plosone-phylo
pone.0015115.g006.png
The Cen-A and Cen-B difference arose long before that between Tel-A and Tel-B.
Three genomic segments with orthologs or paralogs in other higher primates were chosen for divergence time estimation. (A) Shows the three regions used for the analysis and the haplotypes from which they were obtained (human (AC006293/AC011501, AL133414, AY320039, and this study) chimpanzee (BX842589, AC155174), gorilla (CU92894), orangutan (EF014479, AC200148) and rhesus macaque (BX842590, BX842591)). They comprise region I, a 5.5 kb segment including the 5′ part of 3DL3 excluding intron 1, a 14 kb segment from the intergenic region between 3DP1 and KIR2DL4 (region II), and a 16.8 segment beginning in intron 3 of 2DL5A/B extending into the neighboring 2DS3/5 gene (region III). For the latter, both the centromeric and telomeric variants were included in the analysis. (B) Shows the phylogenetic trees for regions I, II and III, with bootstrap values for the nodes. The nodes denoted by dark shaded symbols were those used for divergence time estimates. (C) Plotted here are the divergence time estimates using the same symbols as in panel B. For comparison, the dotted horizontal lines indicate the lower limits for divergence times from the human lineage of rhesus macaque, orangutan, gorilla and chimpanzee as assessed from the fossil record [73]. The left panel examines the divergence of human KIR from KIR in other primates, the right panel examines the divergence of different forms of human KIR and the results from two independent runs of the program are shown. Analysis of region I estimates the divergence time for Cen-A and Cen-B, whereas analysis of region II estimates the divergence of Tel-A and Tel-B, and analysis of region III estimates the time of duplication for 2DL5A and 2DL5B as well as 2DS3 and 2DS5.
pone.0015115.g006.png
The Cen-A and Cen-B difference arose long before that between Tel-A and Tel-B.
Three genomic segments with orthologs or paralogs in other higher primates were chosen for divergence time estimation. (A) Shows the three regions used for the analysis and the haplotypes from which they were obtained (human (AC006293/AC011501, AL133414, AY320039, and this study) chimpanzee (BX842589, AC155174), gorilla (CU92894), orangutan (EF014479, AC200148) and rhesus macaque (BX842590, BX842591)). They comprise region I, a 5.5 kb segment including the 5′ part of 3DL3 excluding intron 1, a 14 kb segment from the intergenic region between 3DP1 and KIR2DL4 (region II), and a 16.8 segment beginning in intron 3 of 2DL5A/B extending into the neighboring 2DS3/5 gene (region III). For the latter, both the centromeric and telomeric variants were included in the analysis. (B) Shows the phylogenetic trees for regions I, II and III, with bootstrap values for the nodes. The nodes denoted by dark shaded symbols were those used for divergence time estimates. (C) Plotted here are the divergence time estimates using the same symbols as in panel B. For comparison, the dotted horizontal lines indicate the lower limits for divergence times from the human lineage of rhesus macaque, orangutan, gorilla and chimpanzee as assessed from the fossil record [73]. The left panel examines the divergence of human KIR from KIR in other primates, the right panel examines the divergence of different forms of human KIR and the results from two independent runs of the program are shown. Analysis of region I estimates the divergence time for Cen-A and Cen-B, whereas analysis of region II estimates the divergence of Tel-A and Tel-B, and analysis of region III estimates the time of duplication for 2DL5A and 2DL5B as well as 2DS3 and 2DS5.