Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores

Abstract

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Phylogenomics and the reconstruction of the tree of life

“…However, this approach suffers from the current lack of evaluation of its accuracy. showed only a limited effect of these factors on the results 52,54 . This suggests that genecontent methods might be more robust to the potential problems of orthology assessment than was first thought.…”

“…Phylogenetic trees reconstructed from gene-content information have generally been reconstructed using distance [50][51][52][53][54][55][56] or parsimony 55-58 methods…”

“…Orthology assessment ideally requires rigorous and time-consuming phylogenetic analyses of individual genes 47,69,70 . showed only a limited effect of these factors on the results 52,54 . This suggests that genecontent methods might be more robust to the potential problems of orthology assessment…”

“…Phylogenetic trees reconstructed from gene-content information have generally been reconstructed using distance [50][51][52][53][54][55][56] or parsimony 55-58 methods (BOX 2). One concern with gene-content analyses is the erroneous grouping of organisms with a similar number of genes 53,56,58,59 .…”

Phylogeny vs genome reshuffling: horizontal gene transfer

“…Thus it is important that at least two criteria are matched for constructing phylogenetic trees: 1) establish orthology relationships between genes; and 2) translate gene presence-absence data into a tree structure. These targets can be achieved by various routes: i) defi ning orthologus as intergenomic best hits (BeTs) and converting it in to intergenomic distances; using these to build hierarchical classifi cation trees [87][88][89] ii) using BLAST E-values to establish homology for computing intergenomic distances and construct trees [90] iii) using intergenomic FASTA z-scores followed by single linkage clustering to identify orthologous groups, then apply PARSIMONY ANALYSIS to reconstruct trees [91,92]; iv) use clusters of orthologous groups of proteins (COGs) [79] and build either parsimony [93] or least-squares trees [94] which are good for small set of gene sequences [57, 95,96]; or apply distance based method, for larger set of gene sequences [97]; v) use the co-effi cient of co-occurrence of genomes in COGs for calculating intergenomic distances and construct neighbour-joining trees [98]; vi) compute the ratio of orthologs (identifi ed as reciprocal BeTs) to the number of genes in the smaller genome and construct least-squares trees [99]; vii) build dendograms on the basis of the predicted protein fold composition of genomes [94,100]. Comparisons of 16S rRNA sequences have revolutionized the understanding of the diversity and phylogenetic relationships of all organisms [101].…”