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Signatures of human European Paleolithic expansion shown by resequencing of nonrecombining X-chromosome segments

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posted on 2016-12-20, 16:34 authored by Pierpaolo Maisano Delser, Rita Neumann, Stéphane Ballereau, Pille Hallast, Chiara Batini, Daniel Zadik, Mark A. Jobling
Human genetic diversity in Europe has been extensively studied using uniparentally-inherited sequences (mitochondrial DNA [mtDNA] and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap SNP data to identify genomewide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as Phylogeographically informative Haplotypes on Autosomes and X chromosome (PHAXs). Three such sequences on the X chromosome spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181 ×. These PHAXs were confirmed to be essentially non-recombining across European samples. All three loci show highly homogeneous patterns across Europe and are highly differentiated from the African sample. Star-like structures of European-specific haplotypes in median-joining networks indicate past population expansions. Bayesian skyline plots and time-to-most-recent-common-ancestor estimates suggest expansions pre-dating the Neolithic transition, a finding that is more compatible with data on mtDNA than the Y chromosome, and with the female bias of Xchromosomal inheritance. This study demonstrates the potential of the use of Xchromosomal haplotype blocks, and the utility of the accurate ascertainment of rare variants for inferring human demographic history.

History

Citation

European Journal of Human Genetics, 2017, 25, pp. 485-492

Author affiliation

/Organisation/COLLEGE OF MEDICINE, BIOLOGICAL SCIENCES AND PSYCHOLOGY/MBSP Non-Medical Departments/Department of Genetics

Version

  • VoR (Version of Record)

Published in

European Journal of Human Genetics

Publisher

Nature Publishing Group for European Society of Human Genetics

issn

1018-4813

eissn

1476-5438

Acceptance date

2016-12-14

Copyright date

2017

Available date

2017-03-14

Publisher version

http://www.nature.com/ejhg/journal/v25/n4/full/ejhg2016207a.html

Language

en

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