Systematics Section / ASPT
McMahon, Michelle , Sanderson, MJ .
Inferring angiosperm phylogeny from EST data with widespread gene duplication.
SPECIES phylogenies are most readily built from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants. A gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead. Despite the complexity of the EST data, a relatively small fraction of usable sequences, a broad range of sampling intensities among taxa, and very high apparent rates of duplication, the gene tree parsimony method performed well.
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1 - University of California, Davis, Section of Evolution and Ecology, One Shields Ave., Davis, California, 95616, USA
2 - University of California, Davis, Section of Evolution and Ecology, One Shields Ave., Davis, California, 95616, USA
gene tree parsimony
Presentation Type: Oral Paper:Papers for Sections
Location: 144/Performing Arts Center
Date: Tuesday, August 1st, 2006
Time: 11:00 AM