Y-DNA Haplogroup E: Basal Eurasian Lineage

The hypothesis that the first Eurasian populations were established on the Arabian Peninsula and that contemporary indigenous Arabs are direct descendants of this ancient population is supported by two major conclusions derived from the combined evidence of this study. First, the analysis results for X/A diversity, the pairwise sequential Markov coalescent, genome-wide admixture, timing of African admixture, local admixture deconvolution, Neanderthal admixture, and application of TreeMix, support the inference that the Q1 (Bedouin) can trace the bulk of their ancestry back to the out-of-Africa migration events. Second, the combination of lower levels of Neanderthal admixture in the Q1 (Bedouin) than European/Asian populations and the outgroup position of the Q1 (Bedouin) compared to non-Africans in the pairwaise similarity clustering of high-density variants measured genome-wide, place the Q1 (Bedouin) as being the most distant relatives of other contemporary non-Africans. 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.



Given the complex history of migration patterns to and from European populations, and the complicated patterns of isolation and intra- and inter-marriage of the indigenous Bedouin populations (Hunter-Zinck et al. 2010; Sandridge et al. 2010), it is not surprising that among the Q1 (Bedouin) are individuals who retain an autosomal signal of being the most distant relatives of non-Africans, while population-level clustering based on migration-shifted allele frequencies places the Q1 (Bedouin) closer to Europeans. 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.



Beyond the importance for disentangling human migration history, an early split of Eurasian lineages in the Arabian Peninsula has implications for the study of disease genetics for indigenous people in the region. For example, for a disease such as type 2 diabetes that has a prevalence of >18% in the Qatari population, associated genetic variants would not a priori be expected to be the same as those discovered in Europeans, when considering that indigenous Arabs are able to trace a significant portion of their ancestry back to ancient lineages on the Arabian Peninsula. More generally, this suggests that for any genome-wide association study (GWAS) or rare variant association study (RVAS) of diabetes or other complex diseases in Qatar, inference of deep ancestry in the Arabian Peninsula, using rare variation sampled by genome or exome sequencing, is critical for identifying new disease risk genes. Given the dearth of next generation sequencing studies conducted in Middle Eastern and Arab populations, these results indicate that a considerable number of variants that make important contributions to disease risk in these populations are yet to be discovered.

This study is the first analysis of Arabian Peninsula migration making use of deeply sequenced genomes from a sample of unrelated inhabitants of the peninsula. Although there have been many analyses of Chr Y and mtDNA sampled from Arab individuals (Abu-Amero et al. 2007, 2008, 2009; Rowold et al. 2007), and there have been previous surveys of genetic variation of people within the peninsula and immediately surrounding regions conducted with genotyping arrays (Behar et al. 2010; Hunter-Zinck et al. 2010; Alsmadi et al. 2013; Markus et al. 2014; Shriner et al. 2014) and deep exome sequencing (Rodriguez-Flores et al. 2012, 2014; Alsmadi et al. 2014), and by individual high-coverage genomes (Alsmadi et al. 2014; John et al. 2015), the sample of rare and common genetic variation throughout the genome in our sample provides a far more complete picture of how both ancient and recent migration events have contributed to the genetics of the modern peoples of the Arabian Peninsula. For understanding how human migration history has determined the structure of modern genomes, our identification of a cluster of Q1 (Bedouin) as the most distant ancestors of non-Africans is of considerable interest, particularly given the suspected route of migration out of Africa and into the surrounding continents. The possibility that the Q1 (Bedouin) are descendants of the first Eurasians provides an additional piece of the puzzle concerning ancient migration routes and the establishment of ancient non-African populations.

Genome Res. 2016. 26: 151-162

A Robust Statistic to Estimate Neandertal Ancestry.
The recent availability of a second high-coverage Neandertal genome allows us to estimate Neandertal ancestry using two Neandertals—an individual from the Altai Mountains, the so-called “Altai Neandertal” (23) and an individual from the Vindija Cave in Croatia, the so-called “Vindija Neandertal” (13). Specifically, we can estimate the proportion of ancestry coming from the Vindija lineage into a modern human (X) using the Altai Neandertal as a second Neandertal in an f4-ratio calculated as f4(Altai, Chimp; X, African)/f4(Altai, Chimp; Vindija, African), which we refer to as a “direct f4-ratio” (Fig. 1C and SI Appendix, Fig. S1). Note that unlike the indirect f4-ratio described previously, the f4-ratio in this formulation does not make assumptions about deep relationships between modern human populations (Fig. 1C and SI Appendix, Fig. S1). Instead, it assumes that any Neandertal population that contributed ancestry to X formed a clade with the Vindija Neandertal. Recent analyses showed that this is the case for all non-African populations studied to date, including the ancient modern humans in this study (13, 24). When calculated on the simulations described above, we find that the direct f4-ratio is more robust than the indirect f4-ratio (Fig. 2). In fact, its temporal trajectory always closely matches the true simulated Neandertal ancestry trajectory, regardless of the specific parameters of gene flow between non-Africans and Africans (Fig. 2). We note that gene flow from West Eurasians into Africans, which introduces introgressed Neandertal alleles into Africa, produces a slight underestimate of Neandertal ancestry in all samples (Fig. 2A). This is in agreement with empirical direct f4-ratio estimates, which vary depending on the African population used in the calculation, with African populations known to carry West Eurasian ancestry (e.g., Mozabite, Saharawi) (17, 25) generating the lowest estimates (SI Appendix, Fig. S4). Crucially, when we use the direct f4-ratio to estimate the trajectory of Neandertal ancestry in ancient and present-day Europeans, we observe nearly constant levels of Neandertal ancestry over time (Fig. 1A, points and solid line) and find that a null model of zero slope can no longer be rejected (Fig. 1A, P = 0.36, estimated via resampling as described in SI Appendix, section S1).

We note that these estimates are based on a relatively small number of individuals, especially for older time points, and that the CIs are wide. For example, we cannot reject a linear decline in Neandertal ancestry of approximately half a percent over the timespan of this dataset (95% CI −0.51–0.37%). Additionally, these analyses are performed on SNPs that were ascertained largely in present day individuals. To examine the effects of such ascertainment, we split the dataset based on the ascertainments used and recalculated the direct and indirect f4-ratios on each of the subsets (SI Appendix, Fig. S5). Although the slopes show some variability, in all but one ascertainment subset the direct f4-ratio cannot reject a slope of 0, whereas the indirect f4-ratio consistently rejects a slope of 0, suggesting that these results are robust to the effects of ascertainment (SI Appendix, Fig. S5). In addition to calculating direct f4-ratio estimates, we estimated Neandertal ancestry proportions using the qpAdm method (26) and obtained similar results (null model of zero slope using Neandertal ancestry point estimates cannot be rejected with P = 0.17).

Our observation that there has been no change in Neandertal ancestry over the past 45,000 y has several implications for our understanding of the fate of Neandertal DNA in modern humans. First, it constrains the timescale during which selection could have significantly affected the average genome-wide Neandertal ancestry in modern humans, an issue addressed below in more detail. Second, a previous analysis of a 40 ky old individual (“Tianyuan”) from East Asia applied the indirect f4-ratio statistic to estimate his Neandertal ancestry proportion at 5% (27). When we apply the direct f4-ratio statistic for this individual, we arrive at a value of ∼2.1% (using Dinka as the African group in the calculation). Third, it has consequences for the so-called “dilution” hypothesis, which suggests that lower levels of Neandertal ancestry in Europeans compared with East Asians can be explained by dilution of Neandertal ancestry in Europeans due to admixture with a hypothetical Basal Eurasian population that carried little to no Neandertal ancestry (19, 28). Previous studies have found Basal Eurasian ancestry in all modern and some ancient Europeans [in this study, four ancient individuals show evidence of Basal Eurasian ancestry: Satsurblia (15 kya), Kotias (10 kya), Ranchot88 (10 kya), and Stuttgart (8 kya), SI Appendix, Fig. S6] (8, 19). Our finding that there is no ongoing decline in Neandertal ancestry in Europeans suggests that Neandertal ancestry in Europe has not been diluted in a significant way by gene flow from Basal Eurasians. Specifically, we find no difference in Neandertal ancestry in European individuals with and without Basal Eurasian ancestry (direct f4-ratio mean 2.31% vs. 2.38%, respectively; P = 0.36). However, given the small number of relevant samples we also cannot exclude that there could be up to 13% less Neandertal ancestry in individuals with Basal Eurasian ancestry, or as much as 6% more Neandertal ancestry in individuals without Basal Eurasian ancestry (95% CI).

In contrast, we do find that present-day Near Easterners carry significantly less Neandertal ancestry than Europeans (direct f4-ratio mean 2.03% vs. 2.33%; P = 0.001; SI Appendix, Fig. S7A). Furthermore, present-day populations in the Near East show even stronger signals of admixture with a deeply divergent modern human lineage than observed in the rest of West Eurasians (SI Appendix, Fig. S7B), suggesting that they carry additional ancestry components that are not present in Europe and that could potentially contribute to lower Neandertal ancestry in the Near East. We note, however, that a simple model of admixture from Africa into Near East would be expected to produce a similar f4 statistics difference between Near East and the rest of West Eurasia and could also explain lower values of Neandertal ancestry in this population.

Long-Term Dynamics of Selection Against Introgressed DNA.
Our observation that Neandertal ancestry levels did not significantly decrease from ∼45,000 y ago until today is seemingly at odds with the hypothesis that lower effective population sizes in Neandertals led to an accumulation of deleterious alleles, which were then subjected to negative selection in modern humans (3, 8⇓–10). To investigate the expected long-term dynamics of selection against Neandertal introgression under this hypothesis, we simulated a model of the human genome with empirical distributions of functional regions and selection coefficients, extending a strategy previously applied by Harris and Nielsen (6). We simulated modern human and Neandertal demography, including a low long-term effective population size (Ne) in Neandertals (Neandertal Ne = 1,000 vs. modern human Ne = 10,000) and 10% introgression at 55 kya (2,200 generations ago, assuming generation time of 25 y). To track the changes in Neandertal ancestry following introgression, we placed fixed Neandertal–human differences as neutral markers, both outside regions that accumulated deleterious mutations (to study the effect of negative selection on linked genome-wide neutral Neandertal variation) as well as within regions directly under selection (to track the effect of negative selection itself) (Fig. 3A).



Fig. 3.
Simulations of selection against Neandertal ancestry. (A) Deleterious mutations (lightning bolts) accumulate in realistically distributed exonic sequence in modern humans and Neandertals. These regions accumulate additive, deleterious mutations, using a mutation rate of 10−8 per base pair per generation. To track the dynamics of Neandertal ancestry over time, neutral Neandertal markers are placed within (blue dots) and between (red dots) exons on all Neandertal chromosomes before introgression. (B) Simulated Neandertal ancestry proportions across 55 ky, in exonic and nonexonic sequence, averaged over 20 simulation replicates. Empirical observations from Fig. 1A are shown for comparison. Initial introgression levels were simulated at 10%. (C) Depletion of simulated Neandertal ancestry at neutral markers over time as a function of distance to regions under selection. Markers in bin 0 are those falling within exons; bins 1–5 represent quintiles of distance to the nearest exon. (D) Changes in frequencies of neutral Neandertal markers and deleterious Neandertal mutations over time, starting from generation 200. Each line shows average allele frequency changes over one simulation replicate. Black lines show smooth fits of these averages over 20 replicates.


Similar to Harris and Nielsen (6), we observed abrupt removal of Neandertal alleles from the modern human population during the first ∼10 generations after introgression, followed by quick stabilization of Neandertal ancestry levels (Fig. 3B). Compared with empirical estimates of Neandertal ancestry, we find a better fit between these simulations and the direct f4-ratio estimate than with the indirect f4-ratio estimate, suggesting that our direct Neandertal ancestry estimates are consistent with theoretical expectations of genome-wide selection against introgression (Fig. 3B). Specifically, simulations show −0.004% change in Neandertal ancestry over 45 ky; in the empirical data this slope is not rejected using the direct f4-ratio (P = 0.29), but is significantly different from the indirect f4-ratio (P < 0.001).

Because many factors can potentially influence the efficacy of negative selection, and no model fully captures all of these, we next sought to determine whether there is a combination of model parameters that could potentially lead to long-term continuous removal of Neandertal ancestry over time. Surprisingly, we failed to find a model which would produce a significant decline over time, although we tried by: (i) decreasing the long-term Neandertal Ne before introgression (making purifying selection in Neandertals even less efficient), (ii) increasing the Ne of modern humans after introgression (i.e., increasing the efficacy of selection against introgressed alleles), (iii) artificially increasing the deleteriousness of Neandertal variants after introgression (approximating a “hybrid incompatibility” scenario), (iv) simulating mixtures of dominance coefficients, or by (v) increasing the total amount of functional sequence (thereby increasing the number of accumulated deleterious variants in Neandertals and modern humans) (SI Appendix, Figs. S9–S13). Varying these factors primarily affected the magnitude of the initial removal of introgressed DNA by increasing the number of perfectly linked deleterious mutations in early Neandertal–modern human offspring (decreasing their fitness compared with individuals with less Neandertal ancestry), which in turn influenced the final level of Neandertal ancestry in the population (SI Appendix, Figs. S9–S13).

The depletion of Neandertal ancestry around functional genomic elements in modern human genomes has also been taken as evidence for selection against Neandertal introgressed DNA (3, 8). We next examined the genomic distribution of Neandertal markers at different time points in our simulations to determine whether our models can recapitulate these signals. In agreement with empirical results in present-day humans (3), we found a strong negative correlation between the proportion of Neandertal introgression surviving at a locus and distance to the nearest region under selection (Fig. 3C). Furthermore, we found that the strength of this correlation increases over time, with the bulk of these changes occurring between 10 and 400 generations postadmixture [mean Pearson’s correlation coefficient ρ = 0.07, 0.79, 0.96 at generations 10, 400, and 2,200, respectively (SI Appendix, Fig. S15)]. We note that this time period predates all existing ancient modern human sequences, frustrating any current comparison with empirical data. However, despite no apparent change in genome-wide Neandertal ancestry proportion over time, we observe a smaller though still significant decrease in linked Neandertal ancestry during the time period for which modern human sequences exist (∼400–2,200 generations post-admixture) (Fig. 3 C and B). Indeed, by looking at the average per-generation changes in frequencies of simulated Neandertal mutations (that is, derivatives of allele frequencies in each generation), we observe the impact of negative selection on linked neutral Neandertal markers until at least ∼700 generations post admixture (Fig. 3D) and find that it closely follows the pattern of introgressed deleterious mutations (Fig. 3D). After this period of gradual removal, selection against linked neutral variation slows down significantly as genome-wide Neandertal ancestry becomes largely unlinked from regions that are under negative selection (Fig. 3D). In contrast, the selected variants themselves are still removed, although at increasingly slower rates (Fig. 3D). Due to this slow rate, and the small contribution these alleles make to genome-wide Neandertal ancestry, their continued removal has little impact on the slope of Neandertal ancestry over time.