Generation of genome-wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation

Recknagel, Hans (author), Močivnik, Luka (author), Zakšek, Valerija (author), Luo, Yonglun (author), Kostanjšek, Rok (author), Trontelj, Peter (author)

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.

• Language: English
• Keywords: amphibians, conservation genetics, environmental DNA, genomics, proteomics, microbial biology, empirical population genetics
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 13 str.
• Numbering: Vol. 24, iss. 7, art. e13995
• PID: 20.500.12556/RUL-161283-d13b8c61-971d-d38e-5c61-7828fbd58d60
• UDC: 575
• ISSN on article: 1755-098X
• DOI: 10.1111/1755-0998.13995
• COBISS.SI-ID: 206423299
• Publication date in RUL: 09.09.2024

Record is a part of a journal

• Title: Molecular ecology resources
• Shortened title: Mol. ecol. resour.
• Publisher: Wiley
• ISSN: 1755-098X
• COBISS.SI-ID: 5711737

Licences

• License: CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
• Link: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Description: The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.

Secondary language

• Language: Slovenian
• Keywords: dvoživke, varstvena genetika, okoljska DNK, genomika, proteomika, mikrobna biologija