@ARTICLE{TreeBASE2Ref19148, author = {Nicholas R Casewell and Simon C Wagstaff and Robert A Harrison and Wolfgang Wuster}, title = {Gene tree parsimony of multi-locus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss}, year = {2010}, keywords = {Key words: gene tree parsimony, multi-gene family, multi-locusple copy genes, snake venom proteins, Bayesian posterior distributions, Serpentes: Viperidae: Echis.}, doi = {}, url = {http://}, pmid = {}, journal = {Molecular Biology and Evolution}, volume = {}, number = {}, pages = {}, abstract = {The proliferation of gene data from multiple loci of large multi-gene families has been greatly facilitated by considerable recent advances in sequence generation. The evolution of such gene families, which often undergo complex histories and different rates of change, combined with increases in sequence data, pose complex problems for traditional phylogenetic analyses, and in particular, those that aim to successfully recover species relationships from gene trees. Here we implement gene tree parsimony analyses on multi-copy gene family datasets of snake venom proteins for two separate groups of taxa, incorporating Bayesian posterior distributions as a rigorous strategy to account for the uncertainty present in gene trees. Bayesian gGene tree parsimony largely failed to infer species trees congruent with each other or with species phylogenies derived from mitochondrial and nuclear sequences. Analysis of four toxin gene families from a large expressed sequence tag dataset from the viper genus Echis failed to produce a consistent topology, and re-analysis of a previously published gene tree parsimony dataset, from the family Elapidae, suggested that species tree topologies were predominantly unsupported. We suggest that gene tree parsimony failure in the family Elapidae is likely the result of unequal and/or incomplete sampling of paralogous genes, and demonstrate that multiple parallel gene losses are likely responsible for the significant species tree conflict observed in the genus Echis. These results highlight the potential for gene tree parsimony analyses to be undermined by rapidly evolving multi-locus gene families under strong natural selection. } }

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