Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: a simple evaluation.
ABSTRACT Recent studies have shown that heterogeneous evolution may mislead phylogenetic analysis, which has been neglected for a long time. We evaluate the effect of heterogeneous evolution on phylogenetic analysis, using 18 fish mitogenomic coding sequences as an example. Using the software DIVERGE, we identify 198 amino acid sites that have experienced heterogeneous evolution. After removing these sites, the rest of sites are shown to be virtually homogeneous in the evolutionary rate. There are some differences between phylogenetic trees built with heterogeneous sites ("before tree") and without heterogeneous sites ("after tree"). Our study demonstrates that for phylogenetic reconstruction, an effective approach is to identify and remove sites with heterogeneous evolution, and suggests that researchers can use the software DIVERGE to remove the influence of heterogeneous evolution before reconstructing phylogenetic trees.
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ABSTRACT: Protein evolution includes the birth and death of structural motifs. For example, a zinc finger or a salt bridge may be present in some, but not all, members of a protein family. We propose that such transitions are manifest in sequence phylogenies as concerted shifts in substitution rates of amino acids that are neighbors in a representative structure. First, we identified rate shifts in a quartet from the Fpg/Nei family of base excision repair enzymes using a method developed by Xun Gu and coworkers. We found the shifts to be spatially correlated, more precisely, associated with a flexible loop involved in bacterial Fpg substrate specificity. Consistent with our result, sequences and structures provide convincing evidence that this loop plays a very different role in other family members. Second, then, we developed a method for identifying latent protein structural characters (LSC) given a set of homologous sequences based on Gu's method and proximity in a high-resolution structure. Third, we identified LSC and assigned states of LSC to clades within the Fpg/Nei family of base excision repair enzymes. We describe seven LSC; an accompanying Proteopedia page (http://proteopedia.org/wiki/index.php/Fpg_Nei_Protein_Family) describes these in greater detail and facilitates 3D viewing. The LSC we found provided a surprisingly complete picture of the interaction of the protein with the DNA capturing familiar examples, such as a Zn finger, as well as more subtle interactions. Their preponderance is consistent with an important role as phylogenetic characters. Phylogenetic inference based on LSC provided convincing evidence of independent losses of Zn fingers. Structural motifs may serve as important phylogenetic characters and modeling transitions involving structural motifs may provide a much deeper understanding of protein evolution.PLoS ONE 01/2011; 6(10):e25246. · 3.53 Impact Factor