Genome-scale approaches to resolving incongruence in molecular phylogenies

Abstract

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.

A history of research on yeasts 8: taxonomy

“…. a recent phylogenetic study of a concatenation of eight commonly used genes for 75 species belonging the 'Saccharomyces complex' found a bootstrap value of 69% in support of a sister group relationship between S. paradoxus and S. mikatae [146], a finding in sharp contrast to our results ( [209] p. 802).…”

Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies

“…However, ME tree [21] was different from the tree of MP and ML when base biases were not adjusted [17,21]. Rokas et al also observed topological differences between the tree obtained from a study on 75 yeast species but only eight commonly sequenced genes and their tree from 106 genes of seven species [17,26]. Although Soltis et al doubted whether the tree is a 'true tree', they advocated the use of multiple-gene or genome-scale approaches [19].…”

“…100% support for the congruent tree from the concatenated alignments of 144 single genes regardless of the phylogenetic methods, even the simplest method such as NJAD, demonstrated power of large datasets by means of the genome-wide data mining approach in resolving the incongruence. Multiple-gene approaches such as three combined genes of angiosperms [19], four combined proteins of eukaryotes [16], six and nine genes of flowering plants [27], 23 proteins of bacteria, archea and eucarya [28], 63 genes of baculovirus [7] and 106 concatenated genes of yeasts [17] strengthened supports and improved the consistence of phylogenies. Those previous results were consistent with the result in this study.…”

“…Concatenated alignments of a couple of genes improved supports [3][4][5][6][7][8][9][10][11][12][13][14][15][16]. Concatenating alignments into one from genome-scale 106 genes based on 7 yeast genomes [17] for phylogenetic analysis proclaimed ending incongruence [18]. However, the tree is doubted whether it is a 'true tree' [19].…”

“…There are some evident limitations for the genome-scale approach [17]. Especially, all of concatenated alignments must include exactly the same set of taxa.…”