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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
(
Avtor
),
ID
Močivnik, Luka
(
Avtor
),
ID
Zakšek, Valerija
(
Avtor
),
ID
Luo, Yonglun
(
Avtor
),
ID
Kostanjšek, Rok
(
Avtor
),
ID
Trontelj, Peter
(
Avtor
)
PDF - Predstavitvena datoteka,
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MD5: 836DFF9019D6BB7C4B89A7B3D7EDDC1C
URL - Izvorni URL, za dostop obiščite
https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13995
Galerija slik
Izvleček
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
Število ogledov:
35
Število prenosov:
13
Metapodatki:
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Objavi na:
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
Projekti
Financer:
ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Številka projekta:
J1-2469
Naslov:
Genomski in transktiptomski vplogled v edinstveno biologijo človeške ribice (Proteus anguinus)
Financer:
ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Številka projekta:
P1-0184
Naslov:
Integrativna zoologija in speleobiologija
Financer:
EC - European Commission
Program financ.:
H2020
Številka projekta:
897695
Naslov:
Genomics of cave evolution in the European olm
Akronim:
GENEVOLCAV
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