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Thread: Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

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    Default Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

    Juan L. Rodriguez-Flores1,8, Khalid Fakhro2,3,8, Francisco Agosto-Perez1,4, Monica D. Ramstetter4, Leonardo Arbiza4, Thomas L. Vincent1, Amal Robay3, Joel A. Malek3, Karsten Suhre5, Lotfi Chouchane3, Ramin Badii6, Ajayeb Al-Nabet Al-Marri6, Charbel Abi Khalil3, Mahmoud Zirie7, Amin Jayyousi7, Jacqueline Salit1, Alon Keinan4, Andrew G. Clark4, Ronald G. Crystal1,9 and Jason G. Mezey1,4,9

    An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.

    Previous analyses of the populations of the Arabian Peninsula (Hunter-Zinck et al. 2010; Alsmadi et al. 2013) have found three distinct clusters that reflect primary ancestry: Q1 (Bedouin); Q2 (Persian-South Asian); and Q3 (African) (Omberg et al. 2012). By assessment of medical records and ancestry-informative SNP genotyping (Supplemental Fig. 2), a sample of 108 purportedly unrelated individuals was selected for sequencing, including 60 Q1 (Bedouin), 20 Q2 (Persian-South Asian), and 20 Q3 (African), as well as 8 Q0 (Subpopulation Unassigned) that could not be cleanly placed in one of these three groups (Supplemental Table I). Each of these genomes was sequenced to a median depth of 37× (minimum 30×) by Illumina technology, identifying a total of 23,784,210 SNPs (see Methods, Supplemental Table II).

    An analysis of inbreeding for these remaining individuals showed the Q1 (Bedouin) to have a more positive inbreeding coefficient than most of the non-admixed 1000 Genomes (The 1000 Genomes Project Consortium 2012) populations (Supplemental Table IV; Supplemental Fig. 4), consistent with the known inbreeding of this group (Hunter-Zinck et al. 2010; Omberg et al. 2012); although we also found the Q1 (Bedouin) to be less inbred than many small and/or isolated populations worldwide represented in the Human Origins samples (Lazaridis et al. 2014) (Supplemental Table V; Supplemental Table VI; Supplemental Fig. 4). The Q2 (Persian-South Asian) had a positive, but slightly lower, inbreeding coefficient than the Q1 (Bedouin). In contrast, the Q3 (African) had a non-negative coefficient that reflects known admixture with African populations (Hunter-Zinck et al. 2010; Omberg et al. 2012).

    These analyses reproduced the population clustering observed previously (Hunter-Zinck et al. 2010; Omberg et al. 2012), with the Q1 (Bedouin) closest to Europeans, the Q2 (Persian-South Asian) between Q1 (Bedouin) and Asians, and the Q3 (African) closest to African populations. A plot of just the Middle Eastern populations on the principal components also showed clustering as expected, with the Q1 (Bedouin) clustering with previously sampled Bedouins and Arabs, Q2 (Persian-South Asians) with Iranians, and Q3 (African) outside of the Middle Eastern cluster (data not shown) (Fig. 1B).


    (As usual, Palestinians, Egyptians and Bedouins cluster very close together)

    We also analyzed the relative ratios of X-linked and autosomal (X/A) diversity in nongenic regions of the female Q1 (Bedouin), Q2 (Persian-South Asian), and Q3 (African) genomes compared to females in African populations of the 1000 Genomes Project (Supplemental Table IX). The relative X/A ratios of both the Q1 (Bedouin) and Q2 (Persian-South Asian) to African populations were slightly higher than when comparing European to African populations (Gottipati et al. 2011; Arbiza et al. 2014). This could indicate a slightly less extreme set of bottleneck events encountered since the out-of-Africa migrations by the direct ancestors of the Q1 (Bedouin) and Q2 (Persian-South Asian) compared to the bottlenecks encountered by the direct ancestors of Europeans. The relative X/A diversity ratios of Q3 (African) to African populations were closer to one, consistent with the known African admixture of this subpopulation (Omberg et al. 2012).

    We next analyzed the full complement of autosomal polymorphisms for signals of ancient bottlenecks by applying the pairwise sequential Markov coalescent (PSMC) (Fig. 3; Li and Durbin 2011). This analysis showed that the Q1 (Bedouin) and Q2 (Persian-South Asian) had clear hallmarks of a bottleneck event, with effective population size hitting a trough in the range of 100,000 to 30,000 yr ago with a minimum at ∼60,000 yr ago. This same pattern is observed for a European individual from the 1000 Genomes Project and is consistent with what has been observed in other non-African human genomes using the pairwise sequential Markov coalescent, as well as related methods (Gronau et al. 2011; Fu et al. 2014; Schiffels and Durbin 2014). These data, therefore, point to the ancestors of Q1 (Bedouin) and Q2 (Persian-South Asian) as having migrated out of Africa at the same time as the ancestors of other non-African populations (Henn et al. 2012). Although PSMC estimates in the more recent past tend to have larger confidence intervals (Li and Durbin 2011), the Q1 (Bedouin) do appear to have a lower population size than the Q2 (Persian-South Asian) in the region <30,000 yr ago, consistent with high levels of inbreeding in the Q1 (Bedouin) (Hunter-Zinck et al. 2010; Sandridge et al. 2010; Mezzavilla et al. 2015). For the Q3 (African), the median effective population size was more similar to an African individual from the 1000 Genomes Project in the range 100,000 to 30,000 yr ago, consistent with Sub-Saharan African ancestry that is relatively recent (Omberg et al. 2012).



    The ADMIXTURE analysis identified K = 12 ancestral populations as having the lowest cross-validation error (Supplemental Fig. 7A). At this level of resolution, the Q1 (Bedouin) had a high average (84%) proportion of ancestry that was also present in the Human Origins Bedouin B population at a high average proportion (93%) (Supplemental Fig. 7B,C), in which this same ancestry was also shared with Saudis, and at lower levels among other Middle Eastern populations. This ancestry therefore appears to be the signal of an indigenous Arab ancestral population. The Bedouin A population also shared this ancestry but at a lower average proportion (45%) and appeared to be more admixed overall. The Q2 (Persian-South Asian) shared a large proportion (45% on average) of ancestry that dominates in Iranians (46% on average), consistent with a Persian ancestral population (Omberg et al. 2012). The Q3 (African) shared the majority of ancestry with African populations as expected and were considerably admixed overall, again consistent with the known history of this subpopulation (Supplemental Fig. 7A; Omberg et al. 2012).

    The higher Neanderthal ancestry in the Q1 (Bedouin) Qatari compared to African populations places the divergence of ancestral Arabs after the out-of-Africa bottleneck. Given the current evidence of the geographic range of Neanderthal populations stretching from Europe and the Mediterranean through Northern and Central Asia (Fu et al. 2014; Hershkovitz et al. 2015), the lower Neanderthal Ancestry in the Q1 (Bedouin) Qatari compared to populations within the ancestral Neanderthal range is also consistent with an early divergence of the ancestors of indigenous Arabs from other lineages that populated Asia and Europe. Yet, since the Neanderthal admixture in the Q1 (Bedouin) cannot be entirely explained by admixture with Europeans, this indicates there was some admixture between Neanderthals and ancestors of the Q1 (Bedouin) in the region of the Arabian Peninsula.

    Given that the Q1 (Bedouin) have the greatest proportion of Arab genetic ancestry measured in contemporary populations (Hodgson et al. 2014; Shriner et al. 2014) and are among the best genetic representatives of the autochthonous population on the Arabian Peninsula, these two conclusions therefore point to the Bedouins being direct descendants of the earliest split after the out-of-Africa migration events that established a basal Eurasian population (Lazaridis et al. 2014). This is also consistent with the majority of Q1 (Bedouin) being able to trace a significant portion of their autosomal ancestry through lineages that never left the peninsula after the out-of-Africa migration events since such deep ancestry would not be expected if the entire Arabian Peninsula population had been reestablished from Africa or a non-African population at a later point.


    The basal position of the Q1 (Bedouin) also has interesting implications for theories about the frequency, timing, and path of major migration waves that established populations in Asia and Europe (Shi et al. 2008; Lazaridis et al. 2014; Shriner et al. 2014). A few isolated Asian populations were previously suspected to be descendants of a separate out-of-Africa migration wave based on Y Chromosome data (Hammer et al. 1998; Shi et al. 2008). Yet, distinct out-of-Africa migration events or separate migration waves emanating from the Arabian Peninsula into Europe and West Asia would be expected to place Bedouins/Europeans and Asians on separate branches of a pairwise clustering tree, distinct from our finding that places the Q1 (Bedouin) as direct descendants of the earliest lineage that split from the ancient non-African population.


    A demographic scenario consistent with the evidence presented here is that the population ancestral to the Q1 (Bedouin) migrated out of Africa, and a subset of this population remained in the peninsula until the present day, while a second subset of this population migrated onward and colonized Eurasia. This migration scenario implies the signal of the same bottleneck would be present in all non-African populations, which has been observed thus far in coalescent analysis of contemporary non-African populations (Gronau et al. 2011; Fu et al. 2014; Schiffels and Durbin 2014) and for an anatomically modern human who lived 45,000 yr ago (Fu et al. 2014). This is also consistent with the recent discovery of another anatomically modern human who lived 55,000 yr ago just northeast of the Arabian Peninsula that had morphological features similar to European peoples (Hershkovitz et al. 2015), where this individual could have been a descendant of the basal Eurasian population that remained on the peninsula. Under this migration scenario, although other waves of migration may have occurred, the descendants of these alternative waves either left no descendants or were integrated into the dominant populations.

    Full study here --> http://genome.cshlp.org/content/26/2/151.full

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    Another good find.
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    Quote Originally Posted by Longbowman View Post
    Another good find.
    What's your opinion on it though?

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