Bayesian Inference of Shared Recombination Hotspots Between Humans and Chimpanzees

Supporting Information

Supporting Information

Supporting Information - Figures S1-S12, Tables S1-S7, and References (PDF, 1 MB)
Figure S1 - The distribution of human-chimpanzee sequence divergence for syntenic regions of humans and chimpanzees on human chromosome 21. (PDF, 40 KB)
Figure S2 - The distribution of the sizes (in bp) of syntenic regions of humans and chimpanzees on human chromosome 21. (PDF, 40 KB)
Figure S3 - The distribution of the sizes (in bp) of syntenic blocks of humans and chimpanzees on human chromosome 21. (PDF, 40 KB)
Figure S4 - The prior probability of hotspot estimated from simulation. (PDF, 70 KB)
Figure S5 - The estimated recombination rates (ρ) from (A) 15504000 to 26362000 bp, (B) 26362000 to 37220000 bp, and (C) 37220000 to 48078000 bp on chromosome 21 for YRI (black lines) and chimpanzee (red lines). (PDF, 868 KB)
Figure S6 - The estimated recombination rates (ρ) across β-globin region using samples of Beni (green) and Chimpanzee (red) (A) and samples of CEPH (blue) and Chimpanzee (red) (B). (PDF, 61 KB)
Figure S7 - The estimated recombination rates (ρ) across HLA region using samples of Beni (green) and Chimpanzee (red) (A) and samples of CEPH (blue) and Chimpanzee (red) B. (PDF, 97 KB)
Figure S8 - Simulation study results from set 1 (A) and results from set 2 (B). (PDF, 47 KB)
Figure S9 - Simulation study results from set 3 (A) and results from set 4 (B). (PDF, 44 KB)
Figure S10 - Simulation study results from set 5 (A) and results from set 6 (B). (PDF, 47 KB)
Figure S11 - The posterior probability of hotspot across the region for CEU (A), BEN (B), Chimp (C) from four independent runs (red, blue, green, and pink lines). (PDF, 51 KB)
Figure S12 - The percentage of hotspot overlapping between species calculated using simulated recombination hotspots based on the prior model used in the analysis. (PDF, 41 KB)
Table S1 - Summary of the polymorphic data from humans and chimpanzees for the β-globin and HLA regions. (PDF, 40 KB)
Table S2 - Positions of human recombination hotspots identified from sperm typing studies for the β-globin (HOLLOWAY et al., 2006) and the HLA regions (JEFFREYS et al., 2001) indicated in Figures 2 and 3 in the main text. (PDF, 46 KB)
Table S3 - The location, BF of shared hotspot, posterior and prior probabilities of hotspot, and recombination rate for the locations within chromosome 21 with BF of shared hotspot for YRI and chimpanzee that is ≥ 100. (PDF, 53 KB)
Table S4 - The location, BF of shared hotspot, posterior and prior probabilities of hotspot, and recombination rate for the locations within β-globin region with BF of shared hotspot for Beni and chimpanzee that is ≥ 100. (PDF, 47 KB)
Table S5 - The location, BF of shared hotspot, posterior and prior probabilities of hotspot, and recombination rate for the locations within β-globin region with BF of shared hotspot for CEPH and chimpanzee that is ≥ 100. (PDF, 47 KB)
Table S6 - The location, BF of shared hotspot, posterior and prior probabilities of hotspot, and recombination rate for the locations within HLA region with BF of shared hotspot for Beni and chimpanzee that is ≥ 100. (PDF, 47 KB)
Table S7 - The location, BF of shared hotspot, posterior and prior probabilities of hotspot, and recombination rate for the locations within HLA region with BF of shared hotspot for CEPH and chimpanzee that is ≥ 100. (PDF, 47 KB)