Abstract
A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the Saccharomyces cerevisiae genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.
Highlights
The advent of the genome era and the availability of a growing number of fully-sequenced genomes have changed the way in which biologists study the evolutionary relationships among groups of organisms
Most of the nodes in such a species tree do represent topologies that are widely represented across the genome
Our analysis only reflects the topological variation found in the yeast phylome and phylogenies of genes not present in S. cerevisiae are not taken into account
Summary
The advent of the genome era and the availability of a growing number of fully-sequenced genomes have changed the way in which biologists study the evolutionary relationships among groups of organisms. The use of phylogenetics in the context of whole genomes, a field known as phylogenomics [1], allows for the combination of evolutionary signals from various genes into a single tree. The use of multiple gene approaches is a way to average out these discrepancies in order to provide a single topology that is expected to reflect the true evolutionary relationships more accurately. The use of multigene approaches, and especially gene concatenation, is becoming the method of choice in most studies aiming to elucidate the evolutionary relationships among a group of species [2]. Such approaches are, not free from criticism. Besides questioning the validity of species trees, these findings have raised doubts regarding the possible sources for the high topological variability and the implications for large-scale phylogenetic inferences such as the prediction of orthology relationships
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