Hybridisation between red deer (Cervus elaphus) and Japanese sika (C. nippon) on the Kintyre Peninsula, Scotland

Hybridisation between introduced and endemic species causes conservation concerns, but also provides us with an opportunity to study the dynamics of gene flow between two species as they first meet. Japanese sika deer (Cervus nippon) were introduced to the British Isles at a number of locations at the beginning of the 20th century. In the intervening time, sika have spread and their range now extends across approximately 40% of Scotland, where they overlap with that of native red deer (C. elaphus), with which they hybridise. In this study we focus on the consequences of one particular introduction that took place at Carradale, on the Kintyre Peninsula in 1893. First, I assessed the current state of hybridisation using a sample of 735 red and sika deer samples collected in 2006/7 from forestry blocks throughout the Kintyre Peninsula. Genetic analysis was conducted with a panel of 22 highly differentiated microsatellite loci and one mtDNA marker. Population admixture analysis of the microsatellite data was conducted with the Bayesian clustering programme STRUCTURE. Over most of the study area, levels of introgression into red and sika deer were low and were consistent with a scenario of very occasional F1 hybridisation followed by backcrossing. There was, however, one forestry block where 43% of individuals could be defined as hybrids. Second, I developed a branching process model of introgression via backcrossing, to assess whether variation in introgression across microsatellite loci could be interpreted as a signature of selection, or could in fact be attributed to stochastic processes. If only a few hybridisation events have contributed to the hybridising population, the pattern of introgression, even with a large number of genetic markers, will be highly stochastic. This pattern of neutral variation in introgression can have high enough variance that it could be mistaken for selection. Therefore, even if strong selection is acting, it may not be possible to distinguish its effects from neutral variation. Third, I analysed trends in hybridisation and introgression over 15 years on the peninsula, through analysis of a dataset of 1513 red and sika deer samples at 20 microsatellite and a mtDNA marker. There was little evidence of change in the extent of hybridisation and introgression over time. MtDNA introgression was predominantly from red deer into sika. Recent introgression into sika on the peninsula can be explained by a very small number of F1 hybridisation events (~10) via analysis of the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population (a similar analysis cannot be conducted for introgression into red deer). Finally, I conducted a regression analysis of genetic hybrid scores against phenotypic traits to assess the effect of hybridisation on phenotype. Hybridisation has caused changes in the weight of sika-like deer and red-like females. Hybridisation has caused changes in incisor arcade breadth of both populations and jaw length (a proxy for skeletal size) in sika-like females. However, there is no evidence that hybridisation has caused changes in kidney fat (a measure of condition) or pregnancy rates in either population. In conclusion, even a small number of F1 hybridisation events can lead to extensive introgression and the timing and spatial distribution of these events is likely to have a large impact on the structure of a recently hybridising population - stochastic factors dominate both the distribution of hybrid individuals and the distribution of the genes that introgress following a hybridisation event. In red deer and sika deer, increasing phenotypic similarities of the two populations caused by hybridisation are likely to facilitate further breakdown between the two species. It is possible that breakdown in assortative mating between the two species could occur across their range

Benefits and pitfalls of captive conservation genetic management: evaluating diversity in scimitar-horned oryx to support reintroduction planning

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

Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland

Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage

Improving cost-efficiency of faecal genotyping:new tools for elephant species

Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples

Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method

Splitting or Lumping? A Conservation Dilemma Exemplified by the Critically Endangered Dama Gazelle (Nanger dama)

Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions

A common statement on anthropogenic hybridization of the European wildcat (Felis silvestris)

Preserving natural genetic diversity and ecological function of wild species is a central goal in conservation biology. As such, anthropogenic hybridization is considered a threat to wild populations, as it can lead to changes in the genetic makeup of wild species and even to the extinction of wild genomes. In European wildcats, the genetic and ecological impacts of gene flow from domestic cats are mostly unknown at the species scale. However, in small and isolated populations, it is known to include genetic swamping of wild genomes. In this context, it is crucial to better understand the dynamics of hybridization across the species range, to inform and implement management measures that maintain the genetic diversity and integrity of the European wildcat. In the present paper, we aim to provide an overview of the current scientific understanding of anthropogenic hybridization in European wildcats, to clarify important aspects regarding the evaluation of hybridization given the available methodologies, and to propose guidelines for management and research priorities.publishedVersio

Towards resolving taxonomic uncertainties in wolf, dog and jackal lineages of Africa, Eurasia and Australasia

Successful conservation depends on accurate taxonomy. Currently, the taxonomy of canids in Africa, Eurasia and Australasia is unstable as recent molecular and morphological studies have questioned earlier phenetic classifications. We review available information on several taxa of Old World and Australasian Canis with phylogenetic uncertainties (namely, African jackals, Asian wolves and Australasian dogs), in order to assess the validity of suggested scientific names and provide a scientific basis for reaching a taxonomic consensus primarily based on molecular data, but also including morphology, biogeography and behavioural ecology. We identify major knowledge gaps, provide recommendations for future research and discuss conservation implications of an updated taxonomic framework. Recent molecular studies indicate that the former Afro-Eurasian 'golden jackal' represents two distinct lineages, the golden jackal (Canis aureus) from Eurasia and the African wolf (C. lupaster) from Africa. Phylogenetic research also indicates that the side-striped and black-backed jackals form a monophyletic group that branched earlier than Canis, Cuon and Lycaon, which should be reassigned to the genus Lupulella as L. adusta and L. mesomelas, respectively. The Himalayan/Tibetan and Indian wolf lineages appear to have diverged earlier and are distinct from all other grey wolves (C. lupus) based on mitochondrial and nuclear genome data. However, until genome-wide data from multiple individuals across the range clarify relationships with other taxa, we suggest referring to the Himalayan/Tibetan wolf lineage as Canis lupus chanco. We support the currently accepted nomenclature for the Indian wolf Canis lupus pallipes for the wolf populations found on the Indian subcontinent and possibly also in south-western Asia (exact geographical boundary pending). The information presented here provides a current and consistent taxonomic framework for use by conservationists and other practitioners, but it is also intended to stimulate further research to resolve current uncertainties affecting the taxonomy of Old World canids.Peer reviewe