title: Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.
abstract: The predictability of evolution is debatable, with recent evidence suggesting that outcomes may be constrained by gene interaction networks [1]. Whole-genome duplication (WGD; polyploidization-ubiquitous in plant evolution [2]) provides the opportunity to evaluate the predictability of genome reduction, a pervasive feature of evolution [3, 4]. Repeated patterns of genome reduction appear to have occurred via duplicated gene (homeolog) loss in divergent species following ancient WGD [5-9], with evidence for preferential retention of duplicates in certain gene classes [8-10]. The speed at which these patterns arise is unknown. We examined presence/absence of 70 homeologous loci in 59 Tragopogon miscellus plants from five natural populations of independent origin; this allotetraploid arose ~80 years ago via hybridization between diploid parents and WGD [11]. Genes were repeatedly retained or lost in clusters, and the gene ontology categories of the missing genes correspond to those lost after ancient WGD in the same family (Asteraceae; sunflower family) [6] and with gene dosage sensitivity [8]. These results provide evidence that the outcomes of WGD are predictable, even in 40 generations, perhaps due to the connectivity of gene products [8, 10, 12]. The high frequency of single-allele losses detected and low frequency of changes fixed within populations provide evidence for ongoing evolution.
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA. r.buggs@qmul.ac.uk
authors.forename: Richard J A
authors.initials: RJ
authors.lastname: Buggs
authors.forename: Srikar
authors.initials: S
authors.lastname: Chamala
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Tate
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.forename: W Brad
authors.initials: WB
authors.lastname: Barbazuk
mesh_terms: D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D018745:Genome, Plant; D011123:Polyploidy; D031188:Tragopogon / Q000235:genetics*