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Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

Gavin M. Douglas, Gesseca Gos, Kim A. Steige, Adriana Salcedo, Karl Holm, Emily B. Josephs, Ramesh Arunkumar, J. Arvid Ågren, Khaled M. Hazzouri, Wei Wang, Adrian E. Platts, Robert J. Williamson, Barbara Neuffer, Martin Lascoux, Tanja Slotte, Stephen I. Wright
doi: https://doi.org/10.1101/006783
Gavin M. Douglas
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Gesseca Gos
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Kim A. Steige
bDepartment of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
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Adriana Salcedo
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Karl Holm
bDepartment of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
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Emily B. Josephs
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Ramesh Arunkumar
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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J. Arvid Ågren
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Khaled M. Hazzouri
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
cCenter for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Wei Wang
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Adrian E. Platts
dMcGill Centre for Bioinformatics, McGill University, Montreal, Canada
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Robert J. Williamson
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Barbara Neuffer
eDepartment of Botany, University of Osnabrück, Osnabrück, Germany
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Martin Lascoux
bDepartment of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
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  • For correspondence: tanja.slotte@su.se stephen.wright@utoronto.ca martin.lascoux@ebc.uu.se
Tanja Slotte
bDepartment of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
fDepartment of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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  • For correspondence: tanja.slotte@su.se stephen.wright@utoronto.ca martin.lascoux@ebc.uu.se
Stephen I. Wright
aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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Abstract

Whole genome duplication events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole genome data provide strong support for recent hybrid origins of the tetraploid species within the last 100-300,000 years from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide, due to the combined effects of demography, selfing and genome redundancy from whole genome duplication. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that non-functionalization can receive a 'head start' through a legacy of deleterious variants and differential expression originating in parental diploid populations.

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Posted January 20, 2015.
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Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
Gavin M. Douglas, Gesseca Gos, Kim A. Steige, Adriana Salcedo, Karl Holm, Emily B. Josephs, Ramesh Arunkumar, J. Arvid Ågren, Khaled M. Hazzouri, Wei Wang, Adrian E. Platts, Robert J. Williamson, Barbara Neuffer, Martin Lascoux, Tanja Slotte, Stephen I. Wright
bioRxiv 006783; doi: https://doi.org/10.1101/006783
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Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
Gavin M. Douglas, Gesseca Gos, Kim A. Steige, Adriana Salcedo, Karl Holm, Emily B. Josephs, Ramesh Arunkumar, J. Arvid Ågren, Khaled M. Hazzouri, Wei Wang, Adrian E. Platts, Robert J. Williamson, Barbara Neuffer, Martin Lascoux, Tanja Slotte, Stephen I. Wright
bioRxiv 006783; doi: https://doi.org/10.1101/006783

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