The perils of intralocus recombination for inferences of molecular convergence

BioRxiv : the Preprint Server for Biology
Fabio K MendesMatthew W Hahn

Abstract

Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence ('hemiplasy') can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and Drosophila, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of Drosophila protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding g...Continue Reading

Related Concepts

Exons
Genes
Trees (plant)
Exon-exon Junction Complex Location
Research Personnel
Recombination, Genetic
Drosophila
Whole Body
Primates
Convergence - Direction

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