title: Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data.
abstract: Whole-genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that the genomes of all angiosperms have experienced at least two ancient WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost. Thus, it can be extremely difficult to identify, let alone characterize, ancient WGDs. In this study, we use a new maximum likelihood estimator to test for evidence of ancient WGDs in land plants and estimate the fraction of new genes copies that are retained following a WGD using gene count data, the number of gene copies in gene families. We identified evidence of many putative ancient WGDs in land plants and found that the genome fractionation rates vary tremendously among ancient WGDs. Analyses of WGDs within Brassicales also indicate that background gene duplication and loss rates vary across land plants, and different gene families have different probabilities of being retained following a WGD. Although our analyses are largely robust to errors in duplication and loss rates and the choice of priors, simulations indicate that this method can have trouble detecting multiple WGDs that occur on the same branch, especially when the gene retention rates for ancient WGDs are very low. They also suggest that we should carefully evaluate evidence for some ancient plant WGD hypotheses.
authors.affiliation: Department of Biology, University of Florida gtiley@ufl.edu.
authors.forename: George P
authors.initials: GP
authors.lastname: Tiley
authors.affiliation: Department of Statistics, University of Wisconsin-Madison Department of Botany, University of Wisconsin-Madison.
authors.forename: Cécile
authors.initials: C
authors.lastname: Ané
authors.affiliation: Department of Biology, University of Florida.
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D003198:Computer Simulation; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D011123:Polyploidy
keywords: gene count; gene duplication and loss; gene family evolution; gene retention; paleopolyploidy; whole-genome duplication