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Thread: [Pre-print] Chabu (Modern HG from SW Ethiopia)

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    [Pre-print] Chabu (Modern HG from SW Ethiopia)

    Source: Biorxiv

    Hunter-gatherer genomes reveal diverse demographic trajectories following the rise of farming in East Africa

    Abstract

    A major outstanding question in human prehistory is the fate of hunting and gathering populations following the rise of agriculture and pastoralism. Genomic analysis of ancient and contemporary Europeans suggests that autochthonous groups were either absorbed into or replaced by expanding farmer populations. Many of the hunter-gatherer populations persisting today live in Africa, perhaps because agropastoral transitions occurred later on the continent. Here, we present the first genomic data from the Chabu, a relatively isolated and marginalized hunting-and-gathering group from the Southwestern Ethiopian highlands. The Chabu are a distinct genetic population that carry the highest levels of Southwestern Ethiopian ancestry of any extant population studied thus far. This ancestry has been in situ for at least 4,500 years. We show that the Chabu are undergoing a severe population bottleneck which began around 40 generations ago. We also study other Eastern African populations and demonstrate divergent patterns of historical population size change over the past 60 generations between even closely related groups. We argue that these patterns demonstrate that, unlike in Europe, Africans hunter-gatherers responded to agropastoralism with diverse strategies.




    Last edited by blackflash16; 01-12-2019 at 08:07 PM.

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    Ethiopia is more diverse than I thought originally, interesting.

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    Interesting! Chabu even appear to lack the minor Afroasiatic-related ancestry detected in Mota in the ADMIXTURE analysis.

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    Quote Originally Posted by Lank View Post
    Afroasiatic-related ancestry
    The yellow Afroasiatic-related cluster seems unstable to me due to the lack of more North African and Arabian samples (the # of samples has influence on the final result). Only using Iberians (without Arabians) as an outgroup was kind of lazy on their part.

    Source:

    A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092366/

    ''Case Study 3: Worldwide human data

    An important consideration in any STRUCTURE analysis is sample size. This is vividly illustrated by the analyses of Friedlaender et al.18 who augmented a pre-existing microsatellite data set from a worldwide collection by a similar number of samples from Melanesia, in order to study genetic relationships between Melanesians, for which purpose their sample was excellent. For K = 2, their analysis infers Papua New Guinea (PNG) as one ancestral population and Western Eurasia and Africa as the other, with East Asians being represented as genetic mixtures (Fig. 5b). This analysis differs from that of Rosenberg et al.19 for K = 2 who had only a small number of Melanesians in their sample, and who found Native Americans rather than Melanesians to be the unadmixed group (Fig. 5f). For K = 6, both models distinguish between all 5 continental groups (Americans, Western Eurasians, Africans, East Asians, and Oceanians). Rosenberg et al. split Native American groups into two ancestral populations while Friedlaender et al. infer that Melanesians have two ancestral populations (Fig. 5a). Rosenberg et al.4 also found the Kalash, an isolated population in Pakistan, to be the sixth cluster.''

    Also, this image is illustrative:

    Last edited by NetNomad; 01-13-2019 at 07:05 PM.

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    Quote Originally Posted by NetNomad View Post
    The yellow Afroasiatic-related cluster seems unstable to me due to the lack of more North African and Arabian samples (the # of samples has influence on the final result). Only using Iberians (without Arabians) as an outgroup was kind of lazy on their part.
    You're right. But you might at least expect the overall results to reflect the most basic differences, such as the Eurasian vs. African affinity of the components. Chabu form one of the poles of variation in the PCA as well.

    Another note: The Shekkacho (Omotic) samples are quite similar to their Oromo neighbors. Shekkacho have the highest Y-DNA J levels (52%) found in Ethiopia so far, followed by the closely related Kefa people. It would be interesting to see the main J subclades found in these groups.
    Last edited by Lank; 01-13-2019 at 08:15 PM.

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    Is that "Afro-Asiatic" component similar to the alleged "Ethio-Somali" compenent? It appears to behave similarly.

    On another note, it seems like the the South Sudan/Sudan/Ethiopia/Kenya border regions are full of genetically distinct people groups. The Nilo-Saharan "language family" is looking less credible on a genetic and linguistic level (at least in Ethiopia).

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    Quote Originally Posted by pgbk87 View Post
    Is that "Afro-Asiatic" component similar to the alleged "Ethio-Somali" compenent? It appears to behave similarly.
    This looks pretty much exactly like Hodgson et al. but just with some new samples, really. It's a pretty nice result seeing the SW Ethiopian component appear in Horners, Somalis included, then suddenly not appear in areas like Sudan. Only the Beni-Amer Beja who are known to intermingle with Tigres show it. Be more interesting to toy with all these samples using something like nMonte, though.
    فار عارابإ آ واجإب اه

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    Interesting case! Usually, we need ancient and ghost populations because a population outside modern variation is needed. Here, the living Chabu are forming a pole of the variation, at the expense of Mota.
    Paternal Y-DNA haplogroup: E-M35>E-Z827>L19>M81>M183
    Maternal [grandfather] Y-DNA: E-M35>E-Z827>L19>M81>M183>PF2477>PF2546
    >Mz90>PF6794>PF6789
    Hidden Content

    Lactase Persistence (LP)
    13910: TT (rs4988235 AA)
    22018: AA (rs182549 TT)

    (my mother's LP: same results)

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    Interesting case! Usually, we need ancient and ghost populations because a population outside modern variation is needed. Here, the living Chabu are forming a pole of the variation, at the expense of Mota.
    Paternal Y-DNA haplogroup: E-M35>E-Z827>L19>M81>M183
    Maternal [grandfather] Y-DNA: E-M35>E-Z827>L19>M81>M183>PF2477>PF2546
    >Mz90>PF6794>PF6789
    Hidden Content

    Lactase Persistence (LP)
    13910: TT (rs4988235 AA)
    22018: AA (rs182549 TT)

    (my mother's LP: same results)

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    Fascinating stuff. I looked up the Chabu. The nature of their language is controversial; some think it's an isolate while others say it's Nilo-Saharan. In any case, physically they resemble the Hadza to my eyes, which makes sense given their admixture results. I guess the purple component (maximized in Mota) is probably ~3/4 Ancient East African HG (roughly Dinka-like) + ~1/4 Southern African HG (San-like).

    Notice that the Sudanese Arabs and Nubians have a lot of that yellow [Afro-Asiatic] "Horner" component, but the Nilotes don't. I really can't wait for ancient DNA from Nubia. I intuit that the West Eurasian admixture in the region predates the Arabization of NE Africa, and that the inhabitants of Nubia and North Sudan were at one point similar to Horn Africans, just with some extra "blue" Nilotic admixture (from hypothetical Nubian language bearers) and probably "green" Egyptian-related admixture, though I suppose some of the latter could have indeed come from the Arabs. Unlike the Nilotes, many NE African groups with the blue component don't have any "green" West African-related admixture, which suggests that the Nilotes were possibly affected by the Bantu migration (with the Nuer being the least affected). Any thoughts?
    Last edited by Michalis Moriopoulos; 01-27-2019 at 06:49 PM.
    Ελευθερία ή θάνατος.

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