Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

Abstract STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of STRUCTURE‐based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,...

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Main Authors: Stephan Michael Funk, Sonya Guedaoura, Rytis Juras, Absul Raziq, Faouzi Landolsi, Cristina Luís, Amparo Martínez Martínez, Abubakar Musa Mayaki, Fernando Mujica, Maria do Mar Oom, Lahoussine Ouragh, Yves‐Marie Stranger, Jose Luis Vega‐Pla, Ernest Gus Cothran
Format: Article
Language:English
Published: Wiley 2020-05-01
Series:Ecology and Evolution
Subjects:
Online Access:https://doi.org/10.1002/ece3.6195
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spelling doaj-e878056f3da1425790d7cbf7bca6a4602021-04-02T11:49:44ZengWileyEcology and Evolution2045-77582020-05-0110104261427910.1002/ece3.6195Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellitesStephan Michael Funk0Sonya Guedaoura1Rytis Juras2Absul Raziq3Faouzi Landolsi4Cristina Luís5Amparo Martínez Martínez6Abubakar Musa Mayaki7Fernando Mujica8Maria do Mar Oom9Lahoussine Ouragh10Yves‐Marie Stranger11Jose Luis Vega‐Pla12Ernest Gus Cothran13Centro de Excelencia de Modelación y Computación Científica Universidad de La Frontera Temuco ChileFaculté des Sciences de la Nature et de la VieUniversité d'El‐Tarf El‐Tarf AlgeriaCollege of Veterinary Medicine and Biomedical Science Texas A&M University College Station TX USASociety of Veterinary, Environment and Agriculture Scientists (SAVES) Quetta PakistanEcole Nationale de Médecine Vétérinaire Sidi Thabet TunisieCentro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT) Faculdade de Ciências Universidade de Lisboa Lisboa PortugalDepartamento de Genética Universidad de Córdoba Córdoba SpainDepartment of Veterinary Medicine Usmanu Danfodiyo University Sokoto NigeriaInstituto de Producción Animal Universidad Austral de Chile Valdivia ChileCE3C – Centre for Ecology, Evolution and Environmental Changes Faculdade de Ciências Universidade de Lisboa Lisboa PortugalInstitut Agronomique et Vétérinaire Hassan II Rabat MoroccoMarmande FranceLaboratorio de Investigación Aplicada Crıa Caballar de las Fuerzas Armadas Cordoba SpainCollege of Veterinary Medicine and Biomedical Science Texas A&M University College Station TX USAAbstract STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of STRUCTURE‐based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters Kopt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (DAPC, FLOCK, PCoA, and STRUCTURE with different run scenarios) all revealed general, broad‐scale breed relationships that largely reflect known breed histories but diverged how they characterized small‐scale patterns. STRUCTURE failed to consistently identify Kopt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a Kopt, was consistent with known breed histories. The over‐reliance on Kopt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.https://doi.org/10.1002/ece3.6195domestic horsepopulation genetic structurePrzewalski horseSTRUCTURE analysis
collection DOAJ
language English
format Article
sources DOAJ
author Stephan Michael Funk
Sonya Guedaoura
Rytis Juras
Absul Raziq
Faouzi Landolsi
Cristina Luís
Amparo Martínez Martínez
Abubakar Musa Mayaki
Fernando Mujica
Maria do Mar Oom
Lahoussine Ouragh
Yves‐Marie Stranger
Jose Luis Vega‐Pla
Ernest Gus Cothran
spellingShingle Stephan Michael Funk
Sonya Guedaoura
Rytis Juras
Absul Raziq
Faouzi Landolsi
Cristina Luís
Amparo Martínez Martínez
Abubakar Musa Mayaki
Fernando Mujica
Maria do Mar Oom
Lahoussine Ouragh
Yves‐Marie Stranger
Jose Luis Vega‐Pla
Ernest Gus Cothran
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
Ecology and Evolution
domestic horse
population genetic structure
Przewalski horse
STRUCTURE analysis
author_facet Stephan Michael Funk
Sonya Guedaoura
Rytis Juras
Absul Raziq
Faouzi Landolsi
Cristina Luís
Amparo Martínez Martínez
Abubakar Musa Mayaki
Fernando Mujica
Maria do Mar Oom
Lahoussine Ouragh
Yves‐Marie Stranger
Jose Luis Vega‐Pla
Ernest Gus Cothran
author_sort Stephan Michael Funk
title Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
title_short Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
title_full Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
title_fullStr Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
title_full_unstemmed Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
title_sort major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
publisher Wiley
series Ecology and Evolution
issn 2045-7758
publishDate 2020-05-01
description Abstract STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of STRUCTURE‐based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters Kopt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (DAPC, FLOCK, PCoA, and STRUCTURE with different run scenarios) all revealed general, broad‐scale breed relationships that largely reflect known breed histories but diverged how they characterized small‐scale patterns. STRUCTURE failed to consistently identify Kopt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a Kopt, was consistent with known breed histories. The over‐reliance on Kopt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.
topic domestic horse
population genetic structure
Przewalski horse
STRUCTURE analysis
url https://doi.org/10.1002/ece3.6195
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