A Comment on the Reliability of Molecular Trees
R. H. Zander
January 31, 2010
A Comment on Reliability of Molecular Trees
Richard H. Zander
Although reliability (as opposed to statistical discriminatory power) of a molecular tree may be estimated in spite of sampling error, incorrect model of sequence evolution, greatly different rates of divergence and extinction, and other problems (Zander 2007a), one might keep in perspective the finding of Guigó et al. (1996) that of 53 different nuclear genes only 17 were perfectly consistent with the accepted species tree of major eucaryote groups, while Chen and Li (2001) found that of 53 different DNA loci, 31 support the Homo-Pan clade, 12 support Pan-Gorilla, and 10 support Homo-Gorilla (although this leaves a chi-square probability of 0.999 that this would not occur by chance alone given random support for all three combinations). Five different phylogenies of mouse, rat, human, seal, cow and whale were supported by one or another of 15 different mitochondrial genes in a study by Årnason and Johnsson (1992). Problems in discrepant gene histories are well known, and are discussed at length most recently by Avise and Robinson (2008) and Duvall et al. (2008). Also, molecular traits may be to a significant extent non-neutral and thus affected by selection. Although protein-coding DNA comprises only two percent of the human genome, of 44 regions studied including 30 million bases, fully 80 percent of the bases were apparently involved in some way in expression of traits, such as gene regulation (Pennisi 2007), and therefore exposed to selection that may lead to false DNA sequence convergence in phylogenetic analysis. Stern and Orgogozo (2008) found that fully 22 percent of identified genetic changes are due to cis-regulatory mutations, which are largely found in non-coding sequence areas, these commonly used in phylogenetic analysis of DNA. Certainly extreme branch length heterogeneity, like that expected for punctuated evolution, can affect the recovery of the true gene tree (Lyons-Weiler and Takahashi 1999). Pollard et al. (2006) suggested that rapidly evolving regions are adaptively significant and should be under positive selection. Yi (2007) summarized evidence for “pervasive natural selection on non-coding and synonymous sites” leading to, for instance, rapid adaptive evolution and accelerated molecular clocks in particular lineages. The molecular analysis must also have accounted for any homoplasy introduced into the analysis by inappropriate technique, e.g. wrong model (Alfaro and Huelsenbeck 2006) or inappropriate data, e.g., incomplete concerted evolution (Doyle 1996).
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See also relevant comments on ancient paraphyly in Evolutionary Systematics page.