Gene diversity patterns at ten X-chromosomal loci in humans and chimpanzees

We have investigated the pattern and extent of nucleotide diversity in 10 X-chromosomal genes where mutations are known to cause mental retardation in humans. For each gene, we sequenced the entire coding regions from cDNA in humans, chimpanzees and orangutans as well as about 3kb of genomic DNA in 20 humans sampled worldwide and in 10 chimpanzees representing two " subspecies ". Overall nucleotide diversity in these genes is about twofold lower in humans than in chimpanzees and nucleotide diversity within and between species is low, suggesting that a high level of functional constraints acts on these genes Strikingly, we find that a summary of the allele frequency spectrum is significantly correlated in humans and chimpanzees, perhaps reflecting very similar levels of constraints at these genes in the two species. A possible exception is FMR2, which shows higher number of non-synonymous than synonymous substitutions on the human lineage, suggesting the action of positive selection.