Data from: Rapid colonisation of synanthropic stone martens in a highly urbanised region: Insights from temporal and spatial analysis

Sample information with sample ID, group ID, sex (empty cells represent gender not know), collection date (or year), and coordinates (Belgian Lambert 72 coordinate system).
Filtered SNP data file with 376 samples of stone marten and 5536 SNPs, with samples in rows and SNPs in columns. In the first two columns the sample ID and the group ID is provided. Missing genotypes are indicated with “NA”.

Medium-sized carnivores, including the synanthropic stone marten (Martes foina Erxleben, 1777), have shown remarkable adaptability to urbanized and fragmented landscapes, facilitating their spread across mainland Europe. This study investigates the recolonisation of a highly urbanised region by stone martens within two decades, examining spatial and temporal genome-wide data (using genotyping by sequencing) to reveal colonisation dynamics, sources, and barriers influencing their expansion. Using genotypes from 5,536 SNPs across 376 stone martens collected between 1995 and 2013, our findings indicate that stone martens successfully expanded through urban environments, yet dispersal was neither entirely random nor strictly distance-dependent. The initial southeastern stronghold (E1) showed the lowest genetic diversity and limited spatial expansion, while other population sources contributed to recolonisation, highlighting a complex, multi-source expansion. Gene flow in the early stages was largely confined to E1, progressing northward and eventually enabling exchange with a second eastern lineage (E2). Meanwhile, the western lineage displayed higher connectivity, occasionally crossing barriers like motorways. Motorways, however, significantly shaped recolonization patterns, reducing gene flow, while other elements such as built-up areas, secondary roads or waterways showed an additional though very small effect. Over the study period, genetic patch size increased, indicating longer dispersal distances. Gene flow strengthened within both eastern (E1 and E2) and western populations. Still, the western population diverged in two subclusters (W1 and W2) of which one became more differentiated. This suggests limited genetic homogenization in the near future. This study provides insights into the genetic and ecological dynamics of carnivore recolonization in highly fragmented landscapes.