Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived
Washburn, Jacob D
Edger, Patrick P
Pires, J Chris
Conant, Gavin C
AffiliationUniv Arizona, Sch Plant Sci, Tucson, AZ 85721 USA
MetadataShow full item record
PublisherOXFORD UNIV PRESS
CitationGenome Biology and Evolution, Volume 10, Issue 3, 1 March 2018, Pages 999–1011, https://doi.org/10.1093/gbe/evy061
JournalGENOME BIOLOGY AND EVOLUTION
Rights© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at firstname.lastname@example.org.
AbstractGenes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes' selective pressures. We analyzed two nested polyploidy events in Brassicaceae: theAt-a genome duplication that is the most recent polyploidy in themodel plant Arabidopsis thaliana and a more recent hexaploidy shared by thegenus Brassica andits relatives. By comparing the strengthanddirectionof thenatural selectionactingat the population andat the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in nonpolyploid outgroup genomes. In both the Arabidopsis and Brassica lineages, we further find evidence for segregating mildly deleterious variants, confirming that the population-level data uncover patterns not visiblewith between-species comparisons. Using theA. thalianametabolic network, we also exploredwhether network position was correlated with the measured selective constraint. At both the population and species level, nodes/genes tended to show similar constraints to their neighbors. Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday's polyploids still have distinct evolutionary trajectories.
NoteOpen access journal.
VersionFinal published version
SponsorsNational Science Foundation [IOS-1339156]; [NSF-DBI-1358997]
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