Analysis of higher-primate phylogeny from transversion differences in nuclear and mitochondrial DNA by Lake's methods of evolutionary parsimony and operator metrics |
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Authors: | Holmquist R; Miyamoto MM; Goodman M |
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Institution: | Space Sciences Laboratory, University of California, Berkeley. |
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Abstract: | In the companion paper (Holmquist et al. 1988), we concluded that there is
no agreement on either the correct branching order or differential rates of
evolution among the higher primates, and we examined in depth why this
uncertainty in the evolutionary understanding of our closest living
relatives persists. Recently, Lake developed two novel methods, based on
group properties of transition and transversion operators, that (a) permit,
in principle, objective resolution of problems of the above type and (b)
attach a statistical significance level to the conclusions drawn. In the
present paper, we develop formulas for using these two methods in tandem
and apply them to study transversion differences in (1) nuclear DNA for a
7-kb segment of the psi eta-globin locus and a 3-kb intergenic region
between the psi beta- and delta- globin loci and (2) mitochondrial DNA for
the 896-bp fragment of Brown et al. Although each of these nucleotide
sequence regions has its characteristic tempo and mode of evolution, the
nuclear and mitochondrial data together, comprising a total of 10,939 base
positions, support a Homo/Pan clade at the 97% confidence level. If we
calibrate the divergence point for humans and chimpanzees at 5 Myr,
consideration of the transversion branch lengths for the combined nuclear
data indicates that the gorilla lineage branched off 600,000- 900,000 years
prior to that, although the 2 sigma sampling errors do not preclude either
a temporal trifurcation for the three species or a considerably more
ancient branch point for the gorilla. To resolve the length of this central
branch to a relative accuracy of 25% and 30% will require a factor of 16
and nine times more data, respectively-- i.e., in excess of 100,000
homologous nucleotides for each of the four primates. For the nuclear
genes, heterogeneity in evolutionary rates between different parts of the
genome is mostly restricted to the human lineage for these two segments.
The lineage leading to chimpanzees has evolved 0.4 (3-kb fragment) to 3.5
(7-kb segment) times as rapidly as the lineage leading to humans, and that
leading to the gorilla has evolved approximately one-fifth to one-half as
rapidly as that leading to chimpanzees. Thus, even local molecular clocks
can "tick" badly. As significant is the fact that virtually contiguous
parts of the genome tick at markedly different rates.(ABSTRACT TRUNCATED AT
400 WORDS)
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