Distinguishing migration events of different timing for wild boar in the Balkans

Panoraia Alexandri, H.J.W.C. Megens, R.P.M.A. Crooijmans, M. Groenen, D.J. Goedbloed, J.M. Herrero Medrano, L.A. Rund, Lawrence B. Schook, Evangelos Chatzinikos, Costas Triantaphyllidis, Alexander Triantafyllidis

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2 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)259-270
JournalJournal of Biogeography
Volume44
Issue number2
DOIs
Publication statusPublished - 1 Oct 2016

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Balkans
wild boars
refugium
refuge habitats
single nucleotide polymorphism
polymorphism
microsatellite repeats
genetic structure
genome
Greece
demographic statistics
nuclear power
hybrid zone
effective population size
genetic drift
phylogeography
linkage disequilibrium
disequilibrium
genotyping
data analysis

Cite this

Alexandri, Panoraia ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Goedbloed, D.J. ; Herrero Medrano, J.M. ; Rund, L.A. ; Schook, Lawrence B. ; Chatzinikos, Evangelos ; Triantaphyllidis, Costas ; Triantafyllidis, Alexander. / Distinguishing migration events of different timing for wild boar in the Balkans. In: Journal of Biogeography. 2016 ; Vol. 44, No. 2. pp. 259-270.
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title = "Distinguishing migration events of different timing for wild boar in the Balkans",
abstract = "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 ofgenetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimationanalysis.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 bottleneckedpopulations.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.",
author = "Panoraia Alexandri and H.J.W.C. Megens and R.P.M.A. Crooijmans and M. Groenen and D.J. Goedbloed and {Herrero Medrano}, J.M. and L.A. Rund and Schook, {Lawrence B.} and Evangelos Chatzinikos and Costas Triantaphyllidis and Alexander Triantafyllidis",
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Alexandri, P, Megens, HJWC, Crooijmans, RPMA, Groenen, M, Goedbloed, DJ, Herrero Medrano, JM, Rund, LA, Schook, LB, Chatzinikos, E, Triantaphyllidis, C & Triantafyllidis, A 2016, 'Distinguishing migration events of different timing for wild boar in the Balkans', Journal of Biogeography, vol. 44, no. 2, pp. 259-270. https://doi.org/10.1111/jbi.12861

Distinguishing migration events of different timing for wild boar in the Balkans. / Alexandri, Panoraia; Megens, H.J.W.C.; Crooijmans, R.P.M.A.; Groenen, M.; Goedbloed, D.J.; Herrero Medrano, J.M.; Rund, L.A.; Schook, Lawrence B.; Chatzinikos, Evangelos; Triantaphyllidis, Costas; Triantafyllidis, Alexander.

In: Journal of Biogeography, Vol. 44, No. 2, 01.10.2016, p. 259-270.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Distinguishing migration events of different timing for wild boar in the Balkans

AU - Alexandri, Panoraia

AU - Megens, H.J.W.C.

AU - Crooijmans, R.P.M.A.

AU - Groenen, M.

AU - Goedbloed, D.J.

AU - Herrero Medrano, J.M.

AU - Rund, L.A.

AU - Schook, Lawrence B.

AU - Chatzinikos, Evangelos

AU - Triantaphyllidis, Costas

AU - Triantafyllidis, Alexander

PY - 2016/10/1

Y1 - 2016/10/1

N2 - 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 ofgenetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimationanalysis.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 bottleneckedpopulations.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.

AB - 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 ofgenetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimationanalysis.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 bottleneckedpopulations.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.

U2 - 10.1111/jbi.12861

DO - 10.1111/jbi.12861

M3 - Article

VL - 44

SP - 259

EP - 270

JO - Journal of Biogeography

JF - Journal of Biogeography

SN - 0305-0270

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ER -