Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

Abstract

Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced Drosophila genomes and nine fungal genomes to address the problem of accurate gene-tree reconstruction across many complete genomes. We show that existing phylogenetic methods that treat each gene tree in isolation show large-scale inaccuracies, largely due to insufficient phylogenetic information in individual genes. However, we find that gene trees exhibit common properties that can be exploited for evolutionary studies and accurate phylogenetic reconstruction. Evolutionary rates can be decoupled into gene-specific and species-specific components, which can be learned across complete genomes. We develop a phylogenetic reconstruction methodology that exploits these properties and achieves significantly higher accuracy, addressing the species-level heterotachy and enabling studies of gene evolution in the context of species evolution.

Mobile male-killer: similar Wolbachia strains kill males of divergent Drosophila hosts

“…Sequences of mitochondrial genes COI and COII of D. borealis, D. innubila and D. recens, and two and three regions of nuclear genes of D. recens and D. innubila, respectively, were aligned with the corresponding regions from the reference genome sequences of nine Drosophila species. Over 20 kb of additional sequence from nine reference species contained 14 genes that yielded method-independent inference of the consensus topology among 12 species of Drosophila in the analysis of Rasmussen and Kellis (2007). A table listing the data included in this supermatrix is available as supplementary material.…”

Unified modeling of gene duplication, loss, and coalescence using a locus tree

“…While these models (which we refer to as dup-loss models) have been successful in many situations, there still remain several important challenges in accurately inferring these events (Li et al 2006;Hahn 2007;Huerta-Cepas et al 2007;Rasmussen and Kellis 2007). These challenges stem from the fact that incongruence can occur due to phenomena other than duplications and losses, and therefore one must use caution when interpreting incongruence.…”

Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds

“…The phylogenomic approach to multigene family evolution has shown recent success in many different clades, such as vertebrates (Zmasek and Eddy, 2002;Storm and Sonnhammer, 2003;Li et al, 2006;Huerta-Cepas et al, 2007) and 16 fungi species (Wapinski et al, 2007). Recently, Rasmussen and Kellis (2007) deduced a pattern of substitution rates within and among Drosophila and yeast species by using machine learning to compare the gene trees in multigene families to the presumed species tree. In addition, Heger and Ponting (2007) developed a comprehensive database of orthologous and paralogous gene sets for several clades, including amniotes.…”