The Study of Racialism

DesertDragon · Regular User Joined: 18 Jul 2007 {Posts: 70 }

Background
Genetic studies of the Arabian Peninsula are scarce even though the region was the center of ancient trade routes and empires and may have been the southern corridor for the earliest human migration from Africa to Asia. A total of 120 mtDNA Saudi Arab lineages were analyzed for HVSI/II sequences and for haplogroup confirmatory coding diagnostic positions. A phylogeny of the most abundant haplogroup (preHV)1 (R0a) was constructed based on 13 whole mtDNA genomes.

Results
The Saudi Arabian group showed greatest similarity to other Arabian Peninsula populations (Bedouin from the Negev desert and Yemeni) and to Levantine populations. Nearly all the main western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade. Saudi Arabs had only a minority sub-Saharan Africa component (7%), similar to the specific North-African contribution (5%). In addition, a small Indian influence (3%) was also detected.

Conclusion
The majority of the Saudi-Arab mitochondrial DNA lineages (85%) have a western Asia provenance. Although the still large confidence intervals, the coalescence and phylogeography of (preHV)1 haplogroup (accounting for 18 % of Saudi Arabian lineages) matches a Neolithic expansion in Saudi Arabia.

Top
Abstract
Background
Results
Discussion
Conclusion
Methods
Authors' contributions
Supplementary Material
References BackgroundThis study represents mtDNA data regarding the population of Saudi Arabia. Geographically, desert is the most prominent feature of the Arabian Peninsula, which comprises the modern countries of Saudi Arabia, Yemen, Oman, the United Arab Emirates, Qatar, Bahrain, and Kuwait. Saudi Arabia occupies eighty percent of the Arabian Peninsula and is divided into five major regions – Central, Northern, Southern, Eastern and Western. From the western coastal region (At-Tihamah), the land rises from sea level to a peninsula-long mountain range (jabal al-Hijaz) beyond which are plateaus to the east. The southwestern 'Asir region has mountains as high as 3,000 metres (9,840 ft) and is known for having the most hospitable climate in the country. The east is primarily rocky or sandy lowland continuing to the shores of the Arabian Gulf. Although vast arid tracts dominate, stretches of coastline along the Arabian Gulf and the Red Sea and several major oases in the central and eastern regions have provided water necessary for human habitation. The coastal areas have been trading centers for centuries with resultant population diversity. In addition, for 1400 years the Haj has brought millions of Muslims annually to the region between Mecca and Jeddah, some of whom have stayed for generations. Traditionally, the central (arid) region of the country has had more population stability. More than 95% of the population now is settled in population centers that are mainly located along the eastern and western coasts and near interior oases such as Hofuf, Buraydah, and Riyadh.

The Arabian Peninsula is a region through which numerous migrations between Africa and Asia took place since ancient times. Anthropological [1,2], archaeological [3], and genetic [4,5] evidence has given support to the hypothesis that modern humans may have dispersed out of Africa, following a southern route through the Arabian Peninsula before they pursued a Levantine route [6]. According to this scenario, the Arabian Peninsula may have been the first step in the colonization of southern and eastern Asia. Middle Palaeolithic artefacts discovered in southwestern areas of the Arabian peninsula are similar to ones recovered in Africa, providing support for the suggestion that the Red Sea coasts may have been important in this southern expansion [7]. The presence of obsidian lithics on the African and Arabian sides of the Red Sea attests to Neolithic contacts as well. Archaeological evidence supports late Neolithic Levantine colonization of the Arabian Peninsula with successive population expansions and contractions depending on climatic conditions [8].

The strategic position of the Arabian Peninsula made it a crucial area for trade, cultural exchange, and warfare after the emergence of Old World Western civilizations. Mesopotamian states invaded the Arabian Peninsula from the north since prehistoric times [9], Ionic and Roman-Byzantine classic cultures took control of strategic trade routes in Arabia, and the Sassinid Persians dominated southern Arabia around 575 AD. Influences from the African side were also present as Pharanoiac Egypt and the Sudanese Meroitic and Abyssinian Askumite kingdoms extended their borders well inside Arabia [10]. Arabian Nabatean and Sabean cultures exerted their influence in turn on the Levant and Ethiopia, although to a lesser degree. Events changed dramatically with the rise of Islam in Arabia during the 7th century AD. In a short span of time, Arabs built a military and cultural empire that extended from Pakistan in the east to the Iberian Peninsula in the west. Even more complete Arabization occurred later in North Africa with the Bedouin Hilalian invasion in the 11th century AD.

The impact of these migrations on the Arab gene pool remains unclear because genetic information about the region has been scarce. Arab populations (Bedouin, Saudi, and Yemenite) are distinct from other Near East populations and from India and Central Asia in an analysis based on classical markers, suggesting the possibility of an ancient expansion from East Africa [11]. Early studies could not discriminate remote from recent contacts, but non-recombining uniparental markers have allowed more refined phylogeographic analysis at both continental [12,13] and regional [14,15] levels.

The rapid mutation rate of mitochondrial DNA (mtDNA) and Y-chromosome microsatellites permits estimates of lineage expansion age and of the most probable geographic origin of these expansions [16,17]. Only two studies regarding the Arabian Peninsula have been based on mtDNA. Lineage classification of a small sample of 29 Bedouins [18] revealed that 25 (86%) had a Eurasian origin, two (7%) belonged to the sub-Saharan Africa L0 and L2 haplogroups, and two were left undetermined. A study of 115 Yemeni mtDNAs showed that Eurasian-specific and African-specific lineages existed in almost equal proportion in that southern Arabian Peninsula sample [19].

In a sample of 120 Saudi Arabs, we sequenced the non-coding HVSI/II mtDNA regions and further characterized haplogroup diagnostic coding region positions by restriction fragment length polymorphism (RFLP) or by partial sequencing in order to estimate the genetic structure of the Arabian Peninsula and to search for archaic N and/or M lineages such as those found in India, Australia, and Southern-east Asia that trace a rapid human expansion outside Africa. The comparison of this sample to 2,204 classified sequences from the Near East and 728 from East Africa allowed us to estimate the relative gene flow between these areas and the Arabian Peninsula. We also provide a detailed mtDNA phylogeny of haplogroup (preHV)1, the most frequent and diverse haplogroup in the Arabian Peninsula. The analysis of this haplogroup, recently renamed R0a [20], is based on complete sequences and a global phylogeographic analysis based on 255 HVSI sequences.

References ResultsThe total number of different haplotypes in our sample of 120 Saudi Arabs were 107 (K = 89%) when HVSI and II variation and RFLP were taken into account [see Additional file 1]; however, the K value dropped to 64% when only partial HVSI variation was used in comparison with other populations (see Table 1). Some lineages had to be included into imprecise groups such as H/HV/R for haplotype and haplogroup frequency comparison, although all Saudi haplotypes were completely sorted into their respective clades and sub-clades [see Additional file 1]. The bulk of individuals (86%) belonged to the Eurasian macrohaplogroup N and its main R branch (75%), while the Sub-Saharan Africa macrohaplogroup L (7%) and the Asian macrohaplogroup M (7%) accounted for a smaller proportion of haplotypes.

Table 1
Haplogroup and macrohaplogroup frequencies in the Near East and eastern-African populations1, gene diversity (H) with standard error (± s.e.) and percentage of number of haplotypes per sample size (K)

Sub-Saharan African macrohaplogroup L lineages
Five of the eight Saudi Arabian L lineages belonged to different L3 sub-clusters. Although L3d is a widespread African clade, the single Saudi representative (Individual 49; [see Additional file 1]) had exact duplicates only in Yemen and Ethiopia [19]. L3f was the most frequent L3 cluster in Yemen and Ethiopia, and the sole Saudi L3f sequence (457) matched an Ethiopian sequence [19]. Sequence 429 was peculiar because it belonged to the recently defined East Africa haplogroup L3i [19] yet lacked the 16223 transition and included the 16318T transversion. The remaining two L3 sequences (221, 430) had L3h designation. One of them (221) harboured 16192–16218 transitions and presented the 16129-16223-16256A-16311-16362 HVSI motif that was first reported in West Africa [21]. The other (430) belonged to the subset of L3h sequences found in Ethiopia [19] and in Tanzania [22] that had the combined 16179–16274 HVSI motif. This haplogroup was present in moderate frequency in Ethiopians and Yemenis [19] but no matches existed between them and the Saudi population. The three remaining Saudi L haplotypes fell into the L2 macrohaplogroup. One of the sequences (433) belonged to the western L2c clade and had matches in West Africa Guineans [21] and in Mozambique [23]. The last two L2 Saudi sequences (225, 452) fell into the widespread L2a cluster [24] and had matches in East Africa and Yemen.
In general the sub-Saharan Africa maternal gene flow to Saudi Arabia was moderate (7%) and fell into the range found for other Arab populations in the Near East [25]. A small portion of this sub-Saharan Africa genetic input could be due to contacts with Yemeni communities from southern Arabia, but the most characteristic Yemeni L6 clade [19] was not present in the Saudi sample.

Macrohaplogroup M
Five of the eight M Saudi Arab lineages clustered into the M1 African haplogroup [26]. Three of them had the 16359 transition that was diagnostic of the M1a East African cluster, and the remaining one belonged to the rare but widespread M1b1 cluster characterized in the HVSI region by 16185 transition and the 16190d deletion that had been identified in the northwest Africa, Jordan, and the Iberian Peninsula [27]. The other three M sequences belonged to Indian clades. One had the basic motif (16126, 16223) of the M3 haplogroup [28]. A second had the 15928 and 16304 transitions that defined haplogroup M25 [29], although this sequence [see Additional file 1] did not match any of the definite or putative M25 sequences found in India [29-31] or Pakistan [26].
The last M sequence (16111A, 16223) has been found with the central motif in Bhoksa from Uttar Pradesh [32] and with the central motif and the 16129 transition in two derivatives in Yerava from South India [33]. Because these lineages were pooled as undetermined M*, we completely sequenced our sample (Ar201) and compared it to 91 complete Indian M sequences [34-36] to know its phylogenetic position. Our Ar201 sequence shared only transition 3010 with the basal mutations that defined haplogroup M34 [35] so that the most parsimonious tree clustered it with this haplogroup (Figure 1). However, we think that Ar201 may be representative of a new Indian branch of macrohaplogroup M because 3010 is a highly recurrent mutation that has independently appeared in the tips (M40) and sub-cluster roots (D4) of other M haplogroups. The M contributions to the Saudi Arab gene pool represented gene flow from East and North Africa (4%) and India (3%) but not from Central Asia.

Figure 1
Phylogenetic position of the haplogroup M Arab 201 sequence. All mutation differences are listed with respect to the revised Cambridge Reference Sequence (rCRS) [66]. This sequence has accession number DQ904234 in GenBank.

Macrohaplogroup N
All the main western Eurasian branches of N (R, N1a, N1b, N1c, I, W, X) were present in Saudi Arabia, with the least common ones (N1a, N1b, N1c, I, W, X) having an infrequent presence in Saudi Arabs (Table 1). N1a was the only one of these haplogroups that seemed to have a consistent presence across the Arabian Peninsula because it was also moderately frequent (6.9%) and diverse (h = 0.89) in Yemeni [19]. N1a frequency dropped to 4% in Saudi Arabs, where it harboured only two different haplotypes. The most abundant one, with the 16147A-16172-16218-16223-16248-16261-16274-16355 HVSI motif and the 41-73-199-204 HVSII motif, had not been observed in the Near East or in East Africa, and the second (16147G-16172-16223-16248-16355) was only shared with Ethiopians.
Saudi Arabs had the main European and western Asian haplogroups (H, J, T, K, U) included in R, the main branch of N, albeit in different frequencies. Haplogroup H was the most frequent cluster in European (45%) and Near East (25%) populations [16] but only accounted for 13% of Saudi lineages, comparable to the frequency in Bedouin and Yemeni. H frequencies significantly diminished with latitude from Turkey to Yemen through the Levant (r = 0.953; two-tail p < 0.01).

Haplogroups K (6%) and T (7%) had similar frequencies in Saudi Arabs to those found in Europe and the Near East [16]. However, the subgroup composition of haplogroup U clearly differed from Europe in Saudi Arabia and in other Near Eastern regions. The most prevalent haplogroup in Europe (U5) was represented in Saudi Arabs by only one U5a1a derived lineage [see Additional file 1]. Likewise, the North-African U6 haplogroup [15] is represented by only one lineage (1%). Several minority European U sub-clades (U1, U2e, U3, U4, and U7) may have had their origins in the Near East [16]. All of them had representative lineages in Saudi Arabs except for U4, U7, which were also absent from Bedouin of the Negev desert, and Yemeni samples (Table 1).

The rare haplogroup U9 was present in our sample with a frequency of 3% (Table 1). This haplogroup was first defined by RFLP-6383 HaeIII and observed only in South Pakistan [26]. It was later proven to be a sister branch of haplogroup U4 [37] on the basis of two complete U9 sequences (one Ethiopian and one Pakistani), both of which shared the 499–5999 motif. In addition to 6386, transitions at 3531, 3834, and 14094 defined the basal motif of U9. The Ethiopian sequence was considered representative of sub-cluster U9a and the Pakistani sequence as representative of sub-cluster U9b. The three Saudi U9 sequences belonged to U9a because all of them shared the HVSI 16051–16278 motif with the Ethiopian sequence while none of them shared any HVSI or HVSII mutations with the U9b Pakistani sequence ([see Additional file 1]; [37]). These three U9a sequences may be different occurrences of an old implantation of this haplogroup in the Arabian Peninsula.

A feature that differentiated Near Eastern populations from European and West Asian populations was the high frequency of haplogroups J and (preHV)1 [16,38], and this was also true for Saudi Arabia. J haplotypes represented 25% of the Saudi sample, and its main contributor was the J1b cluster (12%). Saudi and Bedouin samples showed an identical trend in this respect and were different from Yemenis, whose J1b frequency (4%) was similar to other Near Eastern samples (Table 1). The J1b frequency in the Arabian Peninsula was significantly higher than in the rest of the Near East, even when Yemenis were included (p < 0.0001). However, J1b in Arabia displayed a low level of haplotypic diversity in spite of its relative abundance (h = 0.57). Unlike the derived J1b1 lineage, J1b was scarce in North Africa [39] and practically absent in Europe [39] except for Italy [40].

Haplogroup (preHV)1 was even more frequent than J1b in Saudi Arabs (18%). The frequency of this sequence in Saudi Arabs was not significantly different from that observed in Yemeni Jews (20.4%) and Bedouins of the Negev desert (14%), but it dropped to 3.4% in Yemenis [19] (Table 1). Like J1b, the (preHV)1 frequency in the Arabian Peninsula was significantly higher than in the rest of the Near East (p < 0.001).

Phylogeny of haplogroup (preHV)1 based on complete mtDNA sequences
The relative abundance and diversity of (preHV)1 in the Saudi sample permitted more detailed phylogenetic and phylogeographical analyses of this haplogroup. The phylogenetic tree based on 13 complete mtDNA (preHV)1 sequences (Figure 2) confirmed that the basic motif of this group harboured the 2442, 3847, 13188, 16126 and 16362 transitions [41]. In addition, the transition at 64 was a basic diagnostic mutation for this haplogroup. Three main branches sprouted from this trunk. (preHV)1a was characterized by a transition at 827, while (preHV)1b was defined by the 57i-2355-15674 motif. The 15674 transition was already documented as a defining mutation of a group of (preHV)1 sequences comprising one Druze, one Eritrean, four Ethiopian Jews, and two Yemeni Jews [42]. (preHV)1c was a potential third branch that can be diagnosed by the 9531 transition because this mutation was shared by the EU258 sequence (Figure 2) and a partial sequence from a Moroccan Jew [42]. The Saudi Arab sequences 20, 448, and 505 (Figure 2) constitute a (preHV)1a1 sub-branch within (preHV)1a, defined by transitions 8292, 11761 and 16355. We excluded 58 and 146 as diagnostic positions because 146 was a highly mutable site and because the 58 change was recurrent within (preHV)1 (Figure 2). A (preHV)1b1 sub-cluster was defined by sequences IP969 and Ert41 that shared the 8701 transition. We estimated a radiation age of 18,959 ± 8,478 years for the entire (preHV)1 haplogroup. The (preHV)1a branch, with an age of 9,248 ± 7,604 years, is somewhat younger than the (preHV)1b branch (13,205 ± 7,193).
Figure 2
Haplogroup (preHV)1 phylogeny based on thirteen complete or nearly complete sequences. The Iberian Peninsula (IP969) and the seven Saudi Arab (Ar) sequences are from this study. Five additional sequences were taken from the literature as detailed in Methods. (more ...)

Phylogeography of haplogroup (preHV)1
Figure 3 shows the reduced median network obtained from 255 (preHV)1 haplotypes found in a global search comprising nearly 40,000 HVSI sequences. The basic central motif (16126–16362) was the most abundant and widespread, being present in all of northern Africa and in Eurasia from India to the Iberian Peninsula. However, Saudi Arabs were represented by only a single haplotype. The next most abundant clade, defined by 16355 and encompassing the majority of (preHV)1a1 sequences (Figure 2), was overwhelmingly composed of Near East and North African haplotypes with some European outsiders. Saudi Arabs again occupied more peripheral than central positions. The third most abundant clade was characterized by the 16304 transition and probably constituted a sub-cluster of the (preHV)1b branch represented in the genomic tree by the Ar439 sequence (Figure 2). The Arabian Peninsula was the major contributor to this clade.
Figure 3
Reduced median network relating (preHV)1 HVSI sequences. The central motif (star) differs from rCRS at positions 16126 and 16362 in HVI control region. Numbers along links refer to nucleotide positions minus 16000. Positions not used in diversity estimations (more ...)

In addition, several minority clusters provided valuable information. For instance, the one defined by 16309 was formed exclusively by East African sequences. The one identified by 16126 loss or by 16301 was centrally composed of Pakistani and Iranian sequences and had a derivative Yemeni sequence which pointed to some maternal gene flow to Yemen from those areas. The same could be said of the 16172 branch, although the gene flow was from Ethiopia to Saudi Arabia in this case. Ethiopia seemed to have been a secondary center of (preHV)1 expansions to the Near East, Arabian Peninsula, and northwest Africa, as could be deduced from branches defined by 16114 and the motif 16168–16266. Given the peripheral position of Saudi haplotypes, Saudi Arabia seemed to have acted more as receiver than a focus of (preHV)1 expansions with the exception of the 16304 clade. Radiation ages for the whole (preHV)1 haplogroup based on HVSI sequences were 18,993 ± 6,999 years; 9,624 ± 2,994 years for the 16355 ((preHV)1a1) sub-clade, and more recent for the 16304 subclade.

Population comparisons
We first performed AMOVA using haplogroup and haplotypic frequencies in order to assess the degree of homogeneity within and between the different geographic areas. As customary, the bulk of the variation was found within populations (99.32% for haplotypes and 97.71% for haplogroups). Variance distribution for haplogroups was greater among groups than among populations (1.34% vs. 0.95%), while variance distribution for haplotypes was less among groups than among populations (0.24% vs. 0.44%). Differences were highly significant in all cases (p < 0.001).
Pair-wise FST distances based on haplotype frequencies [see Additional file 3] showed that comparatively high heterogeneity within areas was due to the Druze sample that was significantly different from all the other populations, mainly because of a high frequency of haplotypes (27%) belonging to the minority haplogroup X and to K (20%). The Druze sample was a clear outlier in a graphic representation based on FST distances (Figure 4a), separating from the remaining populations along the first dimension. Founder effects or sample bias were the most likely causes of this deviation, as only two X1 and X2 haplotypes [43] accounted for the X percentage. In addition, Druze had the lowest diversity indices of all studied populations (Table 1). The second dimension of this haplotype analysis included the Arabian samples with those of east Africa, while Egyptians were aligned in the cluster of Near East populations.

Figure 4
Graphical relationships among the studied populations. Codes are as in Table 1. (A) MDS plot based on FST haplotypic distances. Stress value is 0.086. Dimension 1 axe has been shortened to include the Druze sample. (B) PC analysis based on haplogroup (more ...)

A somewhat different picture appeared after PC analysis based on haplogroup frequencies (Figure 4b). In this graph, the Druze were not outliers, most probably due to the fact that its variation is not correlated with that in other populations and therefore not reflected by the two first components. The first component separated all the Near East populations from a cluster including Egyptians and other east African groups. The majority of L haplogroups, pulling positively, and haplogroup H, pulling negatively, were predominantly responsible for this split. The second component divided the Near East cluster into three groups. The first comprised northeastern populations characterized by higher frequencies of H haplogroups and absence of L haplogroups. The second combined the Levantine population with Egypt, and the three Arabian Peninsula samples were left in a third group. The major determinants of the Arabian Peninsula singularity were the comparatively high frequency of (preHV)1, J1b, T5 and M3 haplogroups and the population specificity for other haplogroups such as L4, L6, U9 or U6b. This result was similar to that obtained using classical markers [11]. Saudi and Bedouin samples were relatively homogenous; however, the Arabian Peninsula as a whole was not homogenous because Yemenis were differentiated by a greater African component.

Top
Abstract
Background
Results
Discussion
Conclusion
Methods
Authors' contributions
Supplementary Material
References DiscussionMtDNA genetic analysis of this Saudi Arabian group revealed almost exclusively contributions from Africa and the Near East. All Saudi L, M and N lineages were derived from clades with roots in Africa and west and south Asia. The L4, L5, and L6 haplogroups recently found in Ethiopia and/or Yemen [19] were not detected in the Saudi population. Half of the sub-Saharan African Saudi lineages had exact matches in Ethiopians and/or Yemeni, pointing to these areas as the most likely source. The other half belonged to haplogroups with an East Africa origin or that reached the Red Sea in their eastern radiation [19,24]. The Arab slave trade and the expansion of empires from the Sudan and Ethiopia [25] could explain this moderate sub-Saharan Africa maternal contribution to the present Saudi Arabian gene pool.

The majority of M1 lineages in Saudi Arabia belonged to the eastern Africa M1a sub-clade that is particularly frequent and diverse in Ethiopia [19,44]. Ethiopia was again the most likely source. However, the sole M1b1 Saudi sequence probably reached the Arabian Peninsula from northwest Africa through the Levantine corridor because this sequence has been reported repeatedly in west Africa, the Iberian Peninsula, and Jordan [27], but not yet in Ethiopia. Based on Y-chromosome studies, this northern route was proposed as an important path for bidirectional human migration between north Africa and the Levant [45,46]. The remaining M lineages detected in Saudi Arabs had a clear Indian provenance. The basic Saudi M3 lineage out of India was shared by Yemenis and Iranians. Relatively recent contacts between India and the Arabian Peninsula by continental routes through Iran or by Indian Ocean maritime routes could be responsible of this Indian gene flow.

The overwhelming majority of N lineages present in Saudi Arabia had a clear western Asia provenance. Giving priority to geographically closest neighbors, 47% of the N lineages in Saudi Arabs were shared with other Arabian Peninsula neighbors (Bedouin from the Negev and Yemeni), 31% with Levantine populations, 16% with the Anatolian-Caucasus region, and only 6% with eastern Africa. These data revealed only a modest backflow of Eurasian lineages from Africa to the Arabian Peninsula. The close affinity found among Arabian Peninsula populations was due mainly to sharing Eurasian haplotypes and to similar Eurasian haplogroup frequencies and not to the sub-Saharan African contribution that is prominent in the Yemeni population.

The high frequency of (preHV)1 in Saudi Arabians was not significantly different from that found in Bedouin [18] and in Yemeni Jews (20%). However, this (preHV)1 frequency is significantly different of the non-Jewish Yemeni population [19] and may reflect strong genetic drift in the founding population of Yemeni Jews. The frequencies of L (10%) and J (26%) lineages deduced from published sequences of Yemeni Jews [47] were also similar to Bedouin from Negev desert and Saudi frequencies. In general, Jewish communities have evidenced strong maternal founder effects [47,48]. However, they usually harbor chromosome Y and mtDNA lineages that permit their most probable origin to be traced to the Near East because they share the most common haplotypes with those populations [47-50].

The majority of western Asia lineages found in the Arabian Peninsula had original Paleolithic and Neolithic expansions in the Near East [16] or in Caucasian and Caspian regions [26,51]. Most probably, these expansions reached the Arabian Peninsula as secondary waves when climatic conditions there or cultural improvements such as herding allowed colonization. The Arabian Peninsula has had a relatively low population density, and substantial demographic backflow to the Near East is improbable. However, as for M1, minor N North-African influences have been detected by the presence of an U6 lineage in our Saudi sample. It has been suggested that the rare U9 clade might be another interesting exception because it has been detected only in Pakistan [26], Ethiopia, and Yemen [19], and now in our Saudi sample. U9 occurs frequently only among the Makrani population in Pakistan, which is characterized by a large component of sub-Saharan African lineages, suggesting that U9 lineages in Pakistan might also have an African origin [19]. Makrani sub-Saharan Africa lineages have exact matches in Africa, which is compatible with a recent conection as the result of the East African slave trade [26]. However, the entire sequenced Ethiopian and Pakistani U9 lineages [37] are separated by a mean of 4.5 coding mutations from the common root, placing the split at Paleolithic times. Most probably, Ethiopia received its U9 lineages from the Arabian Peninsula that, in turn, received them from northern areas. The southern geographic distribution of U9 contrasts with the west-northern distribution U4, of its sister clade [52], but this is a pattern shared with other Paleolithic U radiations such as U2, U7 [32], or U8 [53] that have eastern and western branches. An original area west to India and east to the Capsian sea would be an equidistant point to conciliate these early U radiations [54].

It is difficult to differentiate successive gene flows or expansions at a population level because the most recent migration could carry both early and derivative lineages. However, the refined phylogenetic and phylogeographic analysis carried out for haplogroup (preHV)1 allows some inferences regarding Arabian Peninsula population history. The coalescence age for the entire (preHV)1 haplogroup was estimated at around 19,000 years ago, which is coincident with the beginning of the last ice age recession. However, in light of the peripheral distribution of the Arabian lineages in the phylogenetic tree (Figure 3), Arabian Peninsula populations most likely did not actively participate in this Paleolithic expansion. The subsequent radiation of the (preHV)1a1 clade occurred around 10,000 years ago, a date that marks the transition from Mesolithic to Neolithic in the Near East. The ancestral core of this cluster was defined mainly by Near Eastern lineages with important Arabian and Ethiopian participation. Finally, a third detectable expansion involving lineages carrying the 16304 transition seemed to be largely restricted to the Arabian Peninsula. Its coalescence age, most probably placed it in a period of empires flourishing in northern Arabia and on both shores of the Red Sea. The lack of archaic N and/or M autochthonous lineages in the Arabian Peninsula do not offer support for the proposed southern route of Homo sapiens sapiens outside Africa. Nevertheless, these ancient lineages may become apparent in larger samples.

Top
Abstract
Background
Results
Discussion
Conclusion
Methods
Authors' contributions
Supplementary Material
References ConclusionThe majority of Saudi-Arab mitochondrial DNA lineages (85%) have a western Asia provenance. All of the main western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade. The African contribution totalled 12%, with the sub-Saharan Africa (7%) contribution, represented by L macrohaplogroup, being only slightly higher than the M1 and U6 specific North-African contribution (5%). A small Indian influence (3%) was also detected; however, no archaic N and/or M autochthonous lineages in the Arabian Peninsula were found. Although the still large confidence intervals, the coalescence and phylogeography of (preHV)1 haplogroup (accounting for 18 % of Saudi Arabian lineages) matches a Neolithic expansion in Saudi Arabia.

gemini072 · Moderator Joined: 27 Nov 2004 {Posts: 2942 }

(The picture of Saudi Prince Bandar is from Cox Enterprises.)

G-Man · Moderator Joined: 27 Nov 2004 {Posts: 2992 }

Gulf Arabs-to me at least-show considerable African admixture. The ones from the Levant show less. Many of them look no different from Southern Europeans.

anonymouse · Wizard Joined: 09 Oct 2007 {Posts: 677 }

DesertDragon · Regular User Joined: 18 Jul 2007 {Posts: 70 }

DesertDragon · Regular User Joined: 18 Jul 2007 {Posts: 70 }

DesertDragon · Regular User Joined: 18 Jul 2007 {Posts: 70 }

gemini072 · Moderator Joined: 27 Nov 2004 {Posts: 2942 }

William · Posted: Mon 17 Dec 2007 15:30 Post subject: Re: Prince Bandar

Explorer · New User Joined: 07 Jan 2008 {Posts: 14 }

Seeing that M1 was mentioned in the header thread, I have the following to say; please brace yourself for the lengthy [perhaps uncomfortably lengthy for some of us] but perhaps necessary, if not interesting, compilation:

Abstract:

Mitochondrial lineage M1 traces an early human backflow to Africa

Ana M Gonzalez , Jose M Larruga , Khaled K Abu-Amero , Yufei Shi , Jose Pestano and Vicente M Cabrera

BMC Genomics 2007, 8:223 doi:10.1186/1471-2164-8-223

Published 9 July 2007

Abstract (provisional)

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

Background

The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a single origin of haplogroup M in Africa. To test the validity of that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA) sequences and 261 partial sequences belonging to haplogroup M1 was carried out.

Results

The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated.

Conclusions

This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.

And now, MY Response To Ana M. Gonzalez et al.

*First, a quick synopsis of the samplings, with regards to where the n=261 M1 bearing samples come from, aside from the 588 participants mentioned in one of the tables [table 2] in the study:

From my assessment of the table, it comes from the following numbers:

A total of 50 Europeans detected for M1.

A total of 154 for Africans.

A total of 28 Asians, barring 8 unknown Arabian haplotypes.

And a total of 29 Jews, who were lumped together from the various continents.

The sum of the above totals, amount to 261 "known" M1 lineages.

*With regards to the authors claim about M1 or its ancestor, having “had an Asiatic origin”, the following comes to mind:

The authors of the study at hand, themselves admit that they haven't come across M1 ancestor in either south Asia or southwest Asia. They also take note of its highest diversity in Ethiopia and east Africa. Yet through the shaky premise of their M1c expansion time frame estimations, they build a conclusion around it, by tying it to a dispersal(s) "parallel" to that of U6 - another African marker whose immediate common recent ancestor, namely proto-U6, appears to be elusive thus far.

Well, they wouldn’t be the only ones who have failed to come across any proto-M1 ancestor in southwest and south Asia [Indian Subcontinent mainly]:

Based on the high frequency and diversity of haplogroup M in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in Southwest Asia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 in Africa as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3]. Furthermore, the lack of L3 lineages other than M and N (indeed, L3M and L3N) in India is more consistent with the African launch of haplogroup M. On the other hand, one also observes that: i) M1 is the only variant of haplogroup M found in Africa; ii) M1 has a fairly restricted phylogeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly in association with the Afro-Asiatic linguistic phylum – a finding that appears to be inconsistent with the distribution of sub-clades of haplogroups L3 and L2 that have similar time depths. - Mait Metspalu et al.

So, while they acknowledge the highest "frequencies and diversities" of M1 particularly in Ethiopia, and generally in East Africa., the authors base their claims about ’origins’ on their expansion estimations of M1c derivatives, presumably predominant in northwest Africa rather than east Africa, and its relative sporadic distribution in 'Europe' and 'Southwest' Asia. They attempt to buttress this, by invoking a parallel expansion of M1 and U6 "ancestor" lineages into north Africa via the Nile Valley, then an expansion from northwest Africa this time around, of U6 and M1 derivatives northward into Europe and then eastward into "southwest" Asia via the Nile Valley corridor in the Sinai peninsula, presumably with a few derivatives making their way into sub-Saharan east Africa, where they then underwent some expansion, to give rise to yet another, but later, dispersal from there into "southwest Asia" and hence, accounting for the 'majority' of M1 lineages in "southwest Asia" being east African derivatives than the north African [M1c] counterparts.

*Furthermore,

The authors gather that their observations correlate with that of other researchers, namely Olivieri et al. To this extend, they put forth that Olivieri et al.’s M1b corresponds to their M1c, the former’s M1a2 corresponds to their M1b, and the former’s M1a1 corresponds to their M1a. They go onto to add that the coalescence ages arrived by the two research group [that of Olivieri et al. and that of the present authors] also correlate. The present authors note that their coalescence time for M1c (25.7 +/- 6.6 ky) overlaps with Olivieri et al.’s coalescence time for M1b (23.4 +/- 5.6). Similarly, they note that their coalescence age for M1a (22.6 +/- 8.1ky) falls within that of Olivieri et al.’s age for M1a1 at 20.6 +/- 3.4ky. However, this makes way for great discrepancy between the said authors and Olivieri et al., whereby their coalescence age for M1b at 13.7 +/- 4.8ky falls quite short of the latter’s age for M1a2 at 24 +/- 5.7ky. Not only are the subgroup nomenclatures distinct, but this latter discrepancy makes an unsubtle difference, so as to no longer render M1c to be older than M1b, but rather, either place M1c at an age a bit younger or on par with the latter, which should be otherwise according to the present study. Though, by their own admission, the present authors favor Olivieri et al.’s methods over their own:

As our calculations are based only on three lineages and that of Olivieri et al on six, we think that their coalescence time estimation should be more accurate than ours. In fact, when time estimation is based on the eight different lineages (AFR-K143 is common to both sets) a coalescence age of 20.6 +/- ky is obtained.

*But if there is any indication about the tenuous nature of the above thesis, without going into other known details about M1, it would be this alternative viewpoint they came up with:

The alternative idea entertained by the authors, is one where M1 could actually be an autochthonous northwest African lineage, which spread northward into Europe and eastward to "Southwest Asia" and east Africa. Again, to be followed by a yet later dispersal from east Africa, likely sub-Saharan east Africa, particularly the Ethiopian populations.

*The limitations inherent in solely relying on hypervariable segment motifs:

The status quo hasn't changed, not withstanding the hype about the supposed older expansion timeframes from M1c derivatives, predominant in Northwest Africa, according to their study. The authors rely heavily on the hypervariable region of the mtDNA, which even they themselves don't seem to put much faith on, as demonstrated by their noting of the need to proceed cautiously, given that random parallel mutations are known to occur across distinct macro-haplogroups and sub-clades. They also note how hypervariable nature of the control region, can lead to misleading calculations from erratic mutations, as demonstrated by the M1a2 they put forth, leading them to omit them in their lineage coalescence analysis.

*Another thing that hasn't been relayed through this study, is this:

The coding regions transitions are likely to change relatively slower than those of hypervariable segments, and hence, likely to remain intact within a clade. To assist in determining which clade to place a monophyletic unit, key coding region transitions have to be identified. In the case of M1, we were told:

We found 489C (Table 3) in all Indian and eastern-African haplogroup M mtDNAs analysed, but not in the non-M haplogroup controls, including 20 Africans representing all African main lineages (6 L1, 4 L2, 10 L3) and 11 Asians.

These findings, and the lack of positive evidence (given the RFLP status) that the 10400 C->T transition defining M has happened more than once, suggest that it has a single common origin, but do not resolve its geographic origin. Analysis of position 10873 (the MnlI RFLP) revealed that all the M molecules (eastern African, Asian and those sporadically found in our population surveys) were 10873C (Table 3). As for the non-M mtDNAs, the ancient L1 and the L2 African-specific lineages5, as well as most L3 African mtDNAs, also carry 10873C.

Conversely, all non-M mtDNAs of non-African origin analysed so far carry 10873T. These data indicate that the **transition 10400 C-->T, which defines haplogroup M**, arose on an African background characterized by the ancestral state 10873C, which is also present in four primate (common and pygmy chimps, gorilla and orangutan) mtDNA sequences. - Semino et al.

^Which is significant, as other M lineages are devoid of M1 coding region motifs, not to mention the M1 HVS-I package. The above does demonstrate, how M lineages likely arose on an African 'background' by single-event substitutions in the designated African ancestral counterparts. The ancestral transition of 10873C is substituted by 10873T in non-African non-M haplogroups, while the 10400C transition was substituted in M lineages by 10400T.

Furthermore,...

The 489C transition, as noted above and can be seen from the diagram, is peculiar to the M macrohaplogroup, again suggestive of unique event mutations characterizing the family:

The phylogenetic location of the mutations at nt 489 and 10,873 (arrow) was predicted by our analysis. The seemingly shared mutation at nt 16,129 (by G, Z and M1) is very likely an accidental parallelism. The ancestral states 10400C, 10810C and 10873C are fixed in L1 (as analysed so far) and are present in the ape sequences.

The 16129 sharing across the M1 haplogroups, seems to be one of those instances of random parallel mutation, recalling Chang Sun et al.'s observations of random parallel mutations of certain transitions across the M macrohaplogroup.

We also know that "southwest Asian" and "European" M1 lineages are derivatives of African counterparts, and the same is true for southwest Asian non-M1 affiliated M lineages from south Asia:

Compared to India, haplogroup M frequency in Iran is marginally low (5.3%) and there are no distinguished Iranian-specific sub-clades of haplogroup M. All Iranian haplogroup M lineages can be seen as derived from other regional variants of the haplogroup: eleven show affiliation to haplogroup M lineages found in India, twelve in East and Central Asia (D, G, and M8 ) and one in northeast Africa (M1)…

Indian-specific (R5 and Indian-specific M and U2 variants) and East Asian-specific (A, B and East Asian-specific M subgroups) mtDNAs, both, make up less than 4% of the Iranian mtDNA pool. We used Turkey (88.8 ± 4.0%) as the third parental population for evaluating the relative proportions of admixture from India (2.2 ± 1.7%) and China (9.1 ± 4.1%) into Iran. Therefore we can conclude that historic gene flow from India to Iran has been very limited.

With that said, Semino et al.'s older study still remains strong, the way I see it:

haplogroup M originated in eastern Africa approximately 60,000 years ago and was carried toward Asia. This agrees with the proposed date of an out-of-Africa expansion approximately 65,000 years ago10. After its arrival in Asia, the haplogroup M founder group went through a demographic and geographic expansion. The remaining M haplogroup in eastern Africa did not spread, but remained localized up to approximately 10,000−20,000 years ago, after which it started to expand.
- Semino et al.

Elsewhere, I've also talked about some 'basal' M-like lineages in Africa; for instance, at least one of such was identified in the Senegalese sample.

Am. J. Hum. Genet., 66:1362-1383, 2000
mtDNA Variation in the South African Kung and Khwe and Their Genetic Relationships to Other African Populations

"The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage..."

^The 10397 transition is shown in the L3-M linkage, while 10394, which should show up as positive [as exemplified in the above extract] in the M macrohaplogroup, shows up negative in the linkage between L3 and non-M affiliated lineages.

**^To put the above compilation into perspective, and keep it simple, the point is this:

Semino et al.'s demonstration of certain characteristic basic coding transitions of the M super-haplogroup [not including the key coding region motifs unique to the M1 family], springing directly from African ancestral motifs, don't require that M1 has to have a proto "non-African" M1, whereas an Asian origin of M1 would necessitate an Asian proto-M1 lineage that would explain the relatively young expansion ages of M1 and lack of descendancy from pre-existing Asian M lineages. This hasn't been acheived either by the present study or ones prior to it.

Getting to the gist: The studies I posted, suggest that the basal motifs characteristic of the M macrohaplogroup arose in Africa, anywhere between 60-80 ky ago [since they would have likely been in the continent by the time of the 60 ky ago or so OOA migrations] . Sometime between 60 ky and 50 ky ago [some sources place it between 75-60 ky ago], these L3 offshoots were carried outside of Africa, amongst early successful a.m.h migrations, which resulted in the populations now living in the Indian-subcontinent, Melanesia and Australia who have these lineages. Not all the basal African L3M lineages, as Semino et al. convincingly put it, left the continent, as indicated by the basal L3a-M motif detected in Senegal, M1 diversity in Africa, particularly East Africa, both M1 and other M lineages detected in Ugandan samples, and lack of descendancy of M1 from older-coalescent Asian macrohaplogroup. Rather, it appears that the basal L3M lineages which remained in Africa, underwent a relatively limited demographic intra-African expansion until relatively recently, i.e. between 30-10 ky ago, compared to the Asian L3M derivatives, which underwent major expansions, naturally within the quantatively smaller founder immigrant groups, i.e. the founder effect.

M1 is likely the culmination of relatively more recent demographic expansions of basal L3M lineages in the African continent, with M1 derivative being a successful candidate, in what could have possibly involved other derivatives which might not have expanded to the same level intra-continentally, and subsequently, extra-continently as well.

M1 has strongly been correlated with the upper Paleolithic expansion of proto-Afrasan groups across the Sahara to coastal north Africa, and further eastward via the Sinai peninsula.

punjabtrini · Mentor Joined: 04 Sep 2007 {Posts: 253 } Location: USA

The roots of al Arabiyya are in Yemen and Saudi Arabia!
There have always been gene flow exchange between East Africa and the Arabian Peninsula.

ArabianKnight said

William · Posted: Fri 11 Jan 2008 15:12 Post subject:

Splendid job, Explorer, and I agree fully. You have explained it infinitely better than I could ever hope to. I hope you stick around for a while!

It is interesting, but certainly not surprising, that a few non-M1 M-lineages in Africa look to have African (and not Asian) origins as well.

I have long been of the mindset, based on the evidence, that European M1 lineages (mainly found in Iberia, Italy, Greece, Turkey, and the islands of the Mediterranean, notably Sicily) derive ultimately from Africa, and your explanation bears this out.

Thanks for joining and helping to educate us all!

punjabtrini · Mentor Joined: 04 Sep 2007 {Posts: 253 } Location: USA

Explorer,

Thank you! That is science at its apex!
Actually, I look like Bandar in real life.

Explorer · New User Joined: 07 Jan 2008 {Posts: 14 }

To those who appreciated my "lengthy" post,

I'm glad to join a forum that is filled with bright and disciplined posters; trust me, it is a hard thing to come by in many internet discussion forums. So, I'll very likely peep in from time to time to see what I can learn from others here, as well as what I'd like to share with others. Thanks for the feedback.

William · Posted: Mon 14 Jan 2008 03:24 Post subject:

gemini072 · Moderator Joined: 27 Nov 2004 {Posts: 2942 }

The Egyptian Physician, artist and aeromodeller Dr. Khalil Messiha spent more than four years searching about the Hall of records or the secret burial chamber of King Khufu (Cheops ). Sometimes this took place in the early morning or mid-day, or midnight. In the beginning of 1967, he applied officially to the Egyptian Antiquities Department, and was permitted to work under the supervision of their officials. His dowsing instruments indicated the presence of a corridor under the floor of the "Queens room" near its western wall, and that it extends downwards twenty meters, where it led to the Khufu`s burial chamber. The Queen's chamber was covered with a thick layer of mud, ten centimeters thick, that masked any sign of the entrance indicated by dowsing. The workers removed the mud layer, exposing the floor which is made of huge stones (lime stone) of different dimensions, some estimated to weigh over 30 tons. During the process of clearing the mud layer, he found chips of bronze engraving tools and these were sent to the laboratory of the Antiquities Department. The workers found it extremely difficult to move the stones over the entrance and they were content to drill a hole through it, through which they passed a long wire which went down and down. Also through that hole, they procured a sample of powdered "mortar", reddish in color, which was also sent to laboratory. Dr. Khalil was permitted to work for only ten days, after which he received an official order to halt his excavations, and let a "Cosmic Rays" project begin, which had just arrived, sponsored by an American, Dr. Alvarez, and aimed to explore the 2nd pyramid of Khephren rather than the Great pyramid of Khufu. When he discussed this with the officials, they said when the Cosmic Rays work is finished, you can resume his excavations. After four years the Cosmic Rays Project got no definite results, as the force fields (of a radiesthetic nature) led the utilized electronic devices astray. Up to the year 1986 the work of Dr. Khalil Messiha was postponed until a French expedition arrived and drilled holes in the corridor leading to the Queen's chamber. This led Dr. Khalil to meet again with the General Director, Dr. Ahmed Kadry. He asked Dr. Khalil for more experiments at other sites (including the Sphinx), which he finished two years later and found an exciting discoveries. In the year 1986 a Japanese expedition using certain radar devices which can penetrate 2-4 meters into these ancient structures. They also found several cavities, and particularly referred to a cavity near the western wall of the Queen's chamber. But the Japanese electronic devices indicated that it is a long cavity though they could not discern one more than two or three meters in length. But the story didn't reach the end yet, because Dr. Khalil said in the year 1967 that he is the opener of the way to the "Hall of Records", and he will not go inside. He added that the world will not be able to open it until the year 2000. Dr. Khalil Messiha was passed away in peace on 29 Dec. 1998.

http://www.geocities.com/dawoudkhalil/Hallofrecords.htm

He reminds me of Langston Hughes

gemini072 · Moderator Joined: 27 Nov 2004 {Posts: 2942 }

sirius2008 · New User Joined: 26 Mar 2008 {Posts: 38 }

sirius2008 · New User Joined: 26 Mar 2008 {Posts: 38 }

sirius2008 · New User Joined: 26 Mar 2008 {Posts: 38 }

Here are typical people of the Arabian peninsula: