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Generation of genome-wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation
ID
Recknagel, Hans
(
Author
),
ID
Močivnik, Luka
(
Author
),
ID
Zakšek, Valerija
(
Author
),
ID
Luo, Yonglun
(
Author
),
ID
Kostanjšek, Rok
(
Author
),
ID
Trontelj, Peter
(
Author
)
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https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13995
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Abstract
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
Views:
34
Downloads:
13
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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
Projects
Funder:
ARRS - Slovenian Research Agency
Project number:
J1-2469
Name:
Genomski in transktiptomski vplogled v edinstveno biologijo človeške ribice (Proteus anguinus)
Funder:
ARRS - Slovenian Research Agency
Project number:
P1-0184
Name:
Integrativna zoologija in speleobiologija
Funder:
EC - European Commission
Funding programme:
H2020
Project number:
897695
Name:
Genomics of cave evolution in the European olm
Acronym:
GENEVOLCAV
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