The genomic era has led to an unprecedented increase in the availability of genomewide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how

Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.

The Southern birch mouse (Sicista subtilis) is a small-sized rodent species characteristic of the Palearctic steppes with westernmost occurrences in central Europe. The species was considered to be extinct in Transylvania (central Romania), but in our field survey we captured three living individuals near the city of Cluj-Napoca. On the basis of nuclear interphotoreceptor retinoid-binding protein and mitochondrial cytochrome c oxidase subunit 1 sequences, we assessed the taxonomic status of the newly found S. subtilis population by comparing them to available sequences, including the sequences of its subspecies. The Transylvanian samples were found to be genetically closest to the Hungarian samples of S. subtilis trizona. These new records extend the known geographic range of this rediscovered species and provide additional information on its habitat preference and external morphological features. Moreover, our phylogenetic tree reconstruction for seven Sicista taxa provides a basic insight into the phylogenetic relationships of the genus, placing the northern Eurasian taxa (S. betulina and S. subtilis) at the crown of the tree and the central Asian taxa at the base of the tree. The Transylvanian occurrence of S. subtilis trizona, which is endemic to the Carpathian Basin, is of high faunistic value as a result of an increase in the number of known populations of this subspecies -one of the most endangered rodents of Europe -from one to two.

Introduction: From time to time, it could be useful to revise and re-assess the results of long-term programs in conservation and research. This paper overviews an ongoing research program that started 10 years ago in Central Europe and focuses on blind mole-rats, a scarcely investigated and consequently enigmatic group of rodents.Results: Systematics and Taxonomy. By means of molecular biological methods targeting the sequences of mitochondrial genes we conclude that five species of blind mole-rats, representatives of genera Spalax and Nannospalax, occur in the Carpathian Basin. Based on our present knowledge they are the only terrestrial vertebrate species endemic to the region. Mapping of distributions.As recently as one hundred years ago blind mole-rats were widespread and common all over the Carpathian Basin. In the last decade, all the regions in Hungary, the Transylvanian Basin and Vojvodina where previous genuine records were known, were checked systematically. Maps and aerial photography provided information on the exact location of habitat patches that are supposed to be suitable for blind mole-rats even today. In recent years (from 2008 onwards) the survey area was extended to all locations where residents reported on the occurrence of mole-rats.Threatening factors. The main cause of population decline is agricultural development which brought about significant changes in cultivation and land use. The following specific threatening factors were defined: cultivation, tree plantations, natural reafforestation, invasive plants, overgrazing, site developement, genetic bottlenecks, extreme weather conditions, and inadequate legal protection.Risk assessment. Red List categories for all species of Carpathian Basin blind mole-rats were assessed according to the 2001 criteria. Accordingly, one species is proposed to be ranked as Vulnerable, two as Endangered, one as Critically Endangered, and one as Data Deficient (probably extinct). Conclusions:Results from molecular biological and systematic studies, distribution mapping and determination of threatening factors, have had profound effects on practical conservation. These include action plans, wide international co-operations, establishment of a new protected area, updated protected species' list, species-level risk assessment, and the first-ever relocation program of a subterranean mammal.

Introgressive hybridization can pose a serious threat to endangered species which have an overlapping distribution such as in the case of two polecat species, Mustela eversmanii and M. putorius, in Europe. The population size of steppe polecat is known to continuously shrink, whereas its sister species, the European polecat, is still somehow widespread. In this study, we perform an analysis using microsatellite (SSR) and genomic (SNP) data sets to identify natural hybrids between polecats. Four populations were genotyped for eight polymorphic SSR loci, and thousands of unlinked SNPs were generated using a reduced‐representation sequencing approach, RADseq, to characterize the genetic make‐up of allopatric populations and to identify hybrids in the sympatric area. We applied standard population genetic analyses to characterize the populations based on their SSR allelic frequency. Only a single sample out of 48 sympatric samples showed exact intermediacy that we identified as an F1 hybrid. Additionally, one specimen was indicated in the genomic data sets as backcrossed. Other backcrosses, indicated by SSRs, were not validated by SNPs, which highlights the higher efficacy of the genomic method to identify backcrossed individuals. The low frequency of hybridization suggests that the difference in habitat preference of the two species may act as a barrier to admixture. Therefore, it is apparently unlikely that polecat populations are threatened by significant introgression. The two species showed a clear genetic differentiation using both techniques. We found higher genetic diversity values in the sympatric steppe polecat population than in the other studies on polecat populations. Although M. putorius is a hunted species in most countries, genetic diversity values indicate worse conditions in Europe than in the protected sibling species M. eversmanii. Suspending hunting and providing protected status of the former seems to be reasonable and timely.