10.5061/DRYAD.MGQNK98XM
Mahtani-Williams, Sarita
University of Veterinary Medicine Vienna
Fulton, William
University of Veterinary Medicine Vienna
Desvars-Larrive, Amelie
University of Veterinary Medicine Vienna
Lado, Sara
University of Veterinary Medicine Vienna
Elbers, Jean
University of Veterinary Medicine Vienna
Halpern, Bálint
MME Birdlife Hungary
Herczeg, Dávid
Plant Protection Institute
Babocsay, Gergely
Hungarian Natural History Museum
Lauš, Boris
Association HYLA
Nagy, Zoltán Tamás
Independent researcher
Jablonski, Daniel
Comenius University
Kukushkin, Oleg
Russian Academy of Sciences
Orozco-terWengel, Pablo
Cardiff University
Vörös, Judit
Hungarian Natural History Museum
Burger, Pamela
Research Institute of Wildlife Ecology
Landscape genomics of a widely distributed snake (Dolichophis caspius,
Gmelin, 1789) across Eastern Europe and Western Asia
Dryad
dataset
2020
National Research, Development and Innovation Office
https://ror.org/03g2am276
2017-2.2.4-TÉT-AT-2017-00002
FWF Austrian Science Fund
https://ror.org/013tf3c58
P29623-B25
Slovak Research and Development Agency
https://ror.org/037nx0e70
APVV-15-0147
National Research, Development and Innovation Office
https://ror.org/03g2am276
K-124375
YounInvestigators Programme (FiKut) of the Hungarian Academy of Sciences (MTA)*
Slovak Research and Development Agency
https://ror.org/037nx0e70
APVV-19-0076
Austrian Agency for International Cooperation in Education and Research*
HU 02/2018
YounInvestigators Programme (FiKut) of the Hungarian Academy of Sciences (MTA)
Austrian Agency for International Cooperation in Education and Research
HU 02/2018
2021-02-16T00:00:00Z
2021-02-16T00:00:00Z
en
https://doi.org/10.3390/genes11101218
17376010562 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Across the distribution of the Caspian whipsnake (Dolichophis caspius),
populations have become increasingly disconnected due to habitat
alterations. To understand population dynamics and the adaptive potential
of this widespread but locally endangered snake, we investigated
population structure, admixture and effective migration patterns. We took
a landscape-genomic approach to identify selected genotypes associated
with environmental variables relevant to D. caspius. With double-digest
restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting
in 17,518 single nucleotide polymorphisms (SNPs), we identified eight
clusters within D. caspius reflecting complex evolutionary patterns of the
species. Estimated Effective Migration Surfaces (EEMS) revealed
higher-than-average gene flow in most of the Balkan Peninsula and
lower-than-average gene flow along the middle section of the Danube River.
Landscape genomic analysis identified 751 selected genotypes correlated
with seven climatic variables. Isothermality correlated with the highest
number of selected genotypes (478) located in 41 genes, followed by annual
range (127) and annual mean temperature (87). We conclude that
environmental variables, especially the day-to-night temperature
oscillation in comparison to the summer-to-winter oscillation, may have an
important role in the distribution and adaptation of D. caspius.
One hundred twenty-four DNA samples extracted from carcass tissue, shed
skin and blood and buccal swabs originating from eight European and Asian
countries were collected for this study and deposited at the Collection of
Genetic Resources of the Hungarian Natural History Museum in Budapest.
Spatial data (longitude and latitude in decimal degrees) were recorded
using a GPS device for each sampled individual (Figure 1, Table 1). We
extracted DNA from buccal swabs using the blackPREP Swab DNA Kit according
to kit protocols (Analytik Jena AG, Jena, Germany). For shed skin and
carcass (liver and muscle) samples, the DNEasy Blood and Tissue Kit
(Qiagen, Hilden, Germany) was applied following manufacturer’s
instructions but adding 30 μl of Proteinase K (20 mg/μl) to increase lysis
efficacy. Prior to the extraction, skin samples were soaked in water for
24 hours at room temperature and manually sliced into fragments of ~5mm to
facilitate enzymatic lysis. Samples’ DNA quality (measured by absorbance)
was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific,
Waltham, USA). The 96 best extractions were selected based on a
concentration threshold of 10 ng/μL and 260/280 ratio values > 1.85
and used for ddRAD sequencing.