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Beja of Sudan: an intermediate position between Africans and non-Africans 2014
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[QUOTE]Originally posted by Ish Gebor: [QB] [QUOTE] [IMG]http://i63.tinypic.com/10cmfl2.jpg[/IMG] [i]Dataset preparation for population genetic analyses Genotypes were called in [b]GD13a at sites which overlapped those in the Human Origins dataset (Lazaridis et al.17, filtered as described in Jones et al.24)[/b] using GATK Pileup44.[/i] [b]Table S3. f3(X, GD13a; Dinka) where X represents a modern or ancient individual/population. Ancient individuals/populations are shown in bold. [/b] EBA: Early Bronze Age, MN: Middle Neolithic. Populations/individuals with the largest f3 values are shown. [/QUOTE] [QUOTE][b]The mitochondria of GD13a (91.74X) was assigned to haplogroup X,[/b] most likely to the subhaplogroup X2. Haplogroup X2 is present in modern populations from Europe, the Near East, Western and Central Asia, North [b]and East Africa[/b], Siberia, and North America (7). Haplogroup X2 has been associated with an early expansion from the Near East (7, 8) and has been found in early Neolithic samples from Anatolia (9), Hungary (10) and Germany (11). [/QUOTE] [QUOTE] S7. Outgroup f3 statistics show that GD13a shares the most genetic drift with Caucasus Hunter-gatherers We used outgroup f3-statistics to estimate the amount of shared drift between GD13a and contemporary populations. This was performed on the dataset described in section S6 using the qp3Pop program in the ADMIXTOOLS package (13). [b]We computed f3(X, GD13a; Dinka), where X represents a modern population and Dinka, an African population equally related to Eurasians, acts as an outgroup (Fig. S7).[/b] We also repeated this analysis where X represents ancient individuals/populations. Among the ancient populations, Caucasus hunter-gatherers (Kotias and Satsurblia) have the closest affinity to GD13a (Table S3), followed by other ancient individuals from Steppe populations from the Bronze age and modern populations from the Caucasus. […] The phenotypic attributes of GD13a are similar to the neighbouring Anatolian early farmers and Caucasus Hunter-Gatherers. Based on diagnostic SNPs, she had dark, black hair and brown eyes (see Supplementary). [b]She lacked the derived variant (rs16891982) of the SLC45A2 gene associated with light skin pigmentation but likely had at least one copy of the derived SLC24A5 allele (rs1426654) associated with the same trait. [/b] The derived SLC24A5 variant has been found in both Neolithic farmer and Caucasus Hunter-Gatherer groups5,15,24 suggesting that it was already at appreciable frequency before these populations diverged. Finally, she did not have the most common European variant of the LCT gene (rs4988235) associated with the ability to digest raw milk, consistent with the later emergence of this adaptation5,15,21. [/QUOTE]—M. Gallego-Llorente, R. Pinhasi et al. The genetics of an early Neolithic pastoralist from the Zagros, Iran [/QB][/QUOTE]
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