Table 2.
The Ten Regions Identified by HaploPS to Be under Convergent Evolution in Identified Populations
| Chr | Start | End | HSI | Populations | Genesa |
|---|---|---|---|---|---|
| 1 | 35,157,192 | 35,852,095 | 0.85 | CEU, GIH, INS, TSI | ZMYM6, ZNF258, ZMYM1, SFPQ, ZMYM4, NCDN, PSMB2, TFAP2E |
| 1 | 75,238,998 | 75,889,193 | 0.77 | CHB, CHD, CHS, JPT, MAS | LHX8, SLC44A5 |
| 2 | 135,318,981 | 137,528,542 | 0.75 | CEU, MKK | ACMSD, CCNT2, YSK4, RAB3GAP1, ZRANB3, R3HDM1, UBXN4, UBXD2, LCT, MCM6, DARS, CXCR4, THSD7B |
| 6 | 29,388,715 | 31,065,597 | 0.78 | ASW, CEU, CHB, CHD, CHS, GIH, JPT, LWK, TSI, YRI | OR5V1, OR12D3, OR12D2, OR11A1, OR10C1, OR2H1, MAS1L, UBD, GABBR1, SNORD32B, OR2H2, MOG, ZFP57, HLA-F, HLA-G, HLA-A, HLA-H, IFITM4P, HCG4, HCG2P7, HCG4P6, C6orf12, C6orf134, C6orf136, C6orf214, ZNRD1, PPP1R11, PPP1R10, RNF39, TRIM31, TRIM40, TRIM10, TRIM15, TRIM26, TRIM39, GNL1, PRR3, CAT53, MRPS18B, DHX16, NRM, NRM29, MDC1, TUBB, FLOT1, IER3, DDR1, GTF2H4, TFIIH, VARS2, SFTA2, DPCR1, MUC21 |
| 6 | 31,296,179 | 31,556,632 | 0.84 | ASW, CEU, YRI | HLA-C, HLA-B, MICA, HCP5, HCG26 |
| 6 | 33,066,663 | 33,839,447 | 0.89 | ASW, JPT, LWK, MXL, YRI | HLA-DOA, HLA-DPA1, HLA-DPB1, HLA-DPB2, COL11A2, RXRB, SLC39A7, HSD17B8, RING1, VPS52, RPS18, B3GALT4, FP221, WDR46, PFDN6, RGL2, TAPBP, ZBTB22, DAXX, LYPLA2P1, KIFC1, PHF1, CUTA, SYNGAP1, ZBTB9, BAK1, BAK, C6orf227, C6orf125, ITPR3, SBP1, IP6K3 |
| 6 | 65,850,800 | 70,137,233 | 0.84 | MAS, LWK | EYS, UNQ9424, BAI3, BAI |
| 7 | 118,321,619 | 118,579,454 | 0.86 | GIH, INS, MKK | - |
| 12 | 109,915,688 | 111,589,168 | 0.82 | CHB, JPT, TSI | CUX2, FAM109A, SH2B3, ATXN2, BRAP, ACAD10, ALDH2, PNAS1, MAPKAPK5, TMEM116, ERP29, C12orf30, C12orf51, NAP1, TRAFD1, RPL6, PTPN11 |
| 14 | 62,796,468 | 62,834,923 | 0.86 | ASW, INS, MXL | RHOJ |
The ten positive-selection signals were found in multiple populations, and the HSI for each region is less than 0.90. This means that the haplotypes carrying the advantageous variants at each of these ten regions in the different populations is significantly different and thus suggestive of convergent evolution of multiple mutation events, either at the same variant or at different variants in the same genomic region. Abbreviations are as follows: Chr, chromosome; HSI, haplotype similarity index; ASW, African ancestry in southwest USA; CEU, Utah residents with ancestry from northern and western Europe from the CEPH collection; CHB, Han Chinese in Beijing, China; CHD, Chinese in Metropolitan Denver, CO, USA; CHS, Chinese in Singapore; GIH, Gujarati Indians in Houston, TX, USA; INS, Indians in Singapore; JPT, Japanese in Toyko, Japan; LWK, Luhya in Webuye, Kenya; MAS, Malays in Singapore; MKK, Maasai in Kinyawa, Kenya; MXL, Mexican ancestry in Los Angeles, CA, USA; TSI, Toscani in Italia; and YRI, Yoruba in Ibadan, Nigera.
MIM numbers for these genes can be found in Table S2.