10.5061/DRYAD.T722H
Alexandri, Panoraia
Aristotle University of Thessaloniki
Megens, Hendrik-Jan
Animal Breeding and Genomics Centre; 6700AH Wageningen The Netherlands
Crooijmans, Richard P. M. A.
Animal Breeding and Genomics Centre; 6700AH Wageningen The Netherlands
Groenen, Martien A. M.
Animal Breeding and Genomics Centre; 6700AH Wageningen The Netherlands
Goedbloed, Daniel J.
Braunschwein Zoological Institute; Braunschwein Germany
Herrero-Medrano, Juan M.
Animal Breeding and Genomics Centre; 6700AH Wageningen The Netherlands
Rund, Lauretta A.
University of Illinois System
Schook, Lawrence B.
University of Illinois at Urbana Champaign
Chatzinikos, Evangelos
4th Hunting Federation of Sterea Hellas; 10563 Athens Greece
Triantaphyllidis, Costas
Aristotle University of Thessaloniki
Triantafyllidis, Alexandros
Aristotle University of Thessaloniki
Schook, Laurence B.
University of Illinois System
Triantafyllidis, Alexander
Aristotle University of Thessaloniki
Data from: Distinguishing migration events of different timing for wild
boar in the Balkans
Dryad
dataset
2017
mammal
Recent migration
SNPs
Sus scrofa
2017-07-15T00:00:00Z
2017-07-15T00:00:00Z
en
https://doi.org/10.1111/jbi.12861
38412420 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Aim: We compared the power of different nuclear markers to investigate
genetic structure of southern Balkan wild boar. We distinguished between
historic events, such as isolation in different refugia during glacial
periods, from recent demographic processes, such as naturally occurring
expansions. Location: Southern Balkans/Greece. Methods: We sampled 555
wild boars from 20 different locations in southern Balkans/Greece. All
individuals were analysed with 10 microsatellites and a subgroup of 91
with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic
structure and demographic processes were assessed with Bayesian
clustering, linkage disequilibrium and past effective population size
estimation analysis. Results: Both microsatellite and SNP data analyses
detected genetic structure caused by historic events and support the
existence of three groups in the studied area. A hybrid zone between two
of the groups was also detected. We also showed that genome-wide SNP data
analysis can identify recent events in bottlenecked populations. Main
conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp
when populations contracted to different refugia. Our findings
strengthened the evidence that the southern Balkan area was a glacial
refugium including further local smaller refugia. Genome-wide genotyping
inferred a recent population expansion that can mimic a ‘refugium within
refugium’ scenario. It seems that microsatellite data tend to overestimate
genetic structure when genetic drift happens in bottlenecked populations
over a short distance. Therefore, genome-wide SNPs are more powerful at
inferring phylogeography in natural populations, resolving inconsistencies
from mitochondrial and microsatellite data sets.
PA_Wild_boar_ped91 Southern Balkan wild boar genotypes in 49508 SNPs in
.ped format for PLINKWB_SNPs.pedPA_Wild_boar_mapInformation on the 49508
autosomal SNPs in .map file format corresponding to the genotypes in the
PA_Wild_boar.ped file for use in PLINK
softwareWB_SNPs.mapPA_Wild_boar_SNP_structureSTRUCTURE file with 91 wild
boar SNP genotypes from Southern
BalkansWB_SNPs.strPA_Wild_boar_info_SNPsWild boar sample information
corresponding to PA_Wild_boar_ped and
PA_Wild_boar_SNP_structureWB_info_SNPs.txtPA_Wild_boar_micros555 Southern
Balkan wild boar microsatellite
genotypesWB_micros.xlsPA_Wild_boar_micros_structureSTRUCTURE file of 555
Southern Balkan wild boar microsatellite
genotypesWB_micros.strPA_Wild_boar_info_microsWild boar sample information
corresponding to PA_Wild_boar_micros and
PA_Wild_boar_micros_structureWB_info_micros.txtREADMEShort explanation of
file content
Greece
Southern Balkans