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A Comment on the Reliability of
Molecular Trees R. H. Zander Res January 31, 2010 |
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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). Alfaro ME, Huelsenbeck JP (2006)
Comparative performance of Bayesian and AIC-based measured of phylogenetic
model uncertainty. Syst Biol 55:89–96 Årnason U, Johnsson E (1992) The
complete mitrochondrial DNA sequence of the harbor seal, Phoca vitulina. J Mol Evol 34:493–505 Avise JC, Robinson TJ (2008) Hemiplasy: a new term in the
lexicon of phylogenetics. Syst Biol 57:503–507 Chen FC, Li WH (2001) Genomic
divergences between humans and other hominoids and the effective population
size of the common ancestor of humans and chimpanzees. Amer J Human Gen
68:444–456 Doyle JJ (1996) Homoplasy
connections and disconnections: genes and species, molecules and morphology.
In: Sanderson MJ, Hufford L (eds) The recurrence of similarity in evolution.
Academic Press, Duvall MR, Robinson JW, Mattson
JG, Moore A (2008) Phylogenetic analyses of two mitochondrial metabolic genes
sampled in parallel from angiosperms find fundamental interlocus
incongruence. Amer J Bot 95:871–884 Guigó R, Muchnik I, Smith TF
(1996) Reconstruction of ancient molecular phylogeny. Mol Phylog Evol
6:189–213 Lyons-Weiler J, Takahashi K (1999) Branch length heterogeneity
leads to nonindependent branch length estimates and can decrease the
efficiency of methods of phylogenetic inference. J Mol Evol 49:392–405 Pennisi E (2007) DNA study forces rethink of what it means to be
a gene. Science 316:1556--1557 Stern DL, Orgogozo V (2008) The
loci of evolution: how predictable is genetic evolution? Evolution
62:2155–2177 Yi SV (2007) Understanding
neutral genomic molecular clocks. Evol Biol 34:144–151 See also relevant comments on ancient paraphyly in Evolutionary Systematics
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