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

• 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.

Ämnesord

NATURVETENSKAP  -- Biologi -- Ekologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Ecology (hsv//eng)

Nyckelord

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

Publikations- och innehållstyp

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