Hi,
Several months ago there was some discussion about the the 99%
"genetic similarity" number that is often quoted for humans and
chimpanzees. I don't remember if we ever came up with other
estimates aside from the hybridization data for this but I ran
accross the following abstract while trying to find info on sequence
alignment methods and thought I would pass it along. Joel
Genomic divergence between human and chimpanzee estimated from
large-scale alignments of genomic sequences
Chen FC, Vallender EJ, Wang H, Tzeng CS, Li WH
JOURNAL OF HEREDITY
92: (6) 481-489 NOV-DEC 2001
Abstract:
To study the genomic divergence between human and chimpanzee,
large-scale genomic sequence alignments were performed. The genomic
sequences of human and chimpanzee were first masked with the
RepeatMasker and the repeats were excluded before alignments. The
repeats were then reinserted into the alignments of nonrepetitive
segments and entire sequences were aligned again. A total of 2.3
million base pairs (Mb) of genomic sequences, including repeats, were
aligned and the average nucleotide divergence was estimated to be
1.22%. The Jukes-Cantor (JC) distances (nucleotide divergences) in
nonrepetitive (1.44 Mb) and repetitive sequences (0.86 Mb) are 1.14%
and 1.34%, respectively, suggesting a slightly higher average rate in
repetitive sequences. Annotated coding and noncoding regions of
homologous chimpanzee genes were also retrieved from GenBank and
compared. The average synonymous and nonsynonymous divergences in 88
coding genes are 1.48% and 0.55%, respectively. The JC distances in
intron, 5' flanking, 3' flanking, promoter, and pseudogene regions
are 1.47%,1.41%,1.68%, 0.75%, and 1.39%, respectively. It is not
clear why the genetic distances in most of these regions are somewhat
higher than those in genomic sequences. One possible explanation is
that some of the genes may be located in regions with higher mutation
rates.
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