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Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

Novikova, Polina Yu; Hohmann, Nora; Nizhynska, Viktoria; Tsuchimatsu, Takashi; Ali, Jamshaid; Muir, Graham; Guggisberg, Alessia; Paape, Tim; Schmid, Karl and Fedorenko, Olga M., et al. (2016) In Nature Genetics 48(9). p.1077-1082
Abstract

The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared... (More)

The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.

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Nature Genetics
volume
48
issue
9
pages
6 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:84978732423
  • wos:000382398800021
ISSN
1061-4036
DOI
10.1038/ng.3617
language
English
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yes
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c39865f4-e7a6-4a7d-b0b3-226c76a41386
date added to LUP
2016-11-29 14:32:55
date last changed
2017-11-19 04:35:20
@article{c39865f4-e7a6-4a7d-b0b3-226c76a41386,
  abstract     = {<p>The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.</p>},
  author       = {Novikova, Polina Yu and Hohmann, Nora and Nizhynska, Viktoria and Tsuchimatsu, Takashi and Ali, Jamshaid and Muir, Graham and Guggisberg, Alessia and Paape, Tim and Schmid, Karl and Fedorenko, Olga M. and Holm, Svante and Säll, Torbjörn and Schlötterer, Christian and Marhold, Karol and Widmer, Alex and Sese, Jun and Shimizu, Kentaro K. and Weigel, Detlef and Krämer, Ute and Koch, Marcus A. and Nordborg, Magnus},
  issn         = {1061-4036},
  language     = {eng},
  month        = {09},
  number       = {9},
  pages        = {1077--1082},
  publisher    = {Nature Publishing Group},
  series       = {Nature Genetics},
  title        = {Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism},
  url          = {http://dx.doi.org/10.1038/ng.3617},
  volume       = {48},
  year         = {2016},
}