to carry out genetic analyses in situ, at local institutions, field stations, or classrooms. Here, we outline the steps required to perform amplicon sequencing applications, from DNA isolation to nanopore sequencing and downstream data analysis, all of which can be conducted outside of a conventional laboratory environment using miniaturized scientific equipment, without reliance on internet connectivity. Depending on sample type, the protocol (from DNA extraction to full bioinformatic analyses) can be completed within 10 hours and with appropriate quality controls can be used for diagnostic identification of samples independent of core genomic facilities that are required for alternative methods.

The highly valuable timber species Dalbergia cochinchinensis is severely threatened due to habitat loss and illegal logging throughout its distribution in mainland Southeast Asia and is listed on CITES Appendix II. This study proposes a strategy for conservation and sustainable management of the species based on assessment of genetic structure within and among natural populations. We developed SNP markers from RAD sequencing and used these in combination with SSR genotypes from a previous study to assess the genetic diversity in 26 populations of D. cochinchinensis across its entire range in Laos, Thailand, Cambodia and Vietnam. The species is able of clonal reproduction and we found that trees closer than 45 meters from each other can be clones. Genetic diversity and clustering analysis showed a clear division of populations into five geographical groups with differing levels of diversity. Assignment tests correctly identified the region of origin for approximately 90% of the samples, which demonstrates that despite a low number of successfully identified SNPs, the SSR + SNP marker panel has the potential for tracking the geographic origin of D. cochinchinensis timber for use in CITES regulation and enforcement. We propose the five identified groups to be considered as Management Units and that conservation and breeding programs should be based on a network of in situ and ex situ conservation stands representing the genetic variation among and within these units. We recommend that conservation efforts are directed towards community owned and managed lands, as this has proven an effective strategy locally.

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is thefocus of a large-scale and long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management,comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals,we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamicdemographic history that coincided with periods of climate variation during the Pleistocene. Overall,our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangeredspecies.

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management planning. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah)is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

The reintroduction of the scimitar-horned oryx to Chad is a multi-disciplinary endeavour, planned and implemented over the past decade, utilizing a wide range of conservation science applications to maximise the chances of long-term population sustainability. The principle of incorporating genetic diversity information into founder selection for species reintroductions is widely recognized; however, in practice, a full assessment of available ex-situ genetic variation is rarely attempted prior to identifying individuals for release.In this study we present the results of over ten years of research analyzing and interpreting the genetic diversity present in the key source populations for the Chad scimitar-horned oryx reintroduction. Three empirical genetic datasets (mitochondrial DNA sequence, nuclear DNA microsatellite and SNP markers) comprising over 500 individuals sampled from public and private institutions were analysed, accompanied by simulation studies to address applied questions relating to management of the reintroduction.The results strongly demonstrate the importance of conservation genetic analysis in ensuring that founders represent the greatest breadth of evolutionary diversity available. The inclusion of both intensively and lightly managed collections allowed us to bridge the gap between studbook and group managed populations, enabling the inclusion of individuals from populations that lack historic data on their origins, but which may hold unique diversity of significant conservation value. Importantly, however, our study also reveals the potential risks of applying standard population genetic approaches to multiple captive populations, for which small founder sizes are likely to strongly bias results, with potentially serious consequences for the genetic management of conservation breeding programmes.

Conservation efforts are often informed by measures of genetic structure within or between isolated populations. We have established a simulation approach to investigate how isolated or captive populations can display misleading (i.e recently acquired) genetic structure as a result of genetic drift. We utilized a combination of softwares to generate isolated population genetic datasets that allow interrogation of emerging genetic structure under a range of conditions. We have developed a new statistic, S, to describe the extent of differentiation due to genetic drift between two isolated populations within the clustering software, STRUCTURE.A novel method to infer the effects of genetic drift on structure among isolated populationsGraphical AbstractSPECIFICATIONS TABLE

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

European roe deer (Capreolus capreolus L.) are the most common game species in Europe, hunted for meat and trophies. Forensic investigations involving roe deer poaching may often benefit from an individual identification method to link a suspect to a specific incident. The current paper presents a forensically validated DNA profiling system for European roe deer called “STRoe deer”. This DNA profiling system consists of 12 novel unlinked tetranucleotide short tandem repeat (STR) loci and two sex-specific markers, with an allelic ladder to facilitate accurate genotyping. Validation results demonstrate successful amplification of all 14 loci with as little as 0.05 ng of European roe deer DNA. Species-specificity tests showed that other members of the Cervidae family exhibited partial profiles and non-specific peaks, whereas most members of the Bovidae family showed just non-specific cross-species amplification products. Based on 513 European roe deer samples collected from a population from the Swiss Plateau, probability of identity was 3.1 x 10- 12 and the fixation index of 0.0275 indicated that only weak effects of genetic substructure or inbreeding were present in this population. Three different methods to calculate match probabilities for randomly sampled genotypes resulted in median match probabilities ranging from 1.4 x 10-13 to 2.5 x 10-5. These methods accounted for population structure, occurrence of null alleles or relatedness of the involved individuals. Based on these results, we conclude that STRoe deer is a robust genotyping system that should prove a valuable tool for individual identification and sexing of European roe deer to support criminal investigations.

Over recent years, mounting pressure has been placed on countries to assess their role in the ivory trade, with a view to tackling the rapidly declining numbers of elephants, due to poaching. The United Kingdom has been identified as a large re-exporter of ivory. Despite much of this trade being reported as legal or antique ivory, such provision of ivory to meet demand is known to fuel illegal markets and provide trade routes for modern ivory sales. Aside from ivory species and age, further analysis to evaluate geographic provenance, can inform where an elephant had lived, and so identify a source region or population where poaching occurred. The purpose of this study was to determine the age and species of ivory objects surrendered or seized in the UK and assess their likely geographic provenance through comparison of results from mitochondrial DNA and stable isotope analysis to publicly accessible georeferenced African elephant databases. The results demonstrated that the objects tested from an airport seizure were modern and matched existing haplotypes allowing for regional geographic inferences (supported by both techniques) to be obtained for most of these objects. In contrast, antique and modern ivory was detected amongst the amnesty objects, and several new mtDNA haplotypes were identified. Regional geographic inferences were achieved for some but not all of the objects tested. Our findings show this combination of methods provides a wealth of information which, could provide insight into targeted elephant populations and assist in disrupting international wildlife trade networks.

The loss of biological diversity within species has the potential to significantly reduce resilience in the face of environmental change. Conservation of genetic variation needs to consider all available sources of diversity within a species, and approaches are required to integrate population management across traditionally separate wild and captive population domains. Here we report on a study that utilises different types of genetic analysis at different taxonomic scales and across an in situ – ex situ transition to support conservation planning for the Japanese golden eagle, a subspecies in serious regional decline. Mitochondrial DNA sequencing and nuclear DNA profiling are used to investigate subspecies differentiation and diversity in the natural population, revealing relatively high levels of variation in Japan. These results are compared with data from a newly established conservation breeding programme that indicates good representation of wild genetic variation in the captive founders. However, subsequent population viability analysis (PVA) to examine the demographic and genetic future of the captive population demonstrates the severe effects of existing reproductive skews, suggesting that this population is not sustainable without intensive genetic management. Lastly, the use of available molecular tools to validate and reconstruct pedigrees in Japanese golden eagle are evaluated and discussed in the context of captive and wild conservation management. The paper highlights the importance of producing and utilising comparative molecular genetic data across the population management spectrum and the benefits of PVA to support the implementation of integrated conservation plans.