20.500.12556/RUL-161283 Generation of genome-wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation High-density genotyping methods have revolutionized the field of population and conservation genetics in the past decade. To exploit the technological and analytical advances in the field, access to high-quality genetic material is a key component. However, access to such samples in endangered and rare animals is often challenging or even impossible. Here, we used a minimally invasive sampling method (MIS) in the endangered cave salamander Proteus anguinus, the olm, to generate thousands of genetic markers using ddRADseq for population and conservation genomic analyses. Using tail clips and MIS skin swabs taken from the same individual, we investigated genotyping data properties of the two different sampling types. We found that sufficient DNA can be extracted from swab samples to generate up to 200,000 polymorphic SNPs in divergent Proteus lineages. Swab and tissue samples were highly reproducible exhibiting low SNP genotyping error rates. We found that SNPs were most frequently (∼50%) located within genic regions, while the rest mapped to mostly flanking regions of repetitive DNA. The vast majority of DNA recovered from swabbing was host DNA. However, a fraction of DNA recovered from swabs contained additional ecological information on the species, including eDNA from the surrounding environment and bacterial skin fauna. Most exogenous DNA recovered from swabs were bacteria (∼80%), followed by vertebrates (∼20%). Our results demonstrate that MIS can be used to (i) generate tens of thousands of ddRADseq markers for conservation and population genomic analyses and (ii) inform on the species health status and ecology from exogenous DNA. amphibians conservation genetics environmental DNA genomics proteomics microbial biology empirical population genetics dvoživke varstvena genetika okoljska DNK genomika proteomika mikrobna biologija true false true Angleški jezik Slovenski jezik Članek v reviji 2024-09-09 10:26:03 2024-09-09 10:26:05 2025-08-08 13:41:38 0000-00-00 00:00:00 2024 0 0 13 str. iss. 7, art. e13995 Vol. 24 2024 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 575 1755-098X 10.1111/1755-0998.13995 206423299 Molecular_Ecology_Resources_-_2024_-_Recknagel_-_Generation_of_genome‐wide_SNP_markers_from_minimally_invasive_sampling_in.pdf Molecular_Ecology_Resources_-_2024_-_Recknagel_-_Generation_of_genome‐wide_SNP_markers_from_minimally_invasive_sampling_in.pdf 1 836DFF9019D6BB7C4B89A7B3D7EDDC1C bc8b7f10562aec594a9f13b3f7906865f8319e7711c2825633760982a434128e 532051bd-6e85-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=190179 https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13995 0 3db565fa-6e85-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=190178 Biotehniška fakulteta 0 0 0