Long term vs. short term impact of founder relatedness on gene diversity and inbreeding within the European Endangered Species Programme (EEP) of the red panda (Ailurus f. fulgens)

Traditionally, studbooks have been used as the major tool for the scientific management of ex-situ populations organised in breeding programmes. Well documented pedigree information enables managers to sufficiently monitor population size, demographic stability and the level of genetic diversity. However, breeding programes can only maintain the genetic information which is brought into captivity by wild caught founder animals. In most studbooks little is known about those individuals. This is also true for the red panda (Ailurus fulgens), a charismatic but threatened flagship species. Conservation breeding of this remarkable mammal species started in the early 1960s and is nowadays coordinated through a Global Species Management Plan (GSMP). In Europe the Endangered Species Programme (EEP) forms the biggest regional breeding group of red pandas (subspecies A. f. fulgens). Little is known about the true origin of the 23 founders of the EEP and how their unknown relationships may affect their living descendants now and in the future. Studbook data on 1350 individuals were analysed for different assumptions about founder relationships and compared with each other. We provide studbook-based evidence that the annual change in genetic parameters (gene diversity and mean inbreeding) are not affected in long-term by the original founder relationship within strongly intermixed zoo populations managed for mean kinship. Our results point out the importance of good genetic management in the early years of breeding programmes. These early years are crucial in implementing knowledge of founder relationships in the studbook, since a population becomes genetically equalised within the first decades and new information obtained later has no significant effects on subsequent genetic trends

Revealing the origin of wildcat reappearance after presumed long-term absence

Following severe population decline and local extinction due to massive habitat destruction and persecution, wildcats have recently reappeared in several parts of Germany’s low mountain region. It remains unknown how this reemergence occurred, specifically if local populations have been overlooked at low densities or if the species has successfully spread across the highly fragmented anthropogenic landscape. In the central German Rhön Mountains, for instance, wildcats were believed to be extinct during most of the twentieth century, however, the species was recently detected and subsequent genetic monitoring found the presence of a sizeable population. In this study, we used microsatellite and SNP genotypes from 146 wildcat individuals from 2008 to 2017 across a ~ 15,000 km2 area in the central German low mountain region to understand the population re-establishment of wildcats in the region. Bayesian clustering and subsequent analyses revealed that animals in the Rhön Mountains appear to be a mix from the two adjacent populations in the North and South of the area, suggesting a recent range expansion from two different directions. Both populations meet in the Rhön Biosphere Reserve, leading to an admixture of the northern, autochthonous, and the southern reintroduced wildcat population. While we cannot completely exclude the possibility of undetected population persistence, the high genetic homogeneity in the central German wildcat population and the lack of any signatures of past population decline in the Rhön favor a scenario of natural expansion. Our findings thus suggest that wildcats are well capable of rapid range expansion across richly structured landscape mosaics consisting of open land, settlements, and forest patches and document the potential of massive non-invasive genetic sampling when aiming to reconstruct the complex population and range dynamics of wildlife

The genetic characterization of an isolated remnant population of an endangered rodent (Cricetus cricetus L.) using comparative data: implications for conservation

Estimates of genetic diversity and phylogenetic affiliation represent an important resource for biodiversity assessment and a valuable guide to conservation and management. We have found a new population (Jawor—JW) of the common hamster Cricetus cricetus in western Poland that is remote from the nearest populations by 235–300 km. With the objective of genetically characterizing of this population, we compared it with other populations from Poland and Germany by taking into account sequences of four mitochondrial DNA genes and variation at 10 microsatellite loci. The JW population exhibited low levels of genetic diversity and allelic and haplotype richness, which likely reflects its extreme isolation. This factor, coupled with inbreeding and genetic drift, are major threats to JW. A neighbor-joining tree based on mtDNA haplotypes shows that JW clusters among samples representing the Central subgroup that is known from central Germany but that has not yet been identified in Poland. Findings presented here improve our understanding of the spread and diversification of the common hamster. We offer the following hypotheses to explain the observed pattern of mtDNA haplotype distribution: JW could be a byproduct of postglacial migrations or back-migrations from eastern refugia to the western part of Europe, or/and be a result of population and habitat fragmentation. We recommend translocation of individuals as an effective management strategy, both at the level of Central phylogeographic group and at the species level, to overcome the negative consequences of inbreeding and geographical isolation of the JW population

Using eDNA to understand predator–prey interactions influenced by invasive species

Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator–prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator–prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.ISSN:0029-8549ISSN:1432-193

Ex situ versus in situ Eurasian lynx populations: implications for successful breeding and genetic rescue

The main aim of ex situ programmes in conservation is to provide a suitable source of individuals for future reintroductions or reinforcement of existing populations. A fundamental prerequisite is creating and maintaining healthy and sustainable captive populations that show high levels of phenotypic and genetic similarity to their wild counterparts. The Eurasian lynx (Lynx lynx) is a model of a locally extinct species that has been subject to long-term captive breeding and of past and ongoing reintroduction eforts. To test for genetic suitability of ex situ population, a comparative genetic evaluation including in situ populations was undertaken. The assignment analysis of 97 captive lynx from 45 European zoos, wildlife parks and private breeds was performed using 124 lynx from diferent wild Eurasian populations belonging to three evolutionary lineages: the Carpathian, the Northern, and the Siberian lynx. The results showed a high proportion of Siberian lynx (51%) in the European captive lynx population. Remaining captive animals were assigned to either the Carpathian (28%), or the Northern lynx lineage (13%). Admixture between lineages was rather low (8%). Notably, no or very low diference in genetic diversity was detected between the wild and captive lynx populations. Our results support the potential of the captive population to provide genetically suitable individuals for genetic rescue programmes. The transfer of genes between isolated populations, including those in captivity, should become an important management tool to preserve genetic variability and prevent inbreeding depression in native and reintroduced populations of this iconic predator. Captive breeding · Genetic variability · Inbreeding · Large carnivores · Lynx lynx · ReintroductionpublishedVersio

Genome-wide diversity loss in reintroduced Eurasian lynx populations urges immediate conservation management

Reintroductions may produce populations that suffer from decreasing genetic diversity due to isolation, genetic drift and inbreeding if not assisted by careful management. To assess the genetic outcomes of reintroductions in large carnivores, we used the Eurasian lynx (Lynx lynx) as a case study, which was the subject of several reintroduction attempts over the last 50 years. Although some restocking actions initially appeared successful, lynx recovery has stagnated in recent years. To reveal potential genetic causes of slow lynx recovery in Europe, we examined genome-wide patterns of genetic diversity and inbreeding using single nucleotide polymorphisms (SNPs) in all six successfully reintroduced populations in central Europe, as well as twelve natural populations across Europe and Asia. All reintroduced populations showed lower genetic diversity and elevated levels of inbreeding compared to source and other natural populations. Recent inbreeding is prevalent in all reintroduced populations with varying degrees of severity; the most severe cases are those with the lowest number of founding individuals. Interestingly, we found evidence of lower genetic diversity and recent inbreeding in the source population for five reintroduced populations, begging the question if individuals taken from these source populations can safeguard sufficient genetic diversity for future reintroductions. Given the observed genetic consequences, we advocate for standardized regular genomic assessment of source and target populations as well as individuals prior to release. Our study provides compelling evidence for the serious consequences of founder population size on the genetic diversity of reintroduced large carnivore populations, which has broad implications for their conservation. Conservation genomics Inbreeding Large carnivore Runs of homozygosity Species translocation Population management Reintroduction biolog

Genome-wide diversity loss in reintroduced Eurasian lynx populations urges immediate conservation management

Reintroductions may produce populations that suffer from decreasing genetic diversity due to isolation, genetic drift and inbreeding if not assisted by careful management. To assess the genetic outcomes of reintroductions in large carnivores, we used the Eurasian lynx (Lynx lynx) as a case study, which was the subject of several reintroduction attempts over the last 50 years. Although some restocking actions initially appeared successful, lynx recovery has stagnated in recent years. To reveal potential genetic causes of slow lynx recovery in Europe, we examined genome-wide patterns of genetic diversity and inbreeding using single nucleotide polymorphisms (SNPs) in all six successfully reintroduced populations in central Europe, as well as twelve natural populations across Europe and Asia. All reintroduced populations showed lower genetic diversity and elevated levels of inbreeding compared to source and other natural populations. Recent inbreeding is prevalent in all reintroduced populations with varying degrees of severity; the most severe cases are those with the lowest number of founding individuals. Interestingly, we found evidence of lower genetic diversity and recent inbreeding in the source population for five reintroduced populations, begging the question if individuals taken from these source populations can safeguard sufficient genetic diversity for future reintroductions. Given the observed genetic consequences, we advocate for standardized regular genomic assessment of source and target populations as well as individuals prior to release. Our study provides compelling evidence for the serious consequences of founder population size on the genetic diversity of reintroduced large carnivore populations, which has broad implications for their conservation. Conservation genomics Inbreeding Large carnivore Runs of homozygosity Species translocation Population management Reintroduction biologypublishedVersio

Large-scale genetic census of an elusive carnivore, the European wildcat (Felis s. silvestris)

The European wildcat, Felis silvestris silvestris, serves as a prominent target species for the reconnection of central European forest habitats. Monitoring of this species, however, appears difficult due to its elusive behaviour and the ease of confusion with domestic cats. Recently, evidence for multiple wildcat occurrences outside its known distribution has accumulated in several areas across Central Europe, questioning the validity of available distribution data for this species. Our aim was to assess the fine-scale distribution and genetic status of the wildcat in its central European distribution range. We compiled and analysed genetic samples from roadkills and hundreds of recent hair-trapping surveys and applied phylogenetic and genetic clustering methods to discriminate wild and domestic cats and identify population subdivision. 2220 individuals were confirmed as either wildcat (n = 1792) or domestic cat (n = 342), and the remaining 86 (3.9 %) were identified as hybrids between the two. Remarkably, genetic distinction of domestic cats, wildcats and their hybrids was only possible when taking into account the presence of two highly distinct genetic lineages of wildcats, with a suture zone in central Germany. 44 % of the individual wildcats where sampled outside the previously published distribution. Our analyses confirm a relatively continuous spatial presence of wildcats across large parts of the study area in contrast to previous analyses indicating a highly fragmented distribution. Our results suggest that wildcat conservation and management should take advantage of the higher than previously assumed dispersal potential of wildcats, which may use wildlife corridors very efficiently