Molecular Biology and Evolution, Vol 12, 988-1001, Copyright © 1995 by Society for Molecular Biology and Evolution
J Sullivan, KE Holsinger and C Simon
We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and
12S rRNA (12S), for a group of sigmodontine rodents among which
phylogenetic relationships are well understood based on concordance of
morphological, chromosomal, allozyme, and other DNA data sets. Because
these two genes are physically linked on the nonrecombining mitochondrial
genome, they necessarily share the same history. Phylogenetic analysis of
the cyt b gene recovers the well-corroborated relationships, generally with
strong support. None of the methods that we employed, including variously
weighted parsimony, neighbor joining on both single-rate and
gamma-corrected distances, and maximum likelihood, were able to recover
these relationships for the 12S gene. Parsimony analyses of the 12S data
resulted in a relatively strongly supported placement of Peromyscus
eremicus that conflicts with that suggested by cyt b and all other data.
There is extreme among-site rate variation in the 12S sequences and
moderate levels in the cyt b sequences. This highly skewed distribution of
rates in the 12S gene makes phylogenetic analyses of these sequences
particularly susceptible to the misleading effects of nonindependence and
other nonrandom noise, suggesting that phylogenetic analyses of data sets
that contain a great deal of among-site rate variation be interpreted with
caution.
ORIGINAL ARTICLE
Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs 06269-3043, USA.
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