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Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

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Date
09/01/2018
Author
Ma, Tao
Wang, Kun
Hu, Quanjun
Xi, Zhenxiang
Wan, Dongshi
Wang, Qian
Feng, Jianju
Jiang, Dechun
Ahani, Hamid
Abbott, Richard John
Lascoux, Martin
Nevo, Eviatar
Liu, Jianquan
Keywords
Speciation
Paraphyletic
Genome divergence
Natural selection
Gene flow
QH301 Biology
QH426 Genetics
NDAS
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Abstract
How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.
Citation
Ma , T , Wang , K , Hu , Q , Xi , Z , Wan , D , Wang , Q , Feng , J , Jiang , D , Ahani , H , Abbott , R J , Lascoux , M , Nevo , E & Liu , J 2018 , ' Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex ' , Proceedings of the National Academy of Sciences of the United States of America , vol. 115 , no. 2 , pp. E236-E243 . https://doi.org/10.1073/pnas.1713288114
Publication
Proceedings of the National Academy of Sciences of the United States of America
Status
Peer reviewed
DOI
https://doi.org/10.1073/pnas.1713288114
ISSN
0027-8424
Type
Journal article
Rights
Copyright 2017 the Authors. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Collections
  • University of St Andrews Research
URI
http://hdl.handle.net/10023/12423

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