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

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

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.

• Jezik: Angleški jezik
• Ključne besede: amphibians, conservation genetics, environmental DNA, genomics, proteomics, microbial biology, empirical population genetics
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: BF - Biotehniška fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2024
• Št. strani: 13 str.
• Številčenje: Vol. 24, iss. 7, art. e13995
• PID: 20.500.12556/RUL-161283-d13b8c61-971d-d38e-5c61-7828fbd58d60
• UDK: 575
• ISSN pri članku: 1755-098X
• DOI: 10.1111/1755-0998.13995
• COBISS.SI-ID: 206423299
• Datum objave v RUL: 09.09.2024

Gradivo je del revije

• Naslov: Molecular ecology resources
• Skrajšan naslov: Mol. ecol. resour.
• Založnik: Wiley
• ISSN: 1755-098X
• COBISS.SI-ID: 5711737

Licence

• Licenca: CC BY-NC-ND 4.0, Creative Commons Priznanje avtorstva-Nekomercialno-Brez predelav 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by-nc-nd/4.0/deed.sl
• Opis: Najbolj omejujoča licenca Creative Commons. Uporabniki lahko prenesejo in delijo delo v nekomercialne namene in ga ne smejo uporabiti za nobene druge namene.

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: dvoživke, varstvena genetika, okoljska DNK, genomika, proteomika, mikrobna biologija