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How do SNP ascertainment schemes and population demographics affect inferences about population history?

McTavish, Emily Jane; Hillis, David M

Background: The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using F$_{ST}$ and principal components analysis (PCA).
Results: Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group ... mehr

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DOI: 10.5445/IR/1000053056
DOI: 10.1186/s12864-015-1469-5
Zitationen: 20
Web of Science
Zitationen: 20
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Jahr 2015
Sprache Englisch
Identifikator ISSN: 1471-2164
KITopen-ID: 1000053056
Erschienen in BMC genomics
Band 16
Heft 1
Seiten Art.Nr.: 266
Schlagworte Bos taurus, Bos indicus, Gene-flow, Migration, SNP chip
Nachgewiesen in Web of Science
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