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Some samples went as high as 40 percent. Many were had as much sub saharan as me about 22.5 or 25 percent.
We consistently find positive f4 values when NE2 are Natufian/Levant_N and NE1 are other populations (Z = 2.2-11.0 standard error (SE); table S6). Congruent to the outgtoup-f3 results, Natufian shows higher affinity to Taforalt than does Levant_N (Z = 2.2 SE, table S6). This indicates that the early Holocene Levantine populations, overlapping with or postdating our Taforalt individuals by up to 6,000 years (16), are most closely related to Taforalt among Near Eastern populations. Next, we tested if the Taforalt individuals have sub-Saharan African ancestry by calculating f4(Chimpanzee, Test; Natufian, Taforalt). We observe significant positive f4 values for all sub-Saharan African and significant negative values for all Eurasian populations, supporting a substantial contribution from sub-Saharan Africa (Fig. 3B). West Africans, such as Mende and Yoruba most strongly pull out the sub-Saharan African ancestry in Taforalt (Fig. 3B and figs. S15 and S16). We investigated if two first-hand proxies, Natufians and West Africans, are sufficient to explain the Taforalt gene pool or whether a more complex admixture model is required. We thus tested if Natufians could be a sufficient proxy for the Eurasian ancestry in Taforalt without explicit modeling of its African ancestry (fig. S18). This is inspired by proposed archaeological connections between the Iberomaurusian and Upper Paleolithic cultures in southern Europe, either via the Strait of Gibraltar (19) or Sicily (20). If this connection is true, both the Upper Paleolithic European and Natufian ancestries will be required to explain the Taforalt gene pool. For our admixture modeling with qpAdm (16), we chose outgroups that can distinguish sub-Saharan African, Natufian and Paleolithic European ancestries but are blind to differences between sub-Saharan African lineages (11). A two-way admixture model, comprising Natufian and a sub-Saharan African population, does not significantly deviate from our data (χ2 p ≥ 0.128) with 63.5% Natufian and 36.5% sub-Saharan African ancestry on average (table S8). Adding Paleolithic European lineages as a third source only marginally increased the model fit (χ2 p = 0.019 to 0.128; table S9). Consistently, using qpGraph (21) we find that a mixture of Natufian and Yoruba reasonably fits the Taforalt gene pool (|Z| ≤ 3.7; fig. S19 and table S10). Adding gene flow from Paleolithic Europeans does not improve the model fit and provides an ancestry contribution estimate of 0% (fig. S19). We thus find no evidence of gene flow from Paleolithic Europeans into Taforalt within the resolution of our data.
We further characterized the sub-Saharan African-related ancestry in the Taforalt individuals using f4 statistics in the form f4(Chimpanzee, African; Yoruba/Mende, Natufian). We find that Yoruba/Mende and Natufians are symmetrically related to two deeply divergent outgroups, a 2000 yBP ancient South African (“aSouthAfrica”) and Mbuti Pygmy, respectively (|Z| ≤ 1.564 SE; table S11). Since f4 statistics are linear under admixture, we expect Taforalt not to be any closer to these outgroups than Yoruba or Natufians if the two-way admixture model is correct. However, we find instead that Taforalt is significantly closer to both outgroups (“aSouthAfrica” and “Mbuti”) than any combination of Yoruba and Natufians (Z ≥ 2.728 SE; Fig. 4). A similar pattern is observed for the East African outgroups Dinka, Mota and Hadza (table S11 and fig. S20). These results can only be explained by Taforalt harboring an ancestry that contains additional affinity with South, East and Central African outgroups. None of the present-day or ancient Holocene African groups serve as a good proxy for this unknown ancestry, because adding them as the third source is still insufficient to match the model to the Taforalt gene pool (table S12 and fig. S21). However, we can exclude any branch in human genetic diversity more basal than the deepest known one represented by aSouthAfrica (4) as the source of this signal: it would result in a negative affinity to aSouthAfrica, not a positive one as we find (Fig. 4). Both an unknown archaic hominin and the recently proposed deep West African lineage (4) belong to this category and therefore cannot explain the Taforalt gene pool
