Table 1. Performance of ascertainment schemes explored across 12 population quintuplets and assessed as the fraction of all possible admixture graph topologies that are rejected under ascertainment (fit poorly with WR >3 SE) but accepted on all sites (fit well with WR <3 SE).
We also applied the binary classifier to determine if an ascertainment scheme produces unbiased or biased results (the latter cases are highlighted in bold and underlined text). The numbers of population quintuplets or ascertainment schemes affected by bias, or by both bias and low statistical power, are shown in the two rightmost columns and in two bottom rows, respectively. The level of bias is approximated by the fraction of topologies that are rejected under ascertainment but accepted on all sites, and statistical power is approximated by the fraction of topologies that are, vice versa, accepted under ascertainment but rejected on all sites. The composition of the population sets is shown above the table in an abbreviated way: arch, archaic humans, followed by the number of archaic groups in admixture graph models tested; afr, Africans, followed by the number of African groups; nafr, non-Africans or Africans with substantial non-African admixture [67], followed by the number of such groups. The results for five population quintuplets (listed in the footnote) demonstrating no ascertainment bias are collapsed into one column. The SNP counts correspond to sites polymorphic in larger collections of groups from which the analyzed population quintuplets were taken, see S2 Table. SNP counts vary across the population sets, and minimal and maximal values are shown in separate columns.
| percentage of models rejected on asc. data but accepted on all sites | arch 2, afr 3 | arch 1, afr 4 | arch 1, afr 3, nafr 1 | arch 1, afr 2, nafr 2 | afr 4, nafr 1 | afr 3, nafr 2 | afr 1, nafr 4 | afr 5; afr 4, nafr 1; nafr 5 | number of biased pop. sets | number of biased pop. sets, both metrics | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ascertainment type | further details on the ascertainment | min. size of the SNP panel | max. size of the SNP panel | Denisovan, Altai, Yoruba, Dinka, Bulala | Denisovan, Khomani San, Mbuti, Dinka, Mursi | Altai, Ju hoan North, Biaka, Yoruba, Agaw | Altai, Ju hoan North, Luhya, Palestinian, Spanish | Bedzan, Cameroon SMA, Esan, Mozabite, Masai | Mbuti, Biaka, Ngumba, LBK, Iranian | Luo, Bedouin B, Jordanian, Abkhasian, Sardinian | 5 population quintuplets showing no biased results * | ||
| AT/GC | A<>T and G<>C mutations | 805,042 | 1,757,840 | 0.00% | 0.01% | 0.00% | 0.00% | 0.00% | 0.31% | 0.00% | 0.00% | 0 | 0 |
| 1240K | 1240K panel | 501,429 | 663,239 | 0.02% | 1.02% | 7.97% | 5.53% | 0.00% | 0.00% | 0.00% | 0.00% | 3 | 4 |
| 1240K components | Illumina 650Y sites | 256,277 | 304,292 | 0.01% | 0.02% | 7.99% | 5.53% | 0.00% | 0.00% | 0.02% | 0.00% | 2 | 3 |
| sites exclusive to Illumina 650Y | 183,680 | 216,478 | 0.00% | 0.01% | 7.97% | 5.53% | 0.00% | 0.00% | 0.06% | 0.00% | 3 | 4 | |
| sites included in both Illumina 650Y and Human Origins | 72,597 | 87,814 | 0.02% | 0.00% | 7.97% | 5.53% | 0.00% | 0.00% | 0.00% | 0.00% | 2 | 6 | |
| Human Origins sites | 244,922 | 354,460 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% | 1 | 3 | |
| sites exclusive to Human Origins | 171,249 | 266,646 | 0.00% | 0.00% | 6.88% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 2 | |
| 1240K, other sites | 67,096 | 92,301 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 4 | |
| Human Origins (HO) panels | panel 13 based on a San individual and Denisovan | 67,557 | 89,655 | 0.00% | 0.17% | 6.99% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 6 |
| panel 4 based on a San individual | 52,862 | 94,493 | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% | 0 | 4 | |
| panel 5 based on a Yoruba individual | 44,674 | 73,180 | 0.72% | 0.00% | 5.25% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 2 | 8 | |
| panels 4 and 5 | 46,701 | 157,126 | 0.02% | 0.00% | 0.00% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% | 0 | 1 | |
| 1000K & 2200K | 1000K: transversions in 2 Yoruba ind. and in Altai Neand. | 364,079 | 590,775 | 0.00% | 0.00% | 6.89% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% | 1 | 2 |
| 2200K panel = 1000K panel + 1240K panel | 814,915 | 1,190,758 | 0.02% | 0.00% | 7.95% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% | 1 | 1 | |
| archaic asc. | transitions and transversions | 525,014 | 1,555,781 | 10.48% | 0.00% | 6.90% | 0.01% | 0.00% | 0.02% | 0.00% | 0.00% | 2 | 8 |
| transversions | 165,249 | 484,675 | 10.48% | 0.00% | 6.88% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 2 | 8 | |
| MAF | retaining sites with >5% global MAF or: | 2,129,201 | 2,511,335 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 2 |
| >5% MAF in Africans unadmixed with non-Africans | 2,045,769 | 3,231,875 | 1.03% | 0.00% | 6.93% | 0.00% | 0.02% | 0.01% | 0.00% | 0.00% | 2 | 2 | |
| >5% MAF in all Africans | 2,109,808 | 3,120,326 | 0.04% | 0.00% | 6.93% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% | 1 | 1 | |
| >5% MAF in Native Americans | 1,513,207 | 1,764,715 | 0.02% | 0.00% | 7.99% | 5.19% | 0.00% | 0.00% | 0.00% | 0.00% | 2 | 3 | |
| >5% MAF in Central Asians and Siberians | 1,843,262 | 2,150,675 | 0.02% | 0.00% | 7.97% | 0.00% | 0.24% | 0.01% | 0.00% | 0.00% | 1 | 2 | |
| >5% MAF in East Asians | 1,723,831 | 2,020,860 | 0.00% | 0.00% | 7.99% | 5.53% | 0.00% | 0.00% | 0.00% | 0.00% | 2 | 3 | |
| >5% MAF in Europeans | 1,885,336 | 2,192,571 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 2 | |
| >5% MAF in Middle Eastern groups | 2,018,884 | 2,306,319 | 0.01% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 1 | |
| >5% MAF in Papuans and Aboriginal Australians | 1,515,022 | 1,791,390 | 1.03% | 0.00% | 8.00% | 5.53% | 0.24% | 0.31% | 0.00% | 0.00% | 3 | 4 | |
| >5% MAF in South Asians | 1,908,459 | 2,235,024 | 0.00% | 0.00% | 7.97% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 2 | |
| AT/GC MAF | retaining AT/GC sites with >5% global MAF or: | 323,296 | 378,287 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 2 |
| AT/GC, >5% MAF in Africans unadmixed with non-Africans | 309,172 | 486,906 | 0.00% | 0.00% | 6.93% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 1 | |
| AT/GC, >5% MAF in all Africans | 319,053 | 470,070 | 0.00% | 0.01% | 6.93% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 1 | |
| AT/GC, >5% MAF in Native Americans | 229,939 | 266,113 | 0.00% | 0.00% | 7.97% | 6.11% | 0.05% | 0.32% | 0.00% | 0.00% | 2 | 3 | |
| AT/GC, >5% MAF in Central Asians and Siberians | 280,103 | 324,245 | 0.00% | 0.00% | 7.97% | 0.00% | 0.25% | 0.05% | 0.00% | 0.00% | 2 | 3 | |
| AT/GC, >5% MAF in East Asians | 261,857 | 304,567 | 0.00% | 0.00% | 7.99% | 0.00% | 0.00% | 0.32% | 0.00% | 0.00% | 1 | 2 | |
| AT/GC, >5% MAF in Europeans | 285,723 | 330,244 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 3 | |
| AT/GC, >5% MAF in Middle Eastern groups | 306,450 | 347,536 | 0.00% | 0.00% | 7.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 3 | |
| AT/GC, >5% MAF in Papuans and Aboriginal Australians | 230,124 | 272,093 | 1.03% | 0.00% | 8.00% | 5.53% | 0.24% | 0.32% | 0.00% | 0.00% | 3 | 4 | |
| AT/GC, >5% MAF in South Asians | 289,739 | 336,996 | 0.00% | 0.00% | 6.95% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 1 | 3 | |
| * 1) Mbuti, Baka, Laka, Fulani, Bantu Tswana 2) Khomani San, Bakola, Igbo, Mursi, Aari 3) Australian, Quechua, Mayan, Lezgin, French 4) Papuan, Chipewyan, Eskimo Naukan, Finnish, Sardinian 5) Karitiana, Cree, Eskimo Sireniki, Hungarian, Icelandic |
number of biased asc. = > | 6 | 1 | 33 | 9 | 1 | 0 | 1 | 0 | ||||
| number of biased asc., both metrics = > | 6 | 2 | 61 | 9 | 10 | 0 | 5 | 4** | |||||
| ** average number of biased ascertainments per population quintuplet | |||||||||||||