Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula

How was genetic diversity transferred with translocations from ex situ to in situ? A case study of the European mink translocation to Hiiumaa Island in Estonia

The European mink (Mustela lutreola) is one of the most threatened small carnivores, listed as Critically Endangered on the IUCN Red List. Tallinn Zoo started a conservation breeding operation in 1980, which in 1992 was shaped into the European mink EEP Program to maintain a demographically and genetically healthy population in captivity. Since 2000, mink have been translocated on a yearly basis from the breeding facility in the zoo to Hiiumaa Island (Estonia) until the formation of the wild island population in 2016. Maintaining a healthy genetic structure in a captive population was a priority, so genetically the least valuable animals, according to calculations made by a population management program, were used for translocation. This study aims to assess the amount of genetic diversity passed from an ex situ population on to the island population. Comparisons of the genetic diversity were made by mitochondrial, microsatellite and nuclear markers. In addition, our results were combined with the pedigree data from the European mink EEP Studbook to further evaluate the flow of genetic diversity from the founder population to the established wild population. According to the findings, the island population's allelic richness was comparable to that of the founder population, and no evidence was found that its genetic structure had diverged from that of the founder population. It seems that the formation of the island population has been a gradual process of no more than the last seven yearly translocations.

The genetic diversity and structure in the European polecat were not affected by the introduction of the American mink in Poland

The introduction and expansion of an invasive non-native species could have important consequences for the genetic patterns and processes of native species, moreover if the new arrival competes strongly for resources and space. This may result in the demographic decline of the native species. Knowing the effects on the levels of genetic diversity and structure in native species is key in terms of their conservation. We analysed temporal (over 50 years) genetic variation of the population of the European polecat (Mustela putorius), a species under threat in several European countries, in the Białowieża Primeval Forest (BPF), Poland, before and after the invasion of the American mink (Neovison vison). Using 11 microsatellite loci and a fragment of the mitochondrial control region we show that levels of diversity changed in the polecat population over 53 generations (over the period 1959–2012) and after the invasion of mink. When compared with other threatened European polecat populations, high levels of diversity are observed in the population in BPF in both periods, as well as in other areas in Poland. Our data shows that genetic structure was not present either before or after the mink invasion in BPF. This would suggest that the polecat population in Poland was not affected by invasive species and other negative factors and would be a potential good source of individuals for captive breeding or genetic rescue conservation management actions in areas where such actions are needed, for example the UK.

High Genetic Diversity of an Invasive Alien Species: Comparison between Fur-Farmed and Feral American Mink (Neovison vison) in China

Simple Summary

The American mink (Neovison vison) is one of the best-known and most widespread invasive species in China and worldwide. To investigate the genetic characteristics and increase comprehension of the invasiveness process for this species, we compared the genetic characteristics of farmed and feral populations in northeastern China using mitochondrial DNA sequences and microsatellite loci. We found a relatively high diversity among the feral populations that was as high as that of the farmed mink. This demonstrated that high genetic diversity promotes the invasiveness and rapid evolution in the wild.

Abstract

Genetic characteristics play an important role in alien species for achieving high adaptation and rapid evolution in a new environment. The American mink (Neovison vison) is one of the best-known and most widespread invasive species that has successfully invaded the Eurasian mainland over quite a short period, including most parts of northeastern China. However, genetic information on farmed and feral American mink populations introduced in China is completely lacking. In this study, we combined mitochondrial DNA sequences and polymorphic microsatellites to examine the genetic divergence and genetic diversity of farmed and feral American mink populations. Our results suggest that there is admixture of individuals of different genetic characteristics between farmed and feral populations of mink. Furthermore, the genetic diversity of both farmed and feral American mink populations was high, and no bottleneck or population expansion was detected in most of the populations. These findings not only highlight the genetic characteristics of American mink in northeastern China but also contribute to the general understanding of the invasiveness of farmed species.

Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals?

The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.

Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini)

The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.

High-resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile

Easy, economic, precise species authentication is currently necessary in many areas of research and diagnosis in molecular biology applied to conservation studies of endangered species. Here, we present a new method for the identification of three fox species of the Lycalopex genus in Chile. We developed an assay based on high-resolution melt analysis of the mitochondrial cytochrome B gene, allowing a simple, low cost, fast, and accurate species determination. To validate the assay applicability for noninvasive samples, we collected fecal samples in the Atacama Desert, finding unexpectedly one species outside of its known distribution range. We conclude that the assay has a potential to become a valuable tool for a standardized genetic monitoring of the Lycalopex species in Chile.

What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum

The Japanese otter (Lutra nippon), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (L. lutra), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus Lutra and taxonomic status of L. nippon by using the complete sequences of cytochrome b gene of its holotype. The present phylogenic trees supported that the genus Lutra specimens largely formed monophyletic group, with L. sumatrana as a basal to other Lutra species. Within Lutra species, L. nippon was distantly related with L. lutra. The European otter population of L. l. lutra were clustered together with its subspecies, L. l. chinensis rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of L. nippon and L. lutra was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the L. nippon and L. lutra, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. lutra will be reconsidered.

Admixture analyses and phylogeographic relationships reveal complete genetic distinctiveness of Polish farm and wild red foxes (Vulpes vulpes) and the North American origin of farm-bred individuals

A number of studies showed that many mtDNA haplotypes were shared among contemporary farm red foxes bred on different continents and the historical wild red foxes of North American origin. Therefore, in this study, the population genetic structure and phylogeographic relationships of Polish red foxes kept on fur farms and their wild conspecifics were investigated to assess the ancestry of the farm red foxes in Poland. A total of 330 tissue samples (200 from farm foxes and 130 from wild foxes) were used for the genetic analyses. Thirty microsatellite loci and two regions of mtDNA were used to assess the level of admixture between farm- and wild red foxes, to construct haplotype networks and create a phylogenetic tree. The genetic structure analysis clearly indicated two genetic clusters as being the most probable number of genetically distinct populations. The fixation index revealed a significant genetic distance between the farm- and wild red fox populations (F_ST  = 0.27, p < 0.05). Haplotype networks based on frequencies showing relationships between concatenated haplotypes of Polish farm- and wild red foxes and the constructed phylogenetic tree clearly indicated two genetically distinct groups. The results of this study provide strong evidence confirming the North American origin of red foxes bred on Polish farms and the genetic distinctiveness of both studied populations.

Identification of a broad spectrum of mammalian and avian species using the short fragment of the mitochondrially encoded cytochrome b gene

Mitochondrial DNA (mtDNA), especially the gene for cytochrome b (MT-CYB), has been found to be highly informative for species identification. In this study, we present the results of the analysis of a 127 bp long fragment of MT-CYB, amplified using universal primers, variable enough to be used for species identification and discrimination, even in highly degraded animal samples. The total number of analyzed species in this study was 30, including 17 mammalian and 13 bird species. Using a newly created primer pair, we successfully amplified and sequenced the target sequence in almost all tested species. The amplification was incomplete in just two species, and as a result, partial, but still variable sequences, were obtained. Using the target fragment we successfully identified all tested samples. Initial results suggested that the intraspecies genetic diversity of the target region, in all tested species, was low - from 0 to 4.72%. The interspecies genetic diversity of the target region, crucial for successful discrimination, showed relatively high diversity, ranging from 8.36% to 42.52%. Given its short length, the target region should be used for species determination, particularly in samples that are degraded or are low in DNA quantity.

Improved DNA-Based Identification of Cervidae Species in Forensic Investigations

The main reasons for wildlife forensic research are animal poaching, illegal trade, and falsified game meat products. Small trace amounts, old and degraded materials present the most common samples in revealing criminal activities in this field. This is the reason why it is crucial to use adequate and reliable methods and samples to identify animal species killed outside the hunting season or species protected by law. In this study, different endpoint PCR and real-time PCR protocols were compared in the identification of three Cervidae species (Capreolus capreolus, Cervus elaphus, Dama dama) from old and damaged material found in an enclosed area where the animals were kept. From a total of 129 samples, end point PCR provided results for 119 samples, while real-time PCR was successful in all cases. Also, we created and tested a protocol for simultaneous analyses of different types of samples, which is of great importance as when the amplification is carried out simultaneously it is more cost efficient and speeds up the process.

Human umbilical cord-derived mesenchymal stem cells in acute liver injury: Hepatoprotective efficacy, subchronic toxicity, tumorigenicity, and biodistribution

Umbilical cord-derived mesenchymal stem cells (UC-MSCs) therapy might be an alternative to liver transplantation for acute or chronic liver injury. The aim of this study was to evaluate the efficacy of human UC-MSCs on carbon tetrachloride (CCl4)-induced acute liver injury. In addition, its toxicity, tumorigenicity, and biodistribution were determined. Significant hepatoprotective effects of hUC-MSCs with decreased levels of hepatocellular necrosis and lobular neutrophilic infiltration were found. Regarding the safety of hUC-MSCs, no serious hUC-MSCs-related changes (body weight, food/water consumption, clinical symptom, urinalysis, hematology, clinical chemistry, organ weight, and histopathology) were observed in a 13-week subchronic toxicity study. In a 26-week tumorigenicity study, no mice developed tumor related to hUC-MSCs transplantation up to 1 × 108 cells/kg. In particular, human mitochondrial sequence detection revealed that most hUC-MSCs were cleared from the major organs of the mice at 13 weeks after transplantation. There was no systemic toxicity or neoplastic finding either. Taken together, these results suggested that hUC-MSCs have great potential for future clinical treatment of acute liver disease.

Use of Molecular Diagnostic Tools for the Identification of Species Responsible for Snakebite in Nepal: A Pilot Study

Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%). Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42) and the common krait (Bungarus caeruleus; n = 22). When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate "first aid" measures (e.g. tourniquets or local application of remedies). This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

Genetic identification of endangered North African ungulates using noninvasive sampling

North African ungulates include several threatened and emblematic species, yet are poorly studied mainly due to their remoteness and elusiveness. Noninvasive sampling provides a useful approach to obtain ecological and genetic information essential to guide conservation actions. The very first and most important step in conservation planning is to accurately identify species, and molecular genetics has been proved to be a useful tool. Several molecular genetics protocols are available for species identification, even for samples with poor quality DNA, such as faeces, hairs or bones. Most of these protocols use mitochondrial DNA for barcoding despite this marker being especially prone to problems, including mtDNA introgression, nuclear insert copies, high intraspecific diversity or heteroplasmy. In this work, we developed a molecular method based on polymorphisms in small fragments of the mitochondrial cytochrome b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for identifying endangered North African ungulates. These fragments revealed polymorphisms, including species-specific variation, which allowed species identification of nine ungulate species that co-occur in North Africa. The method was validated across more than 400 samples, including different types of noninvasive samples collected in the field. The simplicity, high reliability and relative low cost of the described method make it a promising tool to improve ecological studies of the North African ungulates and consequently, the implementation of more efficient management and conservation plans for these endangered ungulates.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING

Background

Information on polymorphic DNA in organelle genomes is essential for evolutionary and ecological studies. However, it is challenging to perform high-throughput investigations of chloroplast and mitochondrial DNA polymorphisms. In recent years, EcoTILLING stands out as one of the most universal, low-cost, and high-throughput reverse genetic methods, and the identification of natural genetic variants can provide much information about gene function, association mapping and linkage disequilibrium analysis and species evolution. Until now, no report exists on whether this method is applicable to organelle genomes and to what extent it can be used.

Methodology/Principal Findings

To address this problem, we adapted the CEL I-based heteroduplex cleavage strategy used in Targeting Induced Local Lesions in Genomes (TILLING) for the discovery of nucleotide polymorphisms in organelle genomes. To assess the applicability and accuracy of this technology, designated ORG-EcoTILLING, at different taxonomic levels, we sampled two sets of taxa representing accessions from the Brassicaceae with three chloroplast genes (accD, matK and rbcL) and one mitochondrial gene (atp6). The method successfully detected nine, six and one mutation sites in the accD, matK and rbcL genes, respectively, in 96 Brassica accessions. These mutations were confirmed by DNA sequencing, with 100% accuracy at both inter- and intraspecific levels. We also detected 44 putative mutations in accD in 91 accessions from 45 species and 29 genera of seven tribes. Compared with DNA sequencing results, the false negative rate was 36%. However, 17 SNPs detected in atp6 were completely identical to the sequencing results.

Conclusions/Significance

These results suggest that ORG-EcoTILLING is a powerful and cost-effective alternative method for high-throughput genome-wide assessment of inter- and intraspecific chloroplast and mitochondrial DNA polymorphisms. It will play an important role in evolutionary and ecological biology studies, in identification of related genes associated with agronomic importance such as high yield and improved cytoplasmic quality, and for identifying mitochondrial point mutations responsible for diseases in humans and other animals.

DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples

Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA and allowed an assessment of prey DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.

Biogeographical region and host trophic level determine carnivore endoparasite richness in the Iberian Peninsula

We address the question of whether host and/or environmental factors might affect endoparasite richness and distribution, using carnivores as a model. We reviewed studies published in international peer-reviewed journals (34 areas in the Iberian Peninsula), describing parasite prevalence and richness in carnivores, and collected information on site location, host bio-ecology, climate and detected taxa (Helminths, Protozoa andMycobacteriumspp.). Three hypotheses were tested (i) host based, (ii) environmentally based, and (iii) hybrid (combination of environmental and host). Multicollinearity reduced candidate variable number for modelling to 5: host weight, phylogenetic independent contrasts (host weight), mean annual temperature, host trophic level and biogeographical region. General Linear Mixed Modelling was used and the best model was a hybrid model that included biogeographical region and host trophic level. Results revealed that endoparasite richness is higher in Mediterranean areas, especially for the top predators. We suggest that the detected parasites may benefit from mild environmental conditions that occur in southern regions. Top predators have larger home ranges and are likely to be subjected to cascading effects throughout the food web, resulting in more infestation opportunities and potentially higher endoparasite richness. This study suggests that richness may be more affected by historical and regional processes (including climate) than by host ecological processes.

Development of a species-specific AFLP-based SCAR marker for authentication of black muntjac (Muntiacus crinifrons)

Black muntjac is a rare and endangered deer endemic to eastern China. Due to the economic and pharmaceutical value of the meat, antlers and skin, the species has chronically suffered from poaching though it is regarded as the state key protected animal. To provide an effective molecular method for authentication of tissue specimen (such as meat, skin etc.) of the species, we developed a Sequence Characterized Amplified Region (SCAR) derived from a species specific Amplification Fragment Length Polymorphism (AFLP) marker. Initially, a 707-bp species specific DNA fragment of the animal was detected by a pair of AFLP primers (Ep7/Mp8). Subsequently, a species-specific primer pair (P-F/P1-R) was designed based on the specific AFLP fragment sequence, obtaining a 298-bp SCAR for the species. Finally, the reliability of the SCAR primers was verified by two separate PCRs using the designed SCAR primers and a cyt b universal primer pair. As expected, all black muntjac samples presented two bands but the others failed to produce the SCAR by merely showing one band. Our results indicated that the SCAR primers developed in this study may provide a useful tool for forensic authentication of black muntjac samples though further testing with larger sample sizes is warranted.

A novel HURRAH protocol reveals high numbers of monomorphic MHC class II loci and two asymmetric multi-locus haplotypes in the Père David's deer

The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated “HURRAH” based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1) All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2) these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ∼ DRB1 ∼ DRB3 ∼ DQA1 ∼ DQB2 (H1) and DRA1*02 ∼ DRB2 ∼ DRB4 ∼ DQA2 ∼ DQB1 (H2). The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens.

An evaluation of the PCR-RFLP technique to aid molecular-based monitoring of felids and canids in India

Background

The order Carnivora is well represented in India, with 58 of the 250 species found globally, occurring here. However, small carnivores figure very poorly in research and conservation policies in India. This is mainly due to the dearth of tested and standardized techniques that are both cost effective and conducive to small carnivore studies in the field. In this paper we present a non-invasive genetic technique standardized for the study of Indian felids and canids with the use of PCR amplification and restriction enzyme digestion of scat collected in the field.

Findings

Using existing sequences of felids and canids from GenBank, we designed primers from the 16S rRNA region of the mitochondrial genome and tested these on ten species of felids and five canids. We selected restriction enzymes that would cut the selected region differentially for various species within each family. We produced a restriction digestion profile for the potential differentiation of species based on fragment patterns. To test our technique, we used felid PCR primers on scats collected from various habitats in India, representing varied environmental conditions. Amplification success with field collected scats was 52%, while 86% of the products used for restriction digestion could be accurately assigned to species. We verified this through sequencing. A comparison of costs across the various techniques currently used for scat assignment showed that this technique was the most practical and cost effective.

Conclusions

The species-specific key developed in this paper provides a means for detailed investigations in the future that focus on elusive carnivores in India and this approach provides a model for other studies in areas of Asia where many small carnivores co-occur.

DNA detective: a review of molecular approaches to wildlife forensics

Illegal trade of wildlife is growing internationally and is worth more than USD$20 billion per year. DNA technologies are well suited to detect and provide evidence for cases of illicit wildlife trade yet many of the methods have not been verified for forensic applications and the diverse range of methods employed can be confusing for forensic practitioners. In this review, we describe the various genetic techniques used to provide evidence for wildlife cases and thereby exhibit the diversity of forensic questions that can be addressed using currently available genetic technologies. We emphasise that the genetic technologies to provide evidence for wildlife cases are already available, but that the research underpinning their use in forensics is lacking. Finally we advocate and encourage greater collaboration of forensic scientists with conservation geneticists to develop research programs for phylogenetic, phylogeography and population genetics studies to jointly benefit conservation and management of traded species and to provide a scientific basis for the development of forensic methods for the regulation and policing of wildlife trade.