PMC:1271393 / 38266-40036 JSONTXT

{"project":"2_test","denotations":[{"id":"16252244-7800710-2049635","span":{"begin":130,"end":134},"obj":"7800710"},{"id":"16252244-14527305-2049636","span":{"begin":1316,"end":1320},"obj":"14527305"},{"id":"16252244-12433581-2049637","span":{"begin":1469,"end":1473},"obj":"12433581"}],"text":"The low levels of intragenic recombination observed in CD209 allowed maximum-likelihood coalescent analysis (Griffiths and Tavare 1994) for estimation of the time scale of the origin and evolution of this gene. Since this method assumes an infinite-site model without recombination, the same analysis for CD209L was not conducted because of the substantial amount of recombinant haplotypes observed. For CD209, only 29 of the 254 chromosomes analyzed had to be excluded, as did a single segregating site (SNP 939). The resulting CD209 gene tree estimate, rooted with the chimpanzee sequence (i.e., the chimpanzee sequence was used to define ancestral/derived status of human mutations), is shown in figure 6 . The tree is partitioned into two deep branches that correspond to haplotype clusters A and B. African samples were observed in both sides of the deepest node of the tree (i.e., in both clusters A and B), whereas non-African samples are restricted to one branch of the tree (i.e., cluster B). The maximum-likelihood estimate of θ (θML) for CD209 was 8.4. On the basis of this θML value and the estimated mutation rate (1.54×10−4 per gene per generation), the effective population size (N e) was 13,636, a value comparable to most figures reported in the literature (for a review, see Tishkoff and Verrelli [2003]). The T MRCA of the CD209 tree was then estimated at 2.8±0.22 MYA, one of the oldest T MRCA values estimated so far in the human genome (Excoffier 2002).\nFigure 6 CD209 estimated gene tree. Time scale is in MYA. Mutations are represented as black dots and are named for their physical position along CD209. For branches with multiple mutations, order in time is arbitrary. Lineage absolute frequencies in Africa, Europe, and East Asia are reported."}