Egan, Ashley N. , Doyle, Jeff J. .
Exploring sources of incongruence among nuclear genes in generic level phylogenies in the legume subtribe Glycininae.
Rapidly diversifying lineages are often characterized by unresolved or weakly supported, shallow phylogenetic backbones. This may result simply from a lack of characters, but may also be caused by hybridization, recombination, or ancestral polymorphism, processes that increase homoplasy. Furthermore, rate heterogeneity can mimic the effects of recombination. We explore these phenomena as explanations for observed incongruence among nuclear genes in genera produced by a rapid radiation in the legume family (Leguminosae). We focus on Phaseoleae subtribe Glycininae with special interest in the evolutionary relationships surrounding Glycine, a genus of polyploid origin that includes the cultivated soybean (G. max). Past studies have suggested four genera as possible candidates for the closest relative of Glycine, including Amphicarpaea, Teramnus, Pueraria, and tribe Psoraleeae. We use seven nuclear genes, four of which are linked within a 1-Mb region on Glycine chromosome 13, to investigate phylogenetic relationships and incongruence within Glycininae. Evidence for recombination was found within and among genes. However, boundaries for recombination breakpoints are disproportionately correlated with intron/exon boundaries, suggesting the possibility that rate heterogeneity among introns and exons may be mimicking recombination. To further characterize the recombination signals we found, we estimate phylogenies based on individual and combined datasets using maximum parsimony, maximum likelihood, and Bayesian inference. We use gene jackknifing to investigate how robust clades are when genes are deleted from the combined dataset, and similarly test the effect of excluding introns or exons from individual genes. Some groupings seem driven by inclusion of a single gene, Gmw25. Exclusion from the concatenated dataset suggests Teramnus as sister to Glycine while inclusion of Gmw25 suggests Psoraleeae and Amphicarpaea. Analysis of exons only suggests Psoraleeae as sister to Glycine while introns suggest Psoraleeae and Amphicarpaea. These strategies afford a comprehensive exploration of phylogenetic incongruence in the context of recombination, rate heterogeneity, and hybridization.
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1 - Cornell University, Department of Plant Biology, L.H. Bailey Hortorium, 412 Mann Library Building, Ithaca,, New York, 14853-5908, USA
Presentation Type: Oral Paper:Papers for BSA Sections
Location: Maybird/Cliff Lodge - Level C
Date: Monday, July 27th, 2009
Time: 10:00 AM