Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross‐specific and species‐specific amplifications |
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| Authors: | J Queirós R Godinho S Lopes C Gortazar J de la Fuente P C Alves |
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| Affiliation: | 1. CIBIO/InBIO, Centro de Investiga??o em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vair?o, Portugal;2. Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal;3. SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC‐UCLM‐JCCM), Ciudad Real, Spain;4. Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA;5. Wildlife Biology Program, University of Montana, Missoula, MT, USA |
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| Abstract: | Although whole‐genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross‐specific and species‐specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species‐specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity‐fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations. |
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| Keywords: | genome‐wide genetic diversity heterozygosity‐fitness test multilocus heterozygosity randomly vs highly polymorphic microsatellites red deer (Cervus elaphus) |
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