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Demography-adjusted tests of neutrality based on genome-wide SNP data

Artikel i vetenskaplig tidskrift
Författare Marina Rafajlovic
A. Klassmann
A. Eriksson
T. Wiehe
Bernhard Mehlig
Publicerad i Theoretical Population Biology
Volym 95
Sidor 1-12
ISSN 0040-5809
Publiceringsår 2014
Publicerad vid Linnécentrum för marin evolutionsbiologi (CEMEB)
Institutionen för fysik (GU)
Sidor 1-12
Språk en
Länkar dx.doi.org/10.1016/j.tpb.2014.05.00...
Ämnesord Single nucleotide polymorphism, Infinite-sites model, Site frequency spectrum (SFS), Bottleneck, SINGLE-NUCLEOTIDE POLYMORPHISMS, MAXIMUM-LIKELIHOOD-ESTIMATION, FREQUENCY-SPECTRUM, POSITIVE SELECTION, POPULATION PARAMETERS, STATISTICAL TESTS, NATURAL-SELECTION, SEGREGATING SITES, DNA, POLYMORPHISM, HISTORY, Ecology, Evolutionary Biology, Genetics & Heredity, ATES OF AMERICA, V102, P15942, JIMA F, 1989, GENETICS, V123, P585
Ämneskategorier Ekologi

Sammanfattning

Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and the population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. Key ingredients are the first two moments of the site frequency spectrum. We show how these moments can be computed analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima's D, Fay & Wu's H, and Zeng's E. Our results show that demography-adjusted test statistics facilitate the direct comparison between populations and that most of the differences among populations seen in the original unadjusted tests can be explained by their underlying demographies. Upon carrying out whole-genome screens for deviations from neutrality, we identify candidate regions of recent positive selection. We provide track files with values of the adjusted and unadjusted tests for upload to the UCSC genome browser. (C) 2014 Elsevier Inc. All rights reserved.

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