Genetic stratigraphy of key demographic events in Arabia

RESEARCH ARTICLE Genetic Stratigraphy of Key Demographic Events in Arabia Verónica Fernandes 1,2,3 , Petr Triska 1,2,4 , Joana B. Pereira 1,2,3 , Farida Alshamali 5 , Teresa Rito 2 , Alison Machado 2 , Zuzana Fajkošová 2,6 , Bruno Cavadas 1,2 , Viktor Černý 6 , Pedro Soares 2 , Martin B. Richards 3,7☯ , Luísa Pereira 1,2,8☯ * 1Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal, 2Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal, 3School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom, 4Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal, 5General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates, 6Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic, 7Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom, 8Faculdade de Medicina da Universidade do Porto, Porto, Portugal ☯These authors contributed equally to this work. *[email protected]t Abstract At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (*8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa”migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from *2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since *8ka.Themain“back-to-Africa”migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa. PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 1/27 OPEN ACCESS Citation: Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, et al. (2015) Genetic Stratigraphy of Key Demographic Events in Arabia. PLoS ONE 10(3): e0118625. doi:10.1371/journal. pone.0118625 Academic Editor: Gyaneshwer Chaubey, Estonian Biocentre, ESTONIA Received: August 1, 2014 Accepted: January 21, 2015 Published: March 4, 2015 Copyright: © 2015 Fernandes et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All whole-mtDNA sequences generated in this work are available in GenBank database, accession numbers KP316996KP317078. Funding: FCT, the Portuguese Foundation for Science and Technology, supported this work through the research project PTDC/CS-ANT/113832/2009 and the personal grants to V.F. (SFRH/BD/61342/ 2009), J.B.P. (SFRH/BD/45657/2008), and P.S. (SFRH/BPD/64233/2009). P.T. has a PhD grant from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement no. Introduction The issue of admixture in human populations is normally addressed by genome-wide (GW) studies, and several approaches have been developed to date admixture events [1,2,3,4,5]. Admixed populations bear chromosomes with segments of DNA from all contributing source groups, the size of which decreases over successive generations until recombination renders them undetectably short. Several algorithms attempt to date admixture events by inferring the size of the nuclear ancestry segments, and these can work well when dating recent episodes in human history, such as the sub-Saharan African input into the New World [6], but they fail to detect several known episodes that took place at earlier times, such as the African input into Iberia [1] and genetic exchanges across the Red Sea [7]. Simulations with the suite of methods available at the ADMIXTOOLS package indicated that these methods could detect admixture events as early as 500 generation ago, but real data did not allow the tracing of such old events [8]. A recent improved algorithm, called GLOBETROTTER, has been used to tackle the detection of the co-occurrence of several mixture events by decomposing each chromosome into a series of haplotypic chunks and then analysing each chunk independently [3], but the problem of detecting ancient events remains. Its application to the systematic screening of worldwide admixture events was able to reveal around 100 events, but all occurring over only the past 4,000 years [3]. The uniparental markers, characterised by the absence of recombination, do make possible the inference of ancestry for the mitochondrial genome and non-recombining, male-specific portion of the Y chromosome (mtDNA and MSY, respectively), and the dating of some demographic events (those which leave a signature in the genealogy), provided that a mutation rate of these molecules is reliably established. For the mtDNA, in the last couple of years, the application of various methods has led to quite reliable mutation rates with which to convert genetic diversities into time [9,10], while the MSY remains prone to more uncertainty [11], although promising advances are being achieved with whole Y chromosomal mutation rate calibrations [12,13,14]. At the same time, it is important to emphasize that the age of an mtDNA haplogroup cannot be directly associated with a migration event, as the diversity that has arisen in the source population, predating the migration event, would be included in the measurement. Founder analysis is an attempt to overcome this limitation. This approach picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. In a way, the founder analysis allows us to reconstruct the stratigraphy of the migration events responsible for making up a population genetic pool, analogous to the archaeological reconstruction of the history of a site by the analysis of its sequential layers [15,16,17,18]. Some authors have been critical of dating migration events solely based upon the mtDNA evidence, arguing that maternal lineages do not necessarily represent the entire population, and are especially sensitive to drift [19]. Nevertheless, mtDNA-based conclusions for many migrations across various regions of the globe have been subsequently supported by genome-wide results [20,21], despite the limitations of the latter in dating events. In fact, the genealogical approach taken for mtDNA may overcome the effects of drift more effectively than the use of genome-wide SNPs, as we recently demonstrated in the highly-drifted Ashkenazi population: the fine characterisation of mtDNA sequences provided a detailed reconstruction of the maternal Ashkenazi pool, indicating that at least 80% of the lineages had a deep European ancestry [22], an influence not so readily identified in worldwide PCAs based on genome-wide data [23]. Thus, we suggest that for high time-depths, the mtDNA remains at present the most Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 2/27 317184. The authors also thank the Leverhulme Trust (research project grant 10 105/D) (to M.B.R.) and the DeLaszlo Foundation (to M.B.R./P.S.) for support. The Instituto de Patologia e Imunologia Molecular da Universidade do Porto is an Associate Laboratory of the Portuguese Ministry of Science, Technology, and Higher Education and is partially supported by FCT. VČwas supported by the Grant Agency of the Czech Republic (Grant no. 13–37998S-P505). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. informative genetic system with which to infer past migrations and estimate their time frames, allowing us to disentangle the palimpsest that results from the impact of successive migrations. Several distinct disciplines, including climatology, archaeology and genetics, are beginning to suggest that Arabia featured a highly dynamic genetic pool over time, since its successful settlement at *60 thousand years ago (ka) during the out-of-Africa dispersal [16,24]. The Arabian Peninsula was exposed to several climate change episodes, with fluctuations between arid (leading to population contraction) and humid (population expansion) phases, which conditioned its role as a bridge connecting Africa with Eurasia [25,26].This bridge may have been limited, over long periods or in climatically unfavourable times, to three refuge areas: the Red Sea coastal plain; the Dhofar and Mahra Mountains and adjacent littoral zone in Yemen and Oman; and the emerged floodplain within the Persian Gulf basin [27]. In particular, the latter “Gulf Oasis”may have been fundamental for the survival during arid conditions of the ancient N(xR) mtDNA lineages coalescing at *60 ka found in Arabia [24], most likely the relicts of the first migrants; the Gulf was also a preferential contact bridge with the Fertile Crescent. Since these relict lineages are very minor, however, this signal for the settlement of Arabia during the successful out-of-Africa migration does not clarify if it was a continuous process lasting to the present day. The Pleistocene to Holocene continuity versus discontinuity debate has centred on how far the Arabian population was made up from the producers of the Levantine Pre-Pottery Neolithic B (PPNB)-related industry [28]. After rather sparse Late Palaeolithic settlement, the archaeological evidence suggests a significant increase in sites throughout Arabia dating from 9–8ka[29], but it remains unclear if these were the result of newly arrived people [30] or locals who adopted the new food-producing technology [31]. The scarcity of secure stratigraphic reconstructions in the archaeology of the Peninsula has contributed to the uncertainty in dating the major demographic events. We have shown that some of the most frequent South Arabian mtDNA lineages (such as R0a) display signs of introduction and expansion in the post-glacial period [32], thus pre-dating the Neolithic, although the global contribution of this period to the total Arabian maternal gene pool remains to be evaluated. The archaeological evidence is clearer regarding the remarkable maritime trade system that Arabia established with Africa, the Near East and India in the ninth to eighth millennia, probably the earliest worldwide [33]. The maritime traffic was intensified in mid-sixth millennium, with the appearance of the Pre-Dynastic Egyptian period, which dominated long-distance trade in the Red Sea [34], while in the Persian Gulf trade was established between communities in present-day Bahrain, the Oman Peninsula, the Indus Valley and Gujarat [35].This trade contributed to commercial, cultural, linguistic and genetic exchanges. In terms of language expansion in the region, by applying a Bayesian approach to Semitic lexical data, Kitchen et al. [36] concluded for a single entrance of early Ethio-Semitic languages in Africa, from southern Arabia, at around 2800 years ago, a period when South Arabia was influential in northern Ethiopia. A well-documented movement of people occurred through the Arab slave trade established between the 6th and 19th centuries AD [37], bringing African people (from Nubia to Zanzibar) into the Near East, Arabian Peninsula and even India and China. Estimates indicate that 2,400,000 African people were enslaved along the Red Sea and Indian Ocean routes [38], with a 2:1 female to male ratio [39]. This has also been proposed to explain the high levels of African L(xMN) lineages observed in Yemen [37,40], but other potential sources for sub-Saharan African (but also Indian and Southeast Asian) mtDNA lineages in Arabia may be the result of Hadrami men spending several generations in diaspora around the Indian Ocean rim and returning to their homeland with women taken from the diaspora [41]. Kivisild et al. [37] also detected a 12% frequency of haplogroup L6 in their Yemeni population sample from Kuwait, which is only being marginally observed in Ethiopia and almost absent elsewhere in Africa, and hypothesised that L6 originated from the successful out-of-Africa migration at *60 ka. Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 3/27 However, the subsequent characterisation of other Arabian populations, including Yemen and Oman [42,43,44,45,46,47], did not reproduce the high frequency of this mtDNA lineage in South Arabia. In this work, we use mtDNA to provide a detailed stratigraphic characterisation of key demographic events in Arabia since the first successful out-of-Africa migration *60 ka. We performed mtDNA founder analysis for Arabia and neighbouring regions, aiming to ascertain and date the main dispersal episodes. The founder analysis was applied to the unbiased HVS-I database available for the region, and interpreted in the light of the more precise dating information gathered from whole-mtDNA sequences of informative haplogroups [24,32,47,48]. We also updated the phylogenetic trees of haplogroups J, T, L4 and L6, by performing 83 new wholemtDNA sequences. We further tested our inferences from the HVS-I based founder analysis with a whole-mtDNA founder analysis using haplogroups J and T. The mtDNA information is put in perspective with results from genome-wide analyses of published data [3,23,49,50], focused for the first time on inferring the local Arabian population structure, which has been overlooked in the worldwide context of previous autosomal work. Results/Discussion Continuity of Pleistocene/Holocene settlement Previous work has already provided genetic evidence for the exchange of lineages between the Near East and Arabia. This was confirmed with whole-mtDNA sequencing of the Eurasian macrohaplogroup N (including its branches X, I, W, N1a, N1b and some R lineages), which is dominant in Arabia, attaining a frequency of 66%–83% [24,32,47,48]. The obvious missing element in those studies was the whole-mtDNA sequencing of Arabian JT lineages, which we have performed here, providing a detailed phylogeographic analysis in Supplemental Material (outline topology in S1 and S2 Figs.; S1 Text). Following the pattern for the remaining N lineages, the frequency and diversity maps (S3,S4,S5,S7,S12,S13,S16 and S19 Figs.; S3 and S4 Tables) of JT lineages, displaying similarity across the Near East and Arabian Peninsula, as well as the many basal Arabian lineages (S8,S9,S10,S11,S14,S15,S17,S18,S20,S21,S22 and S23 Figs.), suggest that both regions were in close contact throughout the late Pleistocene and Holocene. Haplogroup J assumes a more important role in Arabia overall than haplogroup T, as testified by frequencies (between 7.7–20.6% and 3.2–10.2%, respectively) and the many star-like J sub-clades observed in Arabia, dating to *6–7 ka. These expansions in haplogroup J are reflected in the BSP analysis (S6 Fig.), for which the main increase in effective size was between 8–12 ka in Arabia (S6A Fig.), after the expansion observed in the Near East around 11–15 ka (S6B Fig.). Haplogroup J also shows signs of having crossed into eastern Africa, particularly the sub-clade J1d1a1, necessarily after its emergence in Arabia at *7.1 ka (S14 Fig.). Thus haplogroup JT indicates that demographic expansion in Southwest Asia was a continuous phenomenon from the Late Glacial period to the Neolithic period. In order to dissect the apparent continuous genetic exchange between Arabia and the Near East since the late Pleistocene, we performed a founder analysis for all Eurasian haplogroups assuming the Near East, Iran and Pakistan as source and Arabia as sink (identified founders reported in S6 and S7 Tables). Fig. 1A displays the overall pattern, which seems to favour the periods around 1ka, 10 ka and 16 ka for migrations. Based on this information, we further imposed these dates as migration events to represent broadly, respectively, recent events, the Younger Dryas/Neolithic transition and the Late Glacial period. The results indicate that the Late Glacial period (Fig. 1B) was the most important migratory period, responsible for the introduction of 40–54% of the lineages (mainly belonging to the haplogroups K, U2, U3, U4, N1a1a, N1a1b, H5 and HV1; S24 and S25 Figs. and detailed description in S1 Text). At the Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 4/27 Younger Dryas/Neolithic boundary, 34–41% of lineages, mainly unclassified HV, R0a, J1b, T1a and M1 migrated to Arabia. The remaining 12–19% moved very recently, *1 ka, and consists of derived lineages, (including J1d1a, K1, HV8 and N1a3). Although it is hard to discriminate clearly between the Near Eastern and Pakistan/Iranian influences, due to their largely shared mtDNA pool, the results suggest a higher Pakistan/Iranian impact in the east (41%) than in the west (25%) of Arabia for private founders, but just 14% and 11%, respectively, when considering the overall pool. This seems to indicate that the Pakistan/Iranian contribution was recent, Fig 1. Founder analysis results. Probabilistic distribution of founder clusters across migration times, with time scanned at 200 year intervals from 0–60 ka, using f1 (blue line) and f2 criteria (red line), when considering putative migrations: (A) from the Near East, Iran and Pakistan to Arabia; (C) from Africa into Arabia plus the Near East and Iran; (E) Arabia plus the Near East and Iran into eastern Africa; (G) Arabia plus the Near East and Iran into North Africa; and probabilistic proportion of founder clusters considering different migration events, using f1 (blue bar) and f2 criteria (red bar), when considering putative migrations: (B) from the Near East, Iran and Pakistan to Arabia; (D) from African into Arabia plus the Near East and Iran; (F) Arabia plus the Near East and Iran into eastern Africa; (H) Arabia plus the Near East and Iran into North Africa. doi:10.1371/journal.pone.0118625.g001 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 5/27 as the lineages introduced from this region did not reach high frequencies, and as expected its impact was higher in the eastern Arabian countries. We next tested the robustness of the founder analysis by using whole-mtDNA genomes and HVS-I from haplogroups J and T alone (Fig. 2). The 17 whole-mtDNA founders identified (S8 Table) contributed to the overall pattern of migration displayed in Fig. 2A, which displays two main peaks, at 1 ka and 10 ka. When imposing the model of three migrations (Fig. 2B), 30% of JT lineages were introduced at 1ka, 50% at 10ka and 20% at 16ka. These results match closely the inferences based only on HVS-I information (Fig. 2C,D). We should emphasize that no one-to-one correspondence of founder types between wholemtDNA genomes and HVS-I can be expected, as there is no such precise correspondence between the whole-mtDNA and HVS-I trees, due in part to the differences in resolution but also no doubt to the small samples size at present for the whole-mtDNAs. We must also beware that other factors may also confound the analysis in particular circumstances. An extreme— but very unusual—instance is haplogroup J1d1a. Here, the HVS-I based founder analysis dates the founders to 1.0 ka, while the whole-mtDNA analysis indicates that it expanded in Arabia at least 6.1 ka. This discrepancy is due to 18 HVS-I sequences belonging to the root haplotype largely from central Saudi Arabia, an artefact of the sampling location (central Saudi Arabia is extremely arid and has had historically very low population size, with habitation restricted to oases, undoubtedly leading to severe genetic drift), while the remaining more diverse samples are from Yemen (as for most of the whole-mtDNAs). If the Saudi samples are disregarded, a ρ estimate for the founder age in Arabia increases to *6–7 ka, fitting more closely with the whole-mtDNA result. Allowing for such inevitable noise effects from the datasets, the similarity between the whole-mtDNA and HVS-I analyses is indeed striking, and we conclude that it is reasonable to infer that the picture suggested by the whole-population HVS-I founder analysis is not giving a very misleading impression of the dispersal history of the region. Fig 2. Founder analysis results on JT lineages. Probabilistic distribution of founder clusters across migration times, with time scanned at 200 year intervals from 0–60 ka, using f1 (blue line) and f2 criteria (red line), when considering putative migrations from the Near East, Iran and Pakistan to Arabia for (A) wholemtDNA genomes or (C) HVS-I for haplogroups J and T; and probabilistic proportion of founder clusters considering different migration events, using f1 (blue bar) and f2 criteria (red bar), when considering putative migrations from the Near East, Iran and Pakistan to Arabia for (B) whole-mtDNA genomes or (D) HVS-I for haplogroups J and T. doi:10.1371/journal.pone.0118625.g002 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 6/27 Although it is not possible to date securely events as old as the ones occurring in the Pleistocene/Holocene transition based on genome-wide data alone, it is interesting to observe how the patterns of shared genome-wide ancestry support the inferences made for the mtDNA. All the Arabian populations form a close group with Near East populations in PC analysis (Fig. 3), with the first component explaining 44% of the diversity and partitioning populations along a west–east axis, and the second component explaining 8% and organising populations on a north–south axis. A few individuals in Arabian populations most probably had recent ancestry within Africa (especially for Yemen) or Pakistan (in the United Arab Emirates; UAE). Yemen shows the highest dispersion along the first axis, testifying again the higher African input in the closest country to the Horn of Africa. We confirmed the clustering of Yemeni Jews with Bedouin and Saudi Arabians, already identified previously [23], and probably indicating that they were less open to recent admixture with non-Arabian populations than their Yemeni Arab/ Muslims neighbours. The ADMIXTURE results indicate that K = 6 (Fig. 4 and Table 1; other K plots are displayed in S38 Fig.) is the number of clusters that best represents the population structure of the analysed populations. Here it is already possible to distinguish between a Southwest Asian/Caucasian and an Arabian/North African component; these two components have similar proportions of *30% each in Yemen and UAE, but the Arabian/North African proportion increases to 52–60% in Saudi and Bedouin. In Near Eastern populations, correspondingly, the Southwest Asian/Caucasian component rises to *50% and the Arabian/North African cluster decreases to *20–30%, even in Palestinians (similar to the Samaritans and some of the Fig 3. PCA results. Scatter plot of individuals, showing the first two principal components. Each symbol corresponds to one individual and the colour indicates the region of origin. doi:10.1371/journal.pone.0118625.g003 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 7/27 Druze), highlighting their primarily indigenous origin, with the most extreme values for the Druze, carrying the Southwest Asian/Caucasian component at *80%. European background is higher in Near Eastern populations (around 9–15%) than in Arabia (1.5–5%) while the African ancestry is *25% in Yemen, and then 4–8% in all Arabian and Near East populations except in Samaritans and Druze, with 0–2%. The UAE has a substantial pool from South Asia (21%) similar to the proportion displayed in Iran (24%), which falls to below 10% in all other Arabian and Near Eastern populations, except Turkey (18%). ADMIXTURE allows us to calculate F ST values between the components in order to quantify their similarity (Fig. 5A). For K = 6, Arabia showed a lower distance from the Near East (0.046), than from Europe (0.052), eastern Africa (0.098) and finally western Africa (0.140). Arabia and the Near East have similar genetic distances from eastern African (0.098 and 0.097, respectively), double that of the value between western and eastern Africa (0.046). When evaluating F ST values in pairwise comparisons between Arabian and Near Eastern populations (Fig. 5B), we see that F ST values are higher between Yemen and all other populations (and also for comparisons with Samaritans, but these results may be biased by low sample size). The UAE is closer to Jordan, Syria and Lebanon than Saudi Arabia is; while Saudi are closer to Palestinians, Druze and Samaritans than UAE. Thus, F ST values support lower or similar genetic distances between UAE and Near Eastern populations as between Saudi and Near Eastern populations, while Yemen is clearly more divergent. Exchanges across the Red Sea—from Africa into Arabia Founder analysis of the dispersal of sub-Saharan lineages from Africa into Arabia plus the Near East and Iran (both regions have to be considered together due to the relatively low number of L(xMN) sequences) showed a predominant migration peak at 0–0.8 ka (Fig. 1C). When Fig 4. ADMIXTURE results. Population structure inferred by ADMIXTURE analysis. Each individual is represented by a vertical (100%) stacked column of genetic components proportions shown in colour for K = 6. doi:10.1371/journal.pone.0118625.g004 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 8/27 checking these founders (S9 and S10 Tables), we see that most of them display clearly young ages, but several have ages *13 ka (S15 Table). So, we tested a model based on three periods of migration (Fig. 1D), and their impact was: 31–40% for 1 ka (middle of Arab slave trade, 6 th – Table 1. Estimates of admixture proportions (%) and date of admixture (in generations) calculated in ROLLOFF when using western (Yoruba) and eastern (Maasai) African and Italians + Spanish as ancestral populations. Population Sample Size Western African ancestry proportion (%) ± standard error Eastern African ancestry proportion (%) ± standard error Southwest Asian/ Caucasian ancestry proportion (%) ± standard error Arabian/ North African ancestry proportion (%) ± standard error European ancestry proportion (%) ± standard error South Asian ancestry proportion (%) ± standard error Estimated date of admixture using ROLLOFF using Western African parental population Estimated date of admixture using ROLLOFF using Eastern African parental population Yemen 9*16.935 ± 15.960 7.747 ± 5.333 30.777 ± 9.896 32.398 ± 6.030 3.217 ±2.77 8.926 ± 3.727 21.019 ± 7.450 11.556 ± 3.878 Saudi Arabia 20 1.694 ± 5.223 4.033 ± 4.235 34.227 ± 8.955 52.479 ± 18.957 2.722 ± 3.879 4.844. ± 4.975 30.762 ± 4.907 25.430 ± 3.011 Yemen Jews 15 0.001 ± 0.000 5.105 ± 0.826 47.542 ± 1.525 45.693 ± 1.598 0.565 ± 0.699 1.094 ± 1.187 n/a n/a UAE 14 6.408 ± 9.118 1.817 ± 2.014 34.432 ± 4.312 34.378± 21.632 1.689 ± 1.931 21.276 ± 17.660 8.900 ±1.642 8.923 ±1.795 Bedouin 45 2.005 ± 2.213 4.692 ± 4.246 24.903 ± 19.909 60.057± 30.707 5.400 ± 4.700 2.944 ± 2.285 37.546 ± 3.104 27.734 ± 1.532 Lebanon 7 1.243 ± 4.854 4.670 ± 3.148 51.547 ± 2.519 21.092 ± 4.062 14.543 ± 2.791 6.905 ± 4.854 n/a n/a Syria 16 1.586 ± 1.451 3.413 ± 1.952 49.742 ± 4.880 23.260 ± 5.283 12.864 ± 4.532 9.135 ± 3.387 37.334 ± 4.365 26.181 ± 4.428 Jordan 20 3.205 ± 5.629 7.289 ± 6.404 47.833 ± 7.442 25.055 ± 3.209 11.171 ± 2.436 5.447 ± 2.169 32.871± 4.106 29.470 ± 3.671 Samaritan 3 0.001 ± 0.000 0.190 ± 0.777 63.029 ± 2.282 26.358 ± 2.709 8.946 ± 4.104 0.475 ± 0.496 n/a n/a Druze 42 0.178 ± 0.365 1.869 ± 1.082 80.100 ± 14.498 9.919 ±7.730 6.123 ± 5.089 1.812 ± 1.664 n/a n/a Palestinian 46 2.222 ± 1.760 6.119 ± 2.147 51.538 ± 4.397 27.396 ± 2.153 9.153 ± 1.826 3.572 ± 1.302 29.008 ± 2.194 11.556 ± 3.878 Iran 20 1.701 ± 3.196 1.022 ± 1.818 50.678 ± 4.259 11.850 ± 5.614 11.135 ± 2.916 23.614 ± 3.944 n/a n/a Turkey 19 0.069 ± 0.029 0.194 ± 0.312 49.188 ± 3.258 8.993 ±2.904 23.798 ± 3.503 17.758 ± 2.504 n/a n/a Ethiopia 19 3.911 ± 3.047 58.139 ± 8.479 12.146 ± 5.638 25.469 ± 5.495 0.179 ± 0.442 0.157 ± 0.297 93.223± 9.678 n/a Maasai 19 15.808 ± 12.911 78.060 ± 15.009 0.412 ±0.911 4.120 ±3.043 0.096 ± 0.315 0.736 ± 1.858 47.007± 2.933 n/a Egypt 12 5.553 ± 1.553 15.117 ± 4.878 39.826 ± 5.130 30.499 ± 6.343 8.380 ± 2.245 0.624 ± 0.630 30.034± 3.233 22.766 ± 2.890 Morocco 25 12.199 ± 10.473 12.066 ± 2.951 21.360 ± 4.827 28.872 ± 5.736 25.502 ± 7.971 0.001 ± 0.000 n/a n/a Tunisia 12 9.815 ± 2.927 10.437 ± 1.212 26.002 ± 4.057 30.991 + 6.178 22.754 ± 5.354 0.001 ± 0.000 n/a n/a N/A—not assigned. *By eliminating one individual with a high level of African ancestry. doi:10.1371/journal.pone.0118625.t001 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 9/27 inferring the more eastern contribution into the Arabian Peninsula. In order to assess the error in the Bayesian partitioning across the different migration times realistically, we calculated an effective number of samples for each founder cluster. This was obtained by multiplying the number of samples for each founder cluster by a ratio of the variance assuming a star-like network and the variance calculated as in Saillard et al. [67]. We scanned the distribution of founder ages for each region, defining equally spaced 200year intervals for each migration from 0–70 ka. For each case, we also investigated the proportion of introduction of lineages during putative migrations occurring in certain periods of time. We selected these migration events by combining three distinct lines of evidence: the peaks detected in the founder analysis; historical/archaeological evidence; and dates from wholemtDNA sequences belonging to informative haplogroups in the region (such as R0a, JT, N1, N2, I, L3 and L4/L6). We represented the probabilistic proportions of introduction for each lineage at each of the putative migration periods in graphs resembling the images from the STRUCTURE analysis. In order to further validate the HVS-I founder analysis into Arabia we compared it with the results obtained from a founder analysis using whole-mtDNA genomes belonging to haplogroups J and T. We only used an f1 criterion (since the sampling from the source was too scarce to allow an f2 criterion) and we detected 17 founders (S8 Table). The assumptions of the founder method do not allow the use of a time-dependent clock. Therefore, given the relatively small difference between the mutation rate for time zero (average 2562 years for a mutation to happen) and the mutation rate for the oldest founder (average 2667 years for a mutation to happen) we used the intermediate value (2614 years for a mutation to happen) as an estimate for the overall range. As with the HVS-I founder analysis, we performed a preliminary scan analysis and estimated relative contributions of JT lineages in a three-migration model. Genome-wide database We assembled genome-wide data for 790 samples from eight geographic groups (sub-Saharan Africa, North Africa, Arabian Peninsula, Near East, Iran, Europe, Caucasus and South Asia) from previously published data sets (S13 Table). The samples from Behar et al. [23] were genotyped using Illumina the 610K and 660K bead arrays, while those from Li et al. [49] were screened with Illumina 650K bead arrays, and those from Hellenthal et al. [3] with Illumina 660K bead arrays. We obtained the genotypes from Maasai, an ethnic group located in Kenya, from the HapMap phase III release (http://hapmap.ncbi.nlm.nih.gov/). We used PLINK 1.05 [73] to check that individuals and SNPs had a genotyping success of 97%. We used a Python in-house script to merge genotypes from the various chips and ended up with a total of 309,474 common autosomal single nucleotide polymorphisms (SNPs). We pruned the full dataset for linkage disequilibrium (LD), removing SNPs in strong LD (r 2 >0.4) with nearby markers in a window of 50 SNPs (advanced by 10 SNPs each time); a total of 215,286 SNPs remained for further analyses. Genome-wide statistical analyses We analysed the 790 samples with the ADMIXTURE software [74] which provides a maximum likelihood estimation of the population structure. We tested several numbers of clusters or ancestral populations, K (from three to six), with termination criteria for independent runs for each K value established when the log-likelihood increased by less than 10 −4 between iterations. We performed across-validation to check the K value with the lowest cross-validation error, which would represent the most accurate modelling choice. Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 16 / 27 We carried out the principal component (PC) analysis, which infers worldwide axes of human genetic variation from the allele frequencies of various populations, using the smartpca tool, available in the EIGENSOFT package [75]. We evaluated the statistical significance of each PC through the Tracy-Widom statistics, computed at the EIGENSOFT tool twstats.Aswe were focused in Arabia, we did not include all populations in the analysis, especially the western African ones, in order to maximise the resolution. To estimate the ages of putative admixture events in populations displaying statistical evidence of admixture, we used the ROLLOFF method [1] implemented in the ADMIXTOOLS software package [8]. This method is based on the decay of admixture LD in the target population, performing a local ancestry inference. We ran the ROLLOFF method for Arabia and some Near Eastern populations, using the unpruned set, with Maasai individuals (from the HapMap dataset, selected after the ADMIXTURE analysis, as the ones displaying >80% eastern African ancestry) and Italy plus Spain (extracted from 1000 Genomes database; http:// browser.1000genomes.org/index.html) as ancestral populations. We also performed this analysis by replacing Maasai by Yoruba, from western Africa, to check for the influence of the selected African ancestral population, and as some eastern African populations also have a high western African component (such as Luhya in Webuye, Kenya, in the 1000 Genomes database). We plotted the correlation between SNPs as a function of genetic distance for all chromosomes. Ages (in number of generations) were estimated by fitting an exponential distribution to the decay of these correlation coefficients. The estimated age (in number of generations) for the admixture event is the average of dates for all chromosomes. The F ST values between pairs of ADMIXTURE components (K = 6) were estimated using ADMIXTURE, while the ones between pairs of populations were performed using vcf tools (http://vcftools.sourceforge.net/). Supporting Information S1 Fig. Schematic tree of haplogroup J. Ages (in ka) indicated are maximum likelihood estimates obtained for the whole-mtDNA genome. (TIF) S2 Fig. Schematic tree of haplogroup T. Ages (in ka) indicated are maximum likelihood estimates obtained for the whole-mtDNA genome. (TIF) S3 Fig. Frequency maps based on HVS-I data for haplogroups J (A) and T (B). (TIF) S4 Fig. Distribution maps for haplogroup J for the diversity measures π(A) and ρ(B) based on HVS-I data. (TIF) S5 Fig. Distribution maps for haplogroup T for the diversity measures π(A) and ρ(B) based on HVS-I data. (TIF) S6 Fig. Bayesian skyline plot indicating hypothetical effective population size through time based on data from haplogroup J of Arabia (A) and Near East (B) and from haplogroup T of Arabia (C) and Near East (D). (TIF) Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 17 / 27 S7 Fig. Frequency maps based on HVS-I data for haplogroups J1b. (TIF) S8 Fig. Phylogenetic tree of haplogroup J1b. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; insertions are indicated by a dot followed by the number of repetitions and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S9 Fig. Phylogenetic tree of haplogroup J1b1. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S10 Fig. Phylogenetic tree of haplogroup J1b1a. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S11 Fig. Phylogenetic tree of haplogroup J1b2. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S12 Fig. Frequency maps based on HVS-I data for lineages within haplogroup J defined by the transition at 16193, which mainly corresponds to haplogroup J1d, but can also include haplogroup J2d. (TIF) S13 Fig. Frequency maps based on HVS-I data for the sub-haplogroup J1d1a. (TIF) Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 18 / 27 S14 Fig. Phylogenetic tree of haplogroup J1d1. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; deletions are indicated “d”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S15 Fig. Phylogenetic tree of haplogroup J1d2. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; insertions are indicated by a dot followed by the number of repetition and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S16 Fig. Frequency maps based on HVS-I data for haplogroup J2. (TIF) S17 Fig. Phylogenetic tree of haplogroup J2a2. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S18 Fig. Phylogenetic tree of haplogroup J2a2a. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“ C,”or “T”; insertions are indicated by a dot followed by the number of repetition and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S19 Fig. Frequency maps based on HVS-I data for the haplogroup J2a2b. (TIF) S20 Fig. Phylogenetic tree of haplogroup T1a. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; insertions are indicated by a dot followed by the number of repetition and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 19 / 27 coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S21 Fig. Phylogenetic tree of haplogroup T2a1. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; insertions are indicated by a dot followed by the number of repetition and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S22 Fig. Phylogenetic tree of haplogroup T2c. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; insertions are indicated by a dot followed by the number of repetition and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S23 Fig. Phylogenetic tree of haplogroups T2i and T2g. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; insertions are indicated by a dot followed by the number of repetition and the nucleotide position; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρbased on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S24 Fig. Probabilistic proportion of founder clusters considering three migration periods (1.0, 10.0 and 16.0 ka), using the f1 criterion and by assuming a Near East, Iran and Pakistan source for migrations into Arabian Peninsula. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) S25 Fig. Probabilistic proportion of founder clusters considering three migration periods (1.0, 10.0 and 16.0 ka), using the f2 criterion and by assuming a Near East, Iran and Pakistan source for migrations into Arabian Peninsula. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 20 / 27 S26 Fig. Schematic tree of haplogroups L4 and L6. Ages (in ka) indicated are maximum likelihood estimates obtained with the whole-mtDNA genome. (TIF) S27 Fig. Frequency maps based on HVS-I data for haplogroups L4 (A) and L6 (B). (TIF) S28 Fig. Phylogenetic tree of haplogroup L4a. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S29 Fig. Phylogenetic tree of haplogroup L4b. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S30 Fig. Phylogenetic tree of haplogroup L6. Labels on the branches represent nucleotide positions of transitions, and transversions when followed by a suffix “A,”“G,”“C,”or “T”; reversions by “!”; green indicates synonymous, brown non-synonymous, yellow other coding region, and black control region substitutions. Individual identification is indicated as well as the geographic origin when known (geographic regions are grouped by colour code according to the key). Near the nodes, the TMRCA is indicated (mean and 95% confidence interval) for ρ based on whole-mtDNA sequences (in black), ρbased on synonymous diversity (in green) and for maximum likelihood (in blue). (TIF) S31 Fig. Bayesian Skyline Plot (BSP), indicating the median of the hypothetical effective population size through time based on data from haplogroup L4 (A) and haplogroups L4 and L6 (B), assuming a generation time of 25 years. (TIF) S32 Fig. Probabilistic proportion of founder clusters considering three migration periods (1.0, 2.5 and 13.0 ka), using the f1 criterion and assuming an African source for migrations into Arabian Peninsula plus the Near East and Iran. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) S33 Fig. Probabilistic proportion of founder clusters considering three migration periods (1.0, 2.5 and 13.0 ka), using the f2 criterion and assuming an African source for migrations into Arabian Peninsula plus Near East and Iran. The haplogroup affiliations of the founders Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 21 / 27 are indicated in the bottom. (TIF) S34 Fig. Probabilistic proportion of founder clusters considering three migration periods (2.0, 10.0 and 16.0 ka), using the f1 criterion and assuming Arabian Peninsula plus Near East and Iran migrations into eastern Africa. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) S35 Fig. Probabilistic proportion of founder clusters considering three migration periods (2.0, 10.0 and 16.0 ka), using the f2 criterion and assuming Arabian Peninsula plus Near East and Iran migrations into eastern Africa. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) S36 Fig. Probabilistic proportion of founder clusters considering three migration periods (2.0, 10.0 and 16.0 ka), using f1 criterion and assuming Arabian Peninsula plus Near East and Iran migrations into North Africa. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) S37 Fig. Probabilistic proportion of founder clusters considering three migration periods (2.0, 10.0 and 16.0 ka), using the f2 criterion and assuming Arabian Peninsula plus Near East and Iran migrations into North Africa. The haplogroup affiliations of the founders are indicated in the bottom. (TIF) S38 Fig. Population structure inferred by ADMIXTURE analysis. Each individual is represented by a vertical (100%) stacked column of genetic components proportions shown in colour for K = 3, 4 and 5. (TIF) S1 Table. Haplotypes for whole-mtDNA sequences that were fully characterised in this study and the corresponding geographic region. (DOCX) S2 Table. Published whole-mtDNA sequences used in all phylogenetic tree with the corresponding origin and subclade affiliation. (DOCX) S3 Table. Diversity values of ρand πused for the interpolation maps of the haplogroups J, T and L4. (DOCX) S4 Table. Frequency values used in the reconstruction of the interpolation maps for the haplogroups J, T, J1d1a and J2a2b. (DOCX) S5 Table. Frequency values used in the reconstruction of the interpolation maps for the haplogroups L4 and L6. (DOCX) Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 22 / 27 S6 Table. Founder lineages identified when using f1 criterion from the Near East, Iran and Pakistan to Arabian Peninsula. (DOCX) S7 Table. Founder lineages identified when using f2 criterion from the Near East, Iranand Pakistan to Arabian Peninsula. (DOCX) S8 Table. Founder lineages identified when using a f1 criterion from Near East, Iran and Pakistan to Arabian Peninsula, based on whole-mtDNA JT sequences. (DOCX) S9 Table. Founder lineages identified when using f1 criterion from Africa to Arabian Peninsula, Near East and Iran. (DOCX) S10 Table. Founder lineages identified when using f2 criterion from Africa to Arabian Peninsula, Near East and Iran. (DOCX) S11 Table. Founder lineages identified when using f1 criterion from Arabian Peninsula, Near East and Iran to North Africa and to eastern Africa separately. (DOCX) S12 Table. Founder lineages identified when using f2 criterion from Arabian Peninsula, Near East and Iran to North Africa and to eastern Africa separately. (DOCX) S13 Table. Samples used for genome-wide autosomal analysis. (DOCX) S14 Table. Peaks of rate of population size change through time as obtained from the BSPs and periods of time where the rate of population size increase was of at least one individual per 100 individuals in a period of 100 years. Increment ratio corresponds to the number of times the effective population size increase during this period. (DOCX) S15 Table. Ages for the oldest founders in the migration from Africa into the Arabian Peninsula, Near East and Iran. This is a sub-set of S9 Table. (DOCX) S1 Text. Phylogeographic analyses and supplemental information on founder analyses. Includes 15 tables. (DOCX) Author Contributions Conceived and designed the experiments: MBR LP. Performed the experiments: VF JBP TR AM ZF. Analyzed the data: VF PT BC PS. Contributed reagents/materials/analysis tools: FA VC MBR LP. Wrote the paper: VF MBR LP. References 1. Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, et al. (2011) The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7: e1001373. doi: 10.1371/journal.pgen. 1001373 PMID: 21533020 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 23 / 27 2. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587. PMID: 12930761 3. Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C, et al. (2014) A genetic atlas of human admixture history. Science 343: 747–751. doi: 10.1126/science.1243518 PMID: 24531965 4. Pugach I, Matveyev R, Wollstein A, Kayser M, Stoneking M (2011) Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol 12: R19. doi: 10.1186/gb-2011-12-2r19 PMID: 21352535 5. Pool JE, Nielsen R (2009) Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711–719. doi: 10.1534/genetics.108.098095 PMID: 19087958 6. Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, et al. (2010) Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci U S A 107: 786–791. doi: 10.1073/pnas.0909559107 PMID: 20080753 7. Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL (2014) Early Back-to-Africa Migration into the Horn of Africa. PLoS Genet 10: e1004393. doi: 10.1371/journal.pgen.1004393 PMID: 24921250 8. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, et al. (2012) Ancient admixture in human history. Genetics 192: 1065–1093. doi: 10.1534/genetics.112.145037 PMID: 22960212 9. Soares P, Ermini L, Thomson N, Mormina M, Rito T, et al. (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84: 740–759. doi: 10.1016/j.ajhg. 2009.05.001 PMID: 19500773 10. Fu Q, Mittnik A, Johnson PL, Bos K, Lari M, et al. (2013) A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 23: 553–559. doi: 10.1016/j.cub.2013.02.044 PMID: 23523248 11. Busby GB, Brisighelli F, Sanchez-Diz P, Ramos-Luis E, Martinez-Cadenas C, et al. (2012) The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci 279: 884–892. doi: 10.1098/rspb.2011.1044 PMID: 21865258 12. Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, et al. (2013) A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 23: 388–395. doi: 10.1101/gr.143198.112 PMID: 23038768 13. Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, et al. (2013) Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341: 562–565. doi: 10.1126/science.1237619 PMID: 23908239 14. Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, et al. (2013) Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341: 565–569. doi: 10.1126/ science.1237947 PMID: 23908240 15. Richards M, Macaulay V, Hickey E, Vega E, Sykes B, et al. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67: 1251–1276. PMID: 11032788 16. Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, et al. (2012) The expansion of mtDNA haplogroup L3 within and out of Africa. Mol Biol Evol 29: 915–927. doi: 10.1093/molbev/msr245 PMID: 22096215 17. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, et al. (2008) Climate change and postglacial human dispersals in southeast Asia. Mol Biol Evol 25: 1209–1218. doi: 10.1093/molbev/msn068 PMID: 18359946 18. Forster P, Harding R, Torroni A, Bandelt HJ (1996) Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet 59: 935–945. PMID: 8808611 19. Scally A, Durbin R (2012) Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13: 745–753. doi: 10.1038/nrg3295 PMID: 22965354 20. Mellars P, Gori KC, Carr M, Soares PA, Richards MB (2013) Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proc Natl Acad Sci U S A 110: 10699– 10704. doi: 10.1073/pnas.1306043110 PMID: 23754394 21. Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, et al. (2013) The first modern human dispersals across Africa. PLoS One 8: e80031. doi: 10.1371/journal.pone.0080031 PMID: 24236171 22. Costa MD, Pereira JB, Pala M, Fernandes V, Olivieri A, et al. (2013) A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nat Commun 4: 2543. doi: 10.1038/ncomms3543 PMID: 24104924 23. Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, et al. (2010) The genome-wide structure of the Jewish people. Nature 466: 238–242. doi: 10.1038/nature09103 PMID: 20531471 24. Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, et al. (2012) The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa. Am J Hum Genet 90: 347–355. doi: 10.1016/j.ajhg.2011.12.010 PMID: 22284828 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 24 / 27 25. Petraglia MD, Alsharekh A (2003) The Middle Palaeolithic of Arabia: Implications for modern human origins, behaviour and dispersals Antiquity 77: 671–684 26. Parker AG (2009) Pleistocene Climate Change in Arabia: Developing a Framework for Hominin Dispersal over the Last 350 ka. In: Petraglia MD, Rose J, editors. The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics. The Netherlands: Springer. pp. 39–50. 27. Rose J, Petraglia MD (2009) Tracking the Origin and Evolution of Human Populations in Arabia. In: Petraglia MD, Rose J, editors. The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics. The Netherlands: Springer. pp. 1–14. 28. Drechsler P (2009) The dispersal of the Neolithic over the Arabian Peninsula. Archaeopress, Oxford: British Archaeological Reports International Series S1969. 29. Groucutt HS, Petraglia MD (2012) The prehistory of the Arabian peninsula: deserts, dispersals, and demography. Evol Anthropol 21: 113–125. doi: 10.1002/evan.21308 PMID: 22718479 30. Uerpmann H-P, Potts DT, Uerpmann M (2009) Holocene (Re-) Occupation of Eastern Arabia. In: Petraglia MD, Rose J, editors. The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics. The Netherlands: Springer. pp. 205–214. 31. Fedele FG (2009) Early Holocene in the Highlands: Data on the Peopling of the Eastern Yemen Plateau, with a Note on the Pleistocene Evidence. In: Petraglia MD, Rose J, editors. The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics. The Netherlands: Springer. pp. 215–236. 32. Cerny V, Mulligan CJ, Fernandes V, Silva NM, Alshamali F, et al. (2011) Internal diversification of mitochondrial haplogroup R0a reveals post-last glacial maximum demographic expansions in South Arabia. Mol Biol Evol 28: 71–78. doi: 10.1093/molbev/msq178 PMID: 20643865 33. Boivin N, Blench R, Fuller DQ (2009) Archaeological, Linguistic and Historical Sources on Ancient Seafaring: A Multidisciplinary Approach to the Study of Early Maritime Contact and Exchange in the Arabian peninsula. In: Petraglia MD, Rose J, editors. The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics. The Netherlands: Springer. pp. 251–278. 34. Mitchell P (2005) African connections: archaeological perspectives on Africa and the wider world. Walnut Creek: Altamira Press. pp. 328. 35. Ray PH (2003) The Archaeology of seafaring in ancient South Asia. Cambridge: Cambridge University Press. pp350. 36. Kitchen A, Ehret C, Assefa S, Mulligan CJ (2009) Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East. Proc Biol Sci 276: 2703–2710. doi: 10.1098/rspb.2009.0408 PMID: 19403539 37. Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, et al. (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet 75: 752–770. PMID: 15457403 38. Lovejoy PE (1983) Transformations inSlavery—A history of slavery in Africa. Third Edition ed. New York: Cambridge University Press. pp. 200. 39. Segal R (2002) Islam's Black Slaves—the other black diaspora. London: Atlantic Books. pp 288. 40. Richards M, Rengo C, Cruciani F, Gratrix F, Wilson JF, et al. (2003) Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations. Am J Hum Genet 72: 1058–1064. PMID: 12629598 41. Freitag U, Clarence-Smith WG (1997) Hadhrami traders, scholars, and statesmen in the Indian Ocean. Leiden; New York: Brill. pp 392. 42. Alshamali F, Brandstatter A, Zimmermann B, Parson W (2008) Mitochondrial DNA control region variation in Dubai, United Arab Emirates. Forensic Sci Int Genet 2: e9–10. doi: 10.1016/j.fsigen.2007.11. 001 PMID: 19083802 43. Abu-Amero KK, Gonzalez AM, Larruga JM, Bosley TM, Cabrera VM (2007) Eurasian and African mitochondrial DNA influences in the Saudi Arabian population. BMC evolutionary biology 7: 32. PMID: 17331239 44. Abu-Amero KK, Larruga JM, Cabrera VM, Gonzalez AM (2008) Mitochondrial DNA structure in the Arabian Peninsula. BMC evolutionary biology 8: 45. doi: 10.1186/1471-2148-8-45 PMID: 18269758 45. Cerny V, Mulligan CJ, Ridl J, Zaloudkova M, Edens CM, et al. (2008) Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen. Am J Phys Anthropol 136: 128–137. doi: 10.1002/ajpa.20784 PMID: 18257024 46. Cerny V, Pereira L, Kujanova M, Vasikova A, Hajek M, et al. (2009) Out of Arabia-the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity. Am J Phys Anthropol 138: 439–447. doi: 10.1002/ajpa.20960 PMID: 19012329 Genetic Stratigraphy of Key Demographic Events in Arabia PLOS ONE | DOI:10.1371/journal.pone.0118625 March 4, 2015 25 / 27