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Thread: Ancient DNA from North Africa (this time with formal stats)

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    Ancient DNA from North Africa (this time with formal stats)

    http://science.sciencemag.org/conten...cience.aar8380

    The previous paper about this just used fsts, which led to endless debates about interpretation. This time we have more unequivocal statements.

    North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
    Consistently, we find that all males with sufficient nuclear DNA preservation carry Y haplogroup E1b1b1a1 (M-78; table S16). This haplogroup occurs most frequently in present-day North and East African populations (18). The closely related E1b1b1b (M-123) haplogroup has been reported for Epipaleo- lithic Natufians and Pre-Pottery Neolithic Levantines (“Le- vant_N”) (16). Unsupervised genetic clustering also suggests a connection of Taforalt to the Near East. The three major components that comprise the Taforalt genomes are maxim- ized in early Holocene Levantines, East African hunter-gath- erer Hadza from north-central Tanzania, and West Africans (K = 10; Fig. 2. In contrast, present-day North Africans have smaller sub-Saharan African components with minimal Hadza-related contribution (Fig. 2.
    Also, we have work to do boys:

    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.
    Once the samples are out, qpGraph time.
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

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    It seems like there's some continuity between these guys and the Neolithic Moroccans that were released last year, from the Iberomaurisian to the Capsian, just like some of the old 20th century anthropologists said.

    What a week.
    Last edited by TuaMan; 03-15-2018 at 09:33 PM.

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    From the study:

    Fig. S7. A global PCA plot showing the genetic relatedness of Taforalt to worldwide populations. Taforalt (black filled circles), and other 937 ancient individuals from Africa and the Middle East (black symbols), are projected on the PCs constructed from the genetic variation in 178 global 938 present-day populations (colored symbols). Taforalt fall on an intermediate position between present-day North Africans and sub-Saharan (East) 939 Africans.

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    They're far from being "intermediate" between North and East Africans based solely on their SSA/non-SSA composition, especially without Ethiopian-highlanders and Sudanese-Arabs/Nubians in the PCA.

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    Can someone post details on the Y-DNA calls, if available?

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    Quote Originally Posted by rafc View Post
    Can someone post details on the Y-DNA calls, if available?
    From Rozenfeld's original post in the News thread:

    Code:
    Sample	mtDNA	Y-DNA
    TAF009	U6a6b	E1b1b1a1b1
    TAF010	U6a7b	E1b1b1a1
    TAF011	U6a7	E1b1b1a1
    TAF012	U6a7
    TAF013	U6a7b	E1b1b1a1
    TAF014	M1b	E1b1b1a1
    TAF015	U6a1b	E1b1b

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    Thank you, but aren't there more details available on tested SNP's?

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    Quote Originally Posted by blackflash16 View Post
    From Rozenfeld's original post in the News thread:

    Code:
    Sample	mtDNA	Y-DNA
    TAF009	U6a6b	E1b1b1a1b1
    TAF010	U6a7b	E1b1b1a1
    TAF011	U6a7	E1b1b1a1
    TAF012	U6a7
    TAF013	U6a7b	E1b1b1a1
    TAF014	M1b	E1b1b1a1
    TAF015	U6a1b	E1b1b
    Doesn't E1b1b1a1b1 = V27 or did the naming system change again?
    NW Somali + Eastern Oromo

    Eurogenes K13
    82.9% Somali + 17.1% Ethiopian_Wolayta @ 1.01
    90.5% Somali + 9.5% Ethiopian_Oromo @ 1.38
    96.2% Somali + 3.8% Ethiopian_Ari_cultivator


    My Father's K13
    94.5% Somali + 5.5% Ethiopian_Ari_cultivator @ 2.07
    82.1% Somali + 17.9% Ethiopian_Wolayta @ 2.22

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    Quote Originally Posted by drobbah View Post
    Doesn't E1b1b1a1b1 = V27 or did the naming system change again?
    E1b1b1a1b1 equals L618 since 2013: ISOGG 2013 Y-DNA Haplogroup E.
    But we can be sure only if see SNP names as they are used in the paper.

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    I never thought there'd be too many aDNA papers.

    There is a table of tested SNPs in the supplementary info (Table S16). There is M78 and a bunch at each level upstream of that. No details beyond most being M78. I expect they'll be cousins of E-M78 rather than an existing subclade, but hey, the mtDNA is basically the same as what the IAM (Morocco Neolithic) people had, and still exists in significant amounts in North Africa today.

    So now we have major branches of E-M35 at either end of North Africa, in both the Levant and Morocco, 13 000+ years ago. Looks like Lank is right about its North African origin.

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