4.7 Article

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications

期刊

MOLECULAR ECOLOGY RESOURCES
卷 15, 期 4, 页码 747-760

出版社

WILEY
DOI: 10.1111/1755-0998.12349

关键词

genome-wide genetic diversity; heterozygosity-fitness test; multilocus heterozygosity; randomly vs; highly polymorphic microsatellites; red deer (Cervus elaphus)

资金

  1. Portuguese national funds through the FCT (Fundacao para a Ciencia e a Tecnologia)
  2. FEDER funds (Fundo Europeu de Desenvolvimento Regional) through Programa Operacional Potencial Humano-Quadro de Referencia Estrategico Nacional (POPH-QREN) from the European Social Fund
  3. FEDER funds (Fundo Europeu de Desenvolvimento Regional) through Programa Operacional Potencial Humano-Quadro de Referencia Estrategico Nacional (POPH-QREN) from Portuguese Ministerio da Educacao e Ciencia [SFRH/BD/73732/2010, IF/564/2012, SFRH/BSAB/1278/2012]
  4. FLAD (Luso-American Foundation)
  5. North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF)
  6. Harmonized Approaches in monitoring wildlife Population Health, And Ecology and Abundance (APHAEA) [219235_FP7_ERA-NET_EMIDA]
  7. project 'Genomics and Evolutionary Biology'
  8. Fundação para a Ciência e a Tecnologia [SFRH/BSAB/1278/2012, SFRH/BD/73732/2010] Funding Source: FCT

向作者/读者索取更多资源

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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