The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland

The red fox (Vulpes vulpes) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002–2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management

Estimating the size and structure of Pine Marten populations using non-invasive genetic sampling

The pine marten is one of six mustelid species currently established in Ireland along with the badger, otter, stoat, ferret and the American mink. The ancient origin of the Irish pine marten is unknown but it was possibly introduced into Ireland in the Bronze Age as a commodity species for its luxurious pelt. The species was legally protected in Ireland in 1976 after centuries of persecution with the extensive deforestation of the island and hunting for fur or predator control. The current conservation status is considered to be favourable as the population seems to be expanding its range from core populations in the mid-west, midlands and the south-east of the country. However, the status of these core populations has not been assessed and is very difficult to evaluate based on traditional survey methods. This study aimed to develop the methods required to census pine marten populations based on non-invasive genetic sampling of hair and faeces. Real-time PCR methods which enabled rapid species and sex identification of non-invasively collected samples were developed based on either the hybridisation of species or sex specific probes, or on differences in melting-temperature between amplified DNA sequences of less than 150 nucleotides in length. Genetic variability of the Irish population was assessed at 20 microsatellite loci. The number of alleles per locus (2.29) and expected heterozygosity (0.35) were low and a significant bottleneck signature was detected using a set of 41 road-kill individuals. The historical decline in pine marten distribution and abundance in Ireland has therefore had an impact on genetic diversity. Despite this no significant structuring was identified between regions, suggesting the dispersal ability of the pine marten is sufficient to maintain a panmictic population. A census of two populations in south-east Ireland was then conducted by non-invasive genetic sampling of hair and scats using the methods developed in the project. Species and sex identification success rates were high for both sample types (88-100%), but individual identification was more reliable with plucked hair (94%) than scats (38%). Nine individual pine marten were identified in total in between the two sites by genotyping hair samples with eight microsatellite loci. Independent live trapping surveys carried out after the non-invasive census validated the genetic approach as the same individuals were captured with both survey methods. Remotely plucked hair genotyping is a powerful and non-invasive survey method which can be used to inventory the magnitude and distribution of genetic diversity in pine marten, and other species with similar life history such as the stone marten, to identify any potentially important populations towards which conservation resources should be targeted in the future

Next‐generation phylogeography resolves post‐glacial colonization patterns in a widespread carnivore, the red fox ( Vulpes vulpes ), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.info:eu-repo/semantics/acceptedVersio

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets