Phylogenetic Classification and the Universal Tree

Abstract

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

Towards a unified science of cultural evolution

“…However, we reiterate the point we made in section 2.1.2, that biologists face the same problem, for example, with horizontal gene transfer in bacteria (Doolittle 1999;Rivera & Lake 2004) and plants (Abbott et al 2003). Although we agree with Borgerhoff Mulder et al that it is vital that the parallels between biological and cultural evolution should not blind researchers to the differences, the significance of horizontal transfer to the two disciplines is a matter of degree, not kind.…”

“…However, as noted by , any putative dichotomy contrasting a "divergent, branching biological evolution" with a "convergent, cross-fertilising cultural evolution" is a distortion of both biology and culture. Significant cross-lineage transfer occurs in biological evolution, especially for microbes (Doolittle 1999;Rivera & Lake 2004) and plants (Abbott et al 2003), whereas the convergent nature of culture is an empirically testable hypothesis rather than a statement of fact. Tackling the issue systematically and quantitatively, Tehrani and Collard (2002) found a greater role for branching "phylogenesis" than convergent "ethnogenesis" in Turkmen textile patterns, and Collard et al (2005) have found that the best available cultural data sets show just as good a fit with a branching phylogenetic model as do biological data sets.…”

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

“…Recent research shows that this problem still exists [1][2][3]. Such incongruence is caused by many reasons such as insufficient number of informative sites, lateral gene transfer, unrecognized paralogy and variable evolutionary rates of different genes [3][4]. The comparative genomics results suggest that the simple notion of a single tree of life that would accurately and definitely depict the evolution of all life forms is gone forever [5].…”

“…Kluge believed that phylogenetic analysis should always be performed using all the evidences [14], but Miyamoto and Fitch argued that partitions (including genes) should not be combined [15]. 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].…”

Evolution of protein families: Is it possible to distinguish between domains of life?

“…Until recently, it was widely accepted that the lineage of any species could be represented by a branch in a phylogenetic tree. Recent discoveries have pointed out that processes such as lateral gene transfer also play an important role in evolution, making the redefinition of the "tree of life" one of the "biggest challenges in evolutionary biology" (Doolittle, 1999).…”