Table 1. Polymorphisms for which the low-risk gene variant observed in Neanderthal and/or Denisovan is the ancestral allele.
Column headers: Nea = Neanderthal; Den = Denisovan; Chimp = Chimpanzee; Gor = Gorilla; Ust’-Ishim/Mal’ta (MA-1)/Anzick-1 = Siberian/Siberian/North-American pre-Holocene hunter-gatherer; NE1/BR2 = Neolithic/Bronze Age Hungarian individual; Saqqaq = Palaeo-eskimo; Aus = Aboriginal Australian. Cell shading: light grey = low-risk ancestral variant; dark-grey = high-risk derived variant.
| Gene | Function1) | Extant Humans | AncientHominins | Great Apes | Modern Humans | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Polymorphism | Low3) | High3) | Nea | Den | Chimp | Gor | Ust'-Ishim | MA-1 | Anzick-1 | NE1 | Saqqaq | BR2 | Aus | |||||||||||
| RefSNP Number | HGVS Name2) | (45 kya) | (24 kya) | (12 kya) | (7.2 kya) | (3.9 kya) | (3.2 kya) | (0.1 kya) | ||||||||||||||||
| AHR1 | Regulation | rs2066853 | p.Arg554Lys | A | G | A | A | A | A | A | G | A | G | G | G | G | ─ | |||||||
| rs2282885 | c.66-3946A>G | A | G | A | A | A | A | A | A | A | A | G | A | G | A | G | A | |||||||
| AHRR1 | Regulation | rs2292596 | p.Pro189Ala | C | G | C | C | C | C | C | G | C | G | C | G | C | G | C | G | C | G | |||
| CYP1A1 | Detox. 1 | rs4646903 | c.*1189T>C | T | C | T | T | T | T | T | ─ | T | C | T | T | T | C | C | ||||||
| rs1048943 | p.Ile462Val | A | G | A | A | A | A | A | A | A | G | A | A | A | G | A | ||||||||
| CYP1B1 | Detox. 1 | rs1056836 | p.Leu432Val | G | C | G | G | G | G | G | C | C | C | G | C | C | C | |||||||
| EPHX1 | Detox. 1 | rs1051740 | p.Tyr113His | T | C | T | T | T | T | T | C | T | T | C | T | C | T | T | ||||||
| EPHX2 | Detox. 1 | rs1042064 | c.*93T>C | C | T | C | C | C | C | C | T | C | T | T | C | T | T | |||||||
| GSTA4 | Detox. 2 | rs316133 | c.415-48C>G | G | C | C | G | G | G | G | ─ | G | G | G | G | ─ | ||||||||
| rs3756980 | c.139+176T>C | T | C | C | T | T | T | T | T | T | T | T | T | T | ||||||||||
| GSTM1 | Detox. 2 | - | Null4) | WT | Null | WT | WT | WT | WT | WT | WT | Null | WT | Null | WT | Null | ||||||||
| GSTP1 | rs1138272 | p.Ala114Val | C | T | C | C | C | C | C | C | C | C | C | C | C | |||||||||
| rs762803 | c.232+13C>A | C | A | C | C | C | C | C | A | C | C | A | A | C | C | C | ||||||||
| GSTT1 | Detox. 2 | - | Null4) | WT | Null | WT | WT | WT | WT | WT | WT | WT | Null?5) | Null | WT | Null | ||||||||
| NAT1 | Detox. 2 | c.*215A>T | T | A | T | A | T | Diff.6) | Del.6) | T | T | A | T | A | T | T | ─ | |||||||
| rs4986782 | p.Arg187Gln | G | A | G | G | G | G | G | G | G | G | G | G | ─ | ||||||||||
| rs5030839 | p.Arg187Ter | C | T | C | C | C | C | C | C | C | C | C | T | C | ─ | |||||||||
| rs56379106 | p.Arg64Trp | C | T | C | C | C | C | C | C | C | C | C | C | C | ||||||||||
| rs56318881 | p.Arg33Ter | C | T | C | C | C | C | C | C | C | C | C | C | C | ||||||||||
| rs56172717 | p.Asp251Val | A | T | A | A | A | A | A | A | A | A | A | A | ─ | ||||||||||
| NAT2 | Detox. 2 | rs1801280 | p.Ile114Thr | T | C | T | T | T | T | T | T | T | T | C | T | T | T | |||||||
| rs1799930 | p.Arg197Gln | G | A | G | G | G | G | G | G | G | A | G | G | A | ─ | |||||||||
| CAT1 | Anti-ox. | rs1001179 | c.-330C>T | C | T | C | C | C | C | C | T | T | C | C | C | C | C | |||||||
| SOD2 | Anti-ox. | rs4880 | p.Ala16Val | C | T | C | C | C | C | C | T | T | C | T | C | C | T | C | T | |||||
| rs5746136 | c.*441G>A | G | A | G | G | G | G | G | A | A | G | G | G | G | G | |||||||||
| XPA1 | Repair | rs1800975 | c.-4A>G | G | A | G | G | G | G | G | A | G | G | A | G | A | G | G | A | G | A | |||
1 Detox 1 = Detoxification phase 1; Detox 2 = Detoxification phase 2; Anti-ox = Oxidative stress management; Regulation = Regulation of detoxification gene expression; Repair = Repair of DNA damage.
2 SNP nomenclature as recommended by the Human Genome Variation Society (HGVS) (http://www.hgvs.org/mutnomen/recs.html).
3 Allele associated with a relatively low-risk, respectively, high-risk of adverse reproduction effects based on epidemiological or biochemical studies (details in S1 Text of the Supporting Information).
4 Null variant has a deletion of the entire gene sequence; WT = wild-type allele.
5 Most likely Null for GSTT1, since only reads observed in intron regions, not in exon regions.
6 This A/T polymorphism is the 3'-terminal base of a tandem repeat of four AAT elements that is found full length in modern humans, Neanderthals, and the Denisovan, but is variable in length in chimpanzees (0–4 AAT elements, following position 14,328,777 in assembly CSAC 2.1.4/panTro4). Only the full length 4 x AAT variant encompasses the position corresponding to human polymorphism rs1057126. Diff. indicates that some of the PanMap chimpanzees are clearly or possibly (indicated by? in S2 Table) heterozygous for variants encompassing 0–4 AAT elements. Del. indicates that gorilla misses all 4 AAT elements (= 0 x AAT).