MBE Advance Access published online on February 7, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg037
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
* To whom correspondence should be addressed. E-mail: matthew.webster{at}ebc.uu.se.
We have examined the compositional evolution of non-coding DNA in the primate genome by comparison of lineage-specific substitutions observed in 1.8 Mb of genomic alignments of human, chimpanzee and baboon with 6542 human single nucleotide polymorphisms (SNPs) rooted using chimpanzee sequence. The pattern of compositional evolution, measured in terms of the numbers of GC Key Words:
Keywords: Isochore, base composition, human, chimpanzee, selection, SNP
© 2003 Society for Molecular Biology and Evolution
Original Articles
Compositional evolution of non-coding DNA in the human and chimpanzee genomes
Abstract 
AT and ATGC changes, differs significantly between fixed and polymorphic sites, and indicates that there is a bias towards fixation of ATGC mutations, which could result from weak directional selection or biased gene conversion in favor of high GC content. Comparison of the frequency distributions of a subset of the SNPs revealed no significant difference between GCAT and ATGC polymorphisms, although ATGC polymorphisms in regions of high GC segregate at slightly higher frequencies on average than GCAT polymorphisms, which is consistent with a fixation bias favoring high GC in these regions. However the substitution data suggest that this fixation bias is relatively weak, since the compositional structure of the human and chimpanzee genomes is becoming homogenized, with regions of high GC decreasing in GC content and regions of low GC increasing in GC content. The rate and pattern of nucleotide substitution in 333 Alu repeats within the human-chimpanzee-baboon alignments are not significantly affected by the GC content of the region in which they are inserted, providing further evidence that, since the time of the human-chimpanzee ancestor, there has been little or no regional variation in mutation bias.
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