Wildlife forensic science: A review of genetic geographic origin assignment

Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease

Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.

Review: Wildlife forensic genetics-Biological evidence, DNA markers, analytical approaches, and challenges

Wildlife-related crimes are the second most prevalent lawbreaking offense globally. This illicit trade encompasses hunting, breeding and trafficking. Besides diminishing many species and their habitats and ecosystems, hindering the economic development of local communities that depend on them, undermining the rule of law and financing terrorism, various cross-species transmissions (zoonoses) of pathogens, including COVID-19, can be attributed to wildlife crimes. Wildlife forensics applies interdisciplinary scientific analyses to support law enforcement in investigating wildlife crimes. Its main objectives are to identify the taxonomic species in question, determine if a crime has been committed, link a suspect to the crime and support the conviction and prosecution of the perpetrator. This article reviews wildlife crime and its implications, wildlife forensic science investigation, common forms of wildlife biological evidence, including DNA, wildlife DNA techniques and challenges in wildlife forensic genetics. The article also reviews the contributions of genetic markers such as short tandem repeat (STR) and mitochondrial DNA (mtDNA) markers, which provide the probative genetic data representing the bulk of DNA evidence for solving wildlife crime. This review provides an overview of wildlife DNA databases, which are critical for searching and matching forensic DNA profiles and sequences and establishing how frequent forensic DNA profiles and sequences are in a particular population or geographic region. As such, this review will contain an in-depth analysis of the current status of wildlife forensic genetics, and it will be of general interest to wildlife and conservation biologists, law enforcement officers, and academics interested in combating crimes against wildlife using animal forensic DNA methods.

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics

The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and 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. Here, 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 potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. 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 identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.

Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture

BACKGROUND

Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture.

RESULTS

Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia.

CONCLUSIONS

We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.

A forensically validated genetic toolkit for the species and lineage identification of the highly trafficked shingleback lizard (Tiliqua rugosa)

Shingleback lizards (Tiliqua rugosa) are among the most trafficked native fauna from Australia in the illegal pet trade. There are four morphologically recognised subspecies of shinglebacks, all with differing overseas market values. Shinglebacks from different geographic locales are often trafficked and housed together, which may complicate identifying the State jurisdiction where the poaching event occurred. Additionally, shinglebacks can be housed and trafficked with other species within the same genus, which may complicate DNA analysis, especially in scenarios where indirect evidence (e.g. swabs, faeces) is taken for analysis. In this study, a forensic genetic toolkit was designed and validated to target shingleback DNA for species identification and geographic origin. To do this, field sampling across Australia was conducted to expand the phylogeographic sampling of shinglebacks across their species range and include populations suspected to be poaching hotspots. A commonly used universal reptile primer set (ND4/LEU) was then validated for use in forensic casework related to the genus Tiliqua. Two additional ND4 primer sets were designed and validated. The first primer set was designed and demonstrated to preferentially amplify an ∼510 bp region of the genus Tiliqua over other reptiles and builds on existing data to expand the available phylogeographic database. The second primer set was designed and demonstrated to solely amplify an ∼220 bp region of T. rugosa ND4 over any other reptile species. Through the validation process, all primers were demonstrated to amplify T. rugosa DNA from a variety of sample types (e.g. degraded, low quality and mixed). Two of the primer sets were able to distinguish the genetic lineage of T. rugosa from the phylogeographic database. This work provides the first forensically validated toolkit and phylogeographic genetic database for Squatmate lizards.

Advancing the protection of marine life through genomics

The rapid growth in genomic techniques provides the potential to transform how we protect, manage, and conserve marine life. Further, solutions to boost the resilience of marine species to climate change and other disturbances that characterize the Anthropocene require transformative approaches, made more effective if guided by genomic data. Although genetic techniques have been employed in marine conservation for decades and the availability of genomic data is rapidly expanding, widespread application still lags behind other data types. This Essay reviews how genetics and genomics have been utilized in management initiatives for ocean conservation and restoration, highlights success stories, and presents a pathway forward to enhance the uptake of genomic data for protecting our oceans.

From STRs to SNPs via ddRAD ‐seq: geographic assignment of confiscated tortoises at reduced costs

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost‐effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD‐seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro‐area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re‐assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in‐situ of confiscated animals and their possible re‐allocation in the wild. Our methodological pipeline can easily be extended to other species.

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.

Can DNA help trace the local trade of pangolins? Conservation genetics of white-bellied pangolins from the Dahomey Gap (West Africa)

Background

African pangolins are currently experiencing unprecedented levels of harvesting, feeding both local demands and the illegal international trade. So far, the lack of knowledge on the population genetics of African pangolins has hampered any attempts at assessing their demographic status and tracing their trade at the local scale. We conducted a pioneer study on the genetic tracing of the African pangolin trade in the Dahomey Gap (DG). We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellite loci.

Results

Tree-based assignment procedure showed that the pangolin trade is endemic to the DG region, as it was strictly fed by the the Dahomey Gap lineage (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, important inbreeding levels, and lack of geographic structure. We identified a 92–98% decline in DGL effective population size 200–500 ya—concomitant with major political transformations along the ‘Slave Coast’—leading to contemporaneous estimates being inferior to minimum viable population size (< 500). Genetic tracing suggested that wildlife markets from the DG sourced pangolins through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of a same individual on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies with cross-validation of observed data that traced five traded pangolins to their forest origin, c. 200–300 km away from the markets.

Conclusions

Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the illegal trade in pangolins, our tracing ability was limited by the lack of population structure within the DGL. Given the deleterious combination of genetic, demographic, and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01971-5.

Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo)

Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.

From the river to the ocean: mitochondrial DNA analyses provide evidence of spectacled caimans (Caiman crocodilus Linnaeus 1758) mainland–insular dispersal

There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.

Development and Validation of a Multi-Locus PCR-HRM Method for Species Identification in Mytilus Genus with Food Authenticity Purposes

DNA-based methods using informative markers such as single nucleotide polymorphism (SNPs) are suitable for reliable species identification (SI) needed to enforce compliance with seafood labelling regulations (EU No.1379/2013). We developed a panel of 10 highly informative SNPs to be genotyped by PCR-High resolution melting (HRM) for SI in the Mytilus genus through in silico and in vitro stages. Its fitness for purpose and concordance were assessed by an internal validation process and by the transference to a second laboratory. The method was applicable to identify M. chilensis, M. edulis, M. galloprovincialis and M. trossulus mussels, fresh, frozen and canned with brine, oil and scallop sauce, but not in preserves containing acetic acid (wine vinegar) and tomato sauce. False-positive and negative rates were zero. Sensitivity, expressed as limit of detection (LOD), ranged between 5 and 8 ng/μL. The method was robust against small variations in DNA quality, annealing time and temperature, primer concentration, reaction volume and HRM kit. Reference materials and 220 samples were tested in an inter-laboratory assay obtaining an “almost perfect agreement” (κ = 0.925, p < 0.001). In conclusion, the method was suitable for the intended use and to be applied in the seafood industry.

International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions

International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.

Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

Background

The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets.

Results

Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico.

Conclusions

Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

Mammalian species identification using ISSR-HRM technique

Wildlife trading and the illegal hunting of wildlife are contributing factors to the biodiversity crisis that is presently unfolding across the world. The inability to control the trade of animal body parts or available biological materials is a major challenge for those who investigate wildlife crime. The effective management of this illegal trade is an important facet of wildlife forensic sciences and can be a key factor in the enforcement of effective legislation surrounding the illegal trade of protected and endangered species. However, the science of wildlife forensics is limited by the absence of a comprehensive database for wildlife investigations. Inter-simple sequence repeat markers (ISSR) coupled with high resolution melting analysis (HRM) have been effectively used for species identification of 38 mammalian species. Six primers of the ISSR markers were chosen for species identification analysis. From six ISSR primers resulting in a range of accuracy of 33.3%-100% and 100% in terms of precision in every primer. Furthermore, 161 mammalian samples were 100% distinguished to the correct species using these six ISSR primers. ISSR-HRM analysis was successfully employed in determining mammal identification among varying mammalian species, and thus could serve as an effective alternative tool or technique in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and the ease with which researchers or field practice veterinarians would be able to interpret results in effectively identifying animal parts at wildlife investigation crime scenes.

Marine mammal conservation: over the horizon

Marine mammals can play important ecological roles in aquatic ecosystems, and their presence can be key to community structure and function. Consequently, marine mammals are often considered indicators of ecosystem health and flagship species. Yet, historical population declines caused by exploitation, and additional current threats, such as climate change, fisheries bycatch, pollution and maritime development, continue to impact many marine mammal species, and at least 25% are classified as threatened (Critically Endangered, Endangered or Vulnerable) on the IUCN Red List. Conversely, some species have experienced population increases/recoveries in recent decades, reflecting management interventions, and are heralded as conservation successes. To continue these successes and reverse the downward trajectories of at-risk species, it is necessary to evaluate the threats faced by marine mammals and the conservation mechanisms available to address them. Additionally, there is a need to identify evidence-based priorities of both research and conservation needs across a range of settings and taxa. To that effect we: (1) outline the key threats to marine mammals and their impacts, identify the associated knowledge gaps and recommend actions needed; (2) discuss the merits and downfalls of established and emerging conservation mechanisms; (3) outline the application of research and monitoring techniques; and (4) highlight particular taxa/populations that are in urgent need of focus.

Wildlife crime in Australia

Wildlife crime is on a massive scale by whatever metric is used. The illegal trade in wildlife and related products is leading to the decline and extinction of many iconic species from rhino to tigers. Almost all countries are signatures to CITES and therefore should enforce national legislation if alleged infringements of trade of wildlife occur. No country is immune from this illegal trade although countries like Australia have their own specific wildlife crimes. Australia is home to many reptilian, amphibian and avian species that are highly prized, predominantly as pets. Collection of protected species from the wild is illegal in all jurisdictions yet policing remote areas of the outback, where so much of the native endemic fauna and flora lives, is nearly impossible. The illegal international trade in these species is highlighted by two case studies provided in this review. A further case highlights the issues of each of the six states of Australia having separate legislation, which is compounded when wildlife crime can be inter-state crime. Australia is one of the few countries having an institute, based at the Australian Museum, with an accredited wildlife forensic science laboratory and therefore the capability to undertake forensic testing of seized samples. One way to reduce wildlife crime may be by educating those who buy illegally seized products that there is a direct connection between the dead animal from which it came and the devasting effect this purchase has on the environment.

Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage

Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L, GF-L, and subsequent generations produced by self-crossing [the self-mating offspring of RCC-L (RCC-L-F₂) to the self-mating offspring of RCC-L-F₂ (RCC-L-F₃) and the self-mating offspring of GF-L (GF-L-F₂)]. Paternal mtDNA fragments were stably embedded in the mtDNAs of both lineages, forming chimeric DNA fragments. In addition to these chimeras, several nucleotide positions in the RCC-L and GF-L lineages differed from the parental bases, and were instead identical with RCC and GF, respectively. Moreover, RCC-L and GF-L mtDNA organization and nucleotide composition were more similar to those of RCC and GF, respectively, compared to parental mtDNA. Finally, phylogenetic analyses indicated that RCC-L and GF-L clustered with RCC and GF, not with the parental species. The molecular dating time shows that the divergence time of KOC and GF was about 21.26 Mya [95% highest posterior density (HPD): 24.41-16.67 Mya], which fell within the period of recent. The heritable chimeric DNA fragments and mutant loci identified in the mtDNA of the RCC-L and GF-L lineages provided important evidence that hybridizations might lead to changes in the mtDNA and the subsequent generation of new lineages. Our findings also demonstrated for the first time that the paternal mtDNA was transmitted into the mtDNA of homodiploid lineages (RCC-L and GF-L), which provided evidence that paternal DNA plays a role in inherited mtDNA. These evolutionary analyses in mtDNA suggest that GF might have diverged from RCC after RCC diverged from koi carp.

Mapping the geographic origin of captive and confiscated Hermann's tortoises: A genetic toolkit for conservation and forensic analyses

The illegal trade has been threatening tortoise populations worldwide for decades. Nowadays, however, DNA typing and forensic genetic approaches allow us to investigate the geographic origin of confiscated animals and to relocate them into the wild, providing that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise Testudo hermanni hermanni. Specific allelic ladders were created for each locus and tested on several reference samples. We used the microsatellite panel to (i) increase our understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70 % of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origins of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show that the microsatellite panel and the reference dataset can play a beneficial role in reintroduction and repatriation projects when confiscated individuals need to be re-assigned to their respective macro-area of origin before release, and can assist future forensic genetic applications in detecting the illegal trade and possession of Testudo hermanni individuals.

Tracking a voyager: mitochondrial DNA analyses reveal mainland-to-island dispersal of an American crocodile (Crocodylus acutus) across the Caribbean

Conservation efforts have allowed American crocodile (Crocodylus acutus) populations to recover to the point that dispersal movements are beginning to be documented. The environmental authority of San Andres Island in Colombia reported, for the first time, the arrival of two C. acutus from unknown localities in 2012 and 2018. The former was sacrificed, and the latter was captured and kept in captivity to determining its potential origin. We used wildlife forensics to establish the origin of the animal that arrived in 2018 based on two mitochondrial genes (COI and Cytb). Additionally, five other samples from Tayrona National Natural Park (TNNP), and Salamanca Island Road Park (SIRP) were sequenced for molecular attribution of these populations to the currently described lineages. Phylogenetic and phylogeographic analyses showed that the American crocodile found in San Andrés belongs to a continental evolutionary lineage endemic to Colombia, showing also a strong genetic similarity with animals from SIRP. Thus, the most likely origin for this individual was not the nearest continental area but somewhere around the central Colombian Caribbean, located ~700 km from the island. We discuss the implication of our findings in the systematics and conservation of the species and the potential of mitochondrial DNA analysis to identify such migrants.

Wildlife forensics: A boon for species identification and conservation implications

Wildlife trade and fraudulence in food, artefacts and cosmetic industries had raised serious concern in protection of the wild faunal diversity. Lack of proper tools and molecular based techniques for identification of wild species are some of the major constrains faced by the judiciary and law enforcement agencies while framing charges against poachers and illicit agitator. The emergence of wildlife forensics serves as a boon in solving long pending cases of wildlife crimes. Wildlife forensics have proven to be fast, accurate and reliable criminal investigation processes with comprehensive coverage and easy accessibility. It has also helped resolving taxonomic disputes, determining spatiotemporal genetic divergence, evolutionary history, origins and even endemism. Collaboration among inter-disciplinary fields has even led to engineered signature markers and phylogenetics for several species. Development in fields of genetics, molecular and evolutionary biology and other omics techniques have further contributed in accurate identification of species. Wildlife forensics, with the support of proper international mega database units for population reference, will be fundamental in wildlife investigations through its unlimited information sharing ability. The efficient conservation of species will, however, require a collaborative approach consisting of national policy makers, local stakeholders and implementation agencies in addition to experts from the scientific communities.

Threats from wildlife trade: The importance of genetic data in safeguarding the endangered Four-eyed Turtle (Sacalia quadriocellata)

Wildlife trade has been considered one of the largest threats to biodiversity in Southeast Asia. Many vertebrates, such as pangolins, elephants and turtles have been heavily hunted as a result of high demand from emerging markets in China and other countries in the region. In Vietnam, over-exploitation of turtles over several decades to supply the international trade has extirpated numerous populations and driven several species to the brink of extinction. To reverse this trend, conservation measures, such as re-introduction of confiscated or captive-bred animals to their native habitats, should be implemented to recover severely declined local populations. For species with a complex phylogeographic structure, however, it is crucial to understand geographic patterns of genetically-distinct populations to avoid releasing animals of unknown origin to wrong localities. In this study, we investigate the phylogeographic pattern of the Four-eyed Turtle (Sacalia quadriocellata), a widely traded species, which occurs in southern China, northern and central Laos and much of Vietnam, using samples with known localities and those collected from the local trade. Our range-wide phylogenetic and network study, based on the complete mitochondrial cytochrome b gene, recovered at least three major clades and seven subclades within the species range. Amongst these, two subclades, one from northern Annamites, Vietnam and the other from north-eastern Laos, are newly discovered. The fine scale phylogeographic analysis helped us to assign misidentified sequences from GenBank and those from confiscated animals with unknown origin to well-defined geographic populations. The results highlight the importance of incorporating samples collected from the local trade and the wild in genetic analyses to support both ex-situ and in-situ conservation programmes of highly-threatened species in accordance with the IUCN’s One Plan Approach.

The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method

Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying F_ST. However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.

The visualisation of fingermarks on Pangolin scales using gelatine lifters

Recent media reports document the plight of the Pangolin and its current position as "the most trafficked mammal in the world". They are described by some as scaly anteaters as all species are covered in hard keratinous tissue in the form of overlapping scales acting as a "flexible dermal armour". It is estimated that between 2011 and 2013, 117,000-234,000 pangolins were slaughtered, but the seizures may only represent as little as 10% of the true volume of pangolins being illegally traded. In this paper, methods to visualise fingermarks on Pangolin scales using gelatine lifters is presented. The gelatine lifters provide an easy to use, inexpensive but effective method to help wildlife crime rangers across Africa and Asia to disrupt the trafficking. The gelatine lifting process visualised marks producing clear ridge detail on 52% of the Pangolin scales examined, with a further 30% showing the impression of a finger with limited ridge detail. The paper builds on an initial sociotechnical approach to establishing requirement, then it focuses on the methods and outcomes relating to lifting fingermarks off Pangolin scales using gelatine lifters, providing an evaluation of its use in practice.

Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation

Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.

Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit

Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.

Microsatellite based assignment reveals history of extirpated mountain ungulate

During the early 1900s, Northern chamois (Rupicapra rupicapra) populations in the northern Dinaric Mountains were extirpated. During the 1960s and 1970s there were several reintroductions of individuals from two Northern chamois subspecies (Alpine chamois, R. r. rupicapra and Balkan chamois, R. r. balcanica) from neighbouring areas in the attempt to re-establish the population. Accurate taxonomic classification, at subspecies level, of the autochthonous extirpated population was not known. To clarify which subspecies was present before reintroduction, we genotyped four male chamois skulls originating from Velebit Mountain, collected around 25 years before the population local extinction. DNA was successfully extracted from middle layer and outer sheath of horns. Assignment based on microsatellite loci, using both Bayesian clustering in STRUCTURE (with q values between 0.55 and 0.73) and DAPC (with individual membership probabilities of 0.99 and 1.00) indicated higher assessed likelihood for the Alpine subspecies.

Utility of genetic variation in coat color genes to distinguish wild, domestic and hybrid South American camelids for forensic and judicial applications

A molecular genetic protocol for distinguishing pure and hybrid South American camelids was developed to provide strong, quantifiable, and unbiased species identification. We detail the application of the approach in the context of a criminal case in the Andes Mountains of central Chile where the defendants were alleged to have illegally hunted three wild guanacos (Lama guanicoe), as opposed to hybrid domestic llama (Lama glama)/wild guanaco crosses, which are unregulated. We describe a workflow that differentiates among wild, domestic and hybrid South American camelids (Lama versus Vicugna) based on mitochondrial cytochrome b genetic variation (to distinguish between Lama and Vicugna), and MC1R and exon 4 variation of the ASIP gene (to differentiate wild from domestic species). Additionally, we infer the population origin and sex of each of the three individuals from a panel of 15 autosomal microsatellite loci and the presence or absence of the SRY gene. Our analyses strongly supported the inference that the confiscated carcasses corresponded with 2 male and 1 female guanacos that were hunted illegally. Statistical power analyses suggested that there was an extremely low probability of misidentifying domestic camelids as wild camelids (an estimated 0 % Type I error rate), or using more conservative approached a 1.17 % chance of misidentification of wild species as domestic camelids (Type II error). Our case report and methodological and analytical protocols demonstrate the power of genetic variation in coat color genes to identify hybrids between wild and domestic camelid species and highlight the utility of the approach to help combat illegal wildlife hunting and trafficking.

Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin

Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as "blue crab" and "Product of the USA" may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as "Product of the USA" and "Product of Venezuela." In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F _st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.

A geographical traceability system for Merbau (Intsia palembanica Miq.), an important timber species from peninsular Malaysia

To inform product users about the origin of timber, the implementation of a traceability system is necessary for the forestry industry. In this study, we developed a comprehensive genetic database for the important tropical timber species Merbau, Intsia palembanica, to trace its geographic origin within peninsular Malaysia. A total of 1373 individual trees representing 39 geographically distinct populations of I. palembanica were sampled throughout peninsular Malaysia. We analyzed the samples using a combination of four chloroplast DNA (cpDNA) markers and 14 short tandem repeat (STR) markers to establish both cpDNA haplotype and STR allele frequency databases. A haplotype map was generated through cpDNA sequencing for population identification, resulting in six unique haplotypes based on 10 informative intraspecifically variable sites. Subsequently, an STR allele frequency database was developed from 14 STRs allowing individual identification. Bayesian cluster analysis divided the individuals into two genetic clusters corresponding to the northern and southern regions of peninsular Malaysia. Tests of conservativeness showed that the databases were conservative after the adjustment of the θ values to 0.2000 and 0.2900 for the northern (f = 0.0163) and southern (f = 0.0285) regions, respectively. Using self-assignment tests, we observed that individuals were correctly assigned to populations at rates of 40.54-94.12% and to the identified regions at rates of 79.80-80.62%. Both the cpDNA and STR markers appear to be useful for tracking Merbau timber originating from peninsular Malaysia. The use of these forensic tools in addition to the existing paper-based timber tracking system will help to verify the legality of the origin of I. palembanica and to combat illegal logging issues associated with the species.

Development of HyBeacon® probes for the forensic detection of Panthera, rhinoceros, and pangolin species

The Illegal Wildlife Trade (IWT) represents a multi-billion dollar black-market industry whereby wild species are illegally taken from their natural environment and sold. A common question asked by wildlife forensic scientists pertains to species and/or genus identity, which currently requires multi-step processing. Our work details the development of three HyBeacon® probes, used for the presumptive detection of rhinoceros, pangolin and key target species in the Panthera genus. The approach can be performed in a single tube using melt curve analysis and provide rapid assessment of sample identity. Using synthetic DNA of representative species, early data suggest the approach is sensitive enough to achieve species identification with <10 cells. Future development and assay validation can allow the rapid screening of multiple seized items before confirmatory DNA sequencing.

Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod

Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.

Defining end user requirements for a field-based molecular detection system for wildlife forensic investigations

The increasing use of non-laboratory-based DNA and protein detection methods promise to provide rapid investigative intelligence and support sample prioritisation. Primarily developed for human forensic or medical applications, current systems may also show utility in the field of wildlife forensic science. However, it is currently unknown whether the requirements of the wildlife forensic community can be met by current non-laboratory based tools. Given the diverse array of stakeholders and sample types commonly encountered, it is necessary to first identify the needs of the community and then try and map their needs to current instrumentation. By using a market research style questionnaire, this study identified key requirements for a non-laboratory-based system following feedback from the wildlife forensic community. Data showed that there is strong support for field-based detection methods while highlighting concerns including contamination risks and reduced quality assurance associated with non-laboratory testing. Key species and applications were identified alongside hurdles to implementation and adoption. Broadly, the requirements align with many of the developmental drivers that have led to the rise of in-field portable detection instrumentation, specifically rapid detection within one hour, ease-of-use, and ≥95% accuracy. Several existing platforms exist that met some of the identified requirements but not all. With further collaboration between industry partners and the wildlife forensic community it is possible that new field-based systems can be developed and applied routinely.

Genetic analyses reveal complex dynamics within a marine fish management area

Genetic data have great potential for improving fisheries management by identifying the fundamental management units-that is, the biological populations-and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed-stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.

Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

BACKGROUND

Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several 'omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus.

RESULTS

We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae.

CONCLUSIONS

Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.

The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America

The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider (Petaurus breviceps), endemic to Australia and New Guinea is a popular domestic pet due to its small size and "cute" demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with samples collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the samples tested within this study.

DNA based method for determining source country of the short beaked echidna (Tachyglossus aculeatus) in the illegal wildlife trade

The illegal trade in wild animals being sold as 'captive bred' is an emerging issue in the pet and zoo industry and has both animal welfare and conservation implications. DNA based methods can be a quick, inexpensive, and definitive way to determine the source of these animals, thereby assisting efforts to combat this trade. The short beaked echidna (Tachyglossus aculeatus) is currently one of the species suspected to be targeted in this trade. As this species is distributed throughout Australia and in New Guinea (currently comprising of five recognised sub-species), this project aimed to develop a DNA based method to definitively determine the source country of an echidna and explore the use of non-invasive sampling techniques. Here we use non-invasively sampled echidna quills and demonstrate the extraction of mitochondrial DNA and amplification of a region of the mitochondrial genome. Phylogenetically informative markers for analysis of a 322bp segment of the D-loop region were developed, and subsequently validated, using animals with known source locations allowing us to reliably distinguish between echidnas from New Guinea, and Australia. This research presents the first validated forensic protocols for short beaked echidnas and will be an integral tool in understanding the movement of animals in this emerging trade.

Genetic and genomic monitoring with minimally invasive sampling methods

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

Assessing the Ability of Chloroplast and Nuclear DNA Gene Markers to Verify the Geographic Origin of Jatoba (Hymenaea courbaril L.) Timber

Deforestation-reinforced by illegal logging-is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws that intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on 10 nuclear microsatellites (nSSRs), 13 chloroplast SNPs (cpSNP), and 1 chloroplast indel marker. The chloroplast gene markers have been developed using Illumina DNA sequencing. Bayesian cluster analysis divided the individuals based on the nSSRs into 8 genetic groups. Using self-assignment tests, the power of the genetic reference database to judge on declarations on the location has been tested for 3 different assignment methods. We observed a strong genetic differentiation among locations leading to high and reliable self-assignment rates for the locations between 50% to 100% (average of 88%). Although all 3 assignment methods came up with similar mean self-assignment rates, there were differences for some locations linked to the level of genetic diversity, differentiation, and heterozygosity. Our results show that the nuclear and chloroplast gene markers are effective to be used for a genetic certification system and can provide national and international authorities with a robust tool to confirm legality of timber.

Identification of plant species using variable length chloroplast DNA sequences

The correct identification of species in the highly divergent group of plants is crucial for several forensic investigations. Previous works had difficulties in the establishment of a rapid and robust method for the identification of plants. For instance, DNA barcoding requires the analysis of two or three different genomic regions to attain reasonable levels of discrimination. Therefore, new methods for the molecular identification of plants are clearly needed. Here we tested the utility of variable-length sequences in the chloroplast DNA (cpDNA) as a way to identify plant species. The SPInDel (Species Identification by Insertions/Deletions) approach targets hypervariable genomic regions that contain multiple insertions/deletions (indels) and length variability, which are found interspersed with highly conserved regions. The combination of fragment lengths defines a unique numeric profile for each species, allowing its identification. We analysed more than 44,000 sequences retrieved from public databases belonging to 206 different plant families. Four target regions were identified as suitable for the SPInDel concept: atpF-atpH, psbA-trnH, trnL CD and trnL GH. When considered alone, the discrimination power of each region was low, varying from 5.18% (trnL GH) to 42.54% (trnL CD). However, the discrimination power reached more than 90% when the length of some of these regions is combined. We also observed low diversity in intraspecific data sets for all target regions, suggesting they can be used for identification purposes. Our results demonstrate the utility of the SPInDel concept for the identification of plants.