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

Handle URI:
http://hdl.handle.net/10754/563677
Title:
Demography-adjusted tests of neutrality based on genome-wide SNP data
Authors:
Rafajlović, Marina; Klassmann, Alexander; Eriksson, Anders ( 0000-0003-3436-3726 ) ; Wiehe, Thomas H E; Mehlig, Bernhard
Abstract:
Tests of the neutral evolution hypothesis are usually built on the standard 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. © 2014 Elsevier Inc.
KAUST Department:
Integrative Systems Biology Lab; Bioscience Program
Publisher:
Elsevier BV
Journal:
Theoretical Population Biology
Issue Date:
Aug-2014
DOI:
10.1016/j.tpb.2014.05.002
Type:
Article
ISSN:
00405809
Sponsors:
This work was financially supported by grants from Vetenskapsradet, from the Goran Gustafsson Foundation for Research in Natural Sciences and Medicine, through the Linnaeus Centre for Marine Evolutionary Biology (CeMEB, www.cemeb.science.gu.se) to BM, by a grant of the German Science Foundation (DFG-SFB680) to TW, and AE by the Leverhume Trust and the Biotechnology and Biological Sciences Research Council (Grant BB/H005854/1).
Appears in Collections:
Articles; Bioscience Program

Full metadata record

DC FieldValue Language
dc.contributor.authorRafajlović, Marinaen
dc.contributor.authorKlassmann, Alexanderen
dc.contributor.authorEriksson, Andersen
dc.contributor.authorWiehe, Thomas H Een
dc.contributor.authorMehlig, Bernharden
dc.date.accessioned2015-08-03T12:05:59Zen
dc.date.available2015-08-03T12:05:59Zen
dc.date.issued2014-08en
dc.identifier.issn00405809en
dc.identifier.doi10.1016/j.tpb.2014.05.002en
dc.identifier.urihttp://hdl.handle.net/10754/563677en
dc.description.abstractTests of the neutral evolution hypothesis are usually built on the standard 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. © 2014 Elsevier Inc.en
dc.description.sponsorshipThis work was financially supported by grants from Vetenskapsradet, from the Goran Gustafsson Foundation for Research in Natural Sciences and Medicine, through the Linnaeus Centre for Marine Evolutionary Biology (CeMEB, www.cemeb.science.gu.se) to BM, by a grant of the German Science Foundation (DFG-SFB680) to TW, and AE by the Leverhume Trust and the Biotechnology and Biological Sciences Research Council (Grant BB/H005854/1).en
dc.publisherElsevier BVen
dc.subjectBottlenecken
dc.subjectCoalescent approximationen
dc.subjectInfinite-sites modelen
dc.subjectSingle nucleotide polymorphismen
dc.subjectSite frequency spectrum (SFS)en
dc.titleDemography-adjusted tests of neutrality based on genome-wide SNP dataen
dc.typeArticleen
dc.contributor.departmentIntegrative Systems Biology Laben
dc.contributor.departmentBioscience Programen
dc.identifier.journalTheoretical Population Biologyen
dc.contributor.institutionDepartment of Physics, University of Gothenburg, SE-412 96 Gothenburg, Swedenen
dc.contributor.institutionInstitut für Genetik, Universität zu Köln, 50674 Köln, Germanyen
dc.contributor.institutionDepartment of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdomen
dc.contributor.institutionThe Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, SE-405 30 Gothenburg, Swedenen
kaust.authorEriksson, Andersen
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