Large scale, low coverage population genomics approach to assess genetic variation and structure across vulnerable Swedish sand lizard populations

Genomics has emerged as a powerful tool in conservation biology, offering valuable insights into the genetic diversity, population connectivity and adaptive potential of threatened species. Here, we apply a large-scale, low-coverage whole genome sequencing approach to the conservation genomics of the Swedish sand lizard (Lacerta agilis). Sand lizards occur in fragmented populations across Sweden, with varying population sizes and degrees of isolation, and face significant threats from habitat degradation and land use change. In this study, we sequenced 139 individuals to investigate genetic diversity, population structure and genetic load. We reveal strong population structure among Swedish sand lizards and identify populations with low genetic diversity and realised high genetic load. Genetic diversity in populations declined with increasing latitude, likely reflecting the historical northward expansion process and the subsequent population fragmentation and isolation. We observe strong population structure and reveal genetic distinctiveness of populations; findings with significant conservation implications. For example, the Sormon population, a relict population in central Sweden, appears genetically distinct from all other populations. Further, the northern-most populations in Dalarna appear relatively small, with high genetic load, and thus may require intensive management via e.g., restored open successional habitat to aid population recovery. Our study adds to the growing field of conservation genomics and demonstrates the value of high-resolution whole genome approaches to the conservation efforts for threatened populations. Finally, our research contributes crucial insights for the conservation management of this vulnerable species in Sweden.