Wednesday, December 15, 2010

The Bedouin


Bedouin Chief of Palmyra, Tadmur, Syria between 1890 and 1900

I've mentioned in a previous post that I'm hesitant to associate ADMIXTURE component results with Y-chromosome haplogroups without a strong correlation between the two.  After several months of looking at ADMIXTURE results, it seems clear that one method of analysis is to identify a population that is representative of a particular component.  From there, one can infer other relationships, including Y-chromosome relationships. 

Many of you are aware of the recent Charioni et al paper for the distribution of the y-chromosome J1e haplogroup:

The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations
Chiaroni et al.

"Abstract:  Haplogroup J1 is a prevalent Y-chromosome lineage within the Near East. We report the frequency and YSTR diversity data for its major sub-clade (J1e). The overall expansion time estimated from 453 chromosomes is 10,000 years. Moreover, the previously described J1 (DYS388=13) chromosomes, frequently found in the Caucasus and eastern Anatolian populations, were ancestral to J1e and displayed an expansion time of 9,000 years. For J1e, the Zagros/Taurus mountain region displays the highest haplotype diversity, although the J1e frequency increases toward the peripheral of the Arabian Peninsula. The southerly pattern of decreasing expansion time estimates is consistent with the serial drift and founder effect processes. The first such migration is predicted to have occurred at the onset of the Neolithic, and accordingly J1e parallels the establishment of rain-fed agriculture and semi-nomadic herders throughout the Fertile Crescent. Subsequently, J1e lineages might have been involved in episodes of the expansion of pastoralists into arid habitats coinciding with the spread of Arabic and other Semitic-speaking populations."

Because J1e (also named J1c3) has its highest haplotype diversity in the Zagros/Taurus mountain range, it is likely to have originated there. The expansion time cited in this paper for J1e is concurrent with the domestication of goats and sheep.  Domestication would have allowed hunter-gatherer groups to expand beyond the range of the animals they hunted.

In my previous post, I looked at the advance of domesticated animals along the Levantine Corridor.  The slow advance (0.3km/year) southward in the Levant suggests that shephards encountered an already populated region.  This might have made it attractive to move eastward into the less inhabited Arabian desert. 

During the Terminal Pleistocene, hyperaridity and climatic instability would have made the Syro-Arabian desert uninhabitable, but following this period, this region experienced greater humidity(See Reference 1):

"The onset of conditions is related to the northwards migration of the Inter Tropical Convergence Zone (ITCZ) owing to increased heating across the northern Hemisphere (sensu de Menocal et al, 2000).  Stalactitie records from Southern Oman (Fleitmann et al, 2007) record the northwards movement of the ITCZ and incursion of the IOM [Indian Ocean Monsoon] by 10.3 kya into southern Oman and northern Oman by 9.6ka (Neff et al, 2001).  At Awafi the cessation of dune emplacement occured at 9.0kya (Goodie et al, 2000) and the onset of lacustrine sedimentation did not take place until 8.5 kya (Parker et al. 2004).  Thus, it took ~1,800 years for the IOM to move from Southern Arabia (15 dregrees N) to Northern Arabia (25 degrees N). This provides important information on the time lag and northwards migration and latitudinal position of the summer ITCZ and incursion of monsoon rainfall across the eastern sector of the Arabia during the Early Holocene.  The impact of human migration into and across Arabia during the Early Holocene would have been profoundly influenced by this variation in moisture across the peninsula.

"Evidence from Awafi, UAE, indicates that the dune field became stabilized and vegetated during the Early Holocene with a predominant mix of C3 grasslands and scatters of woody elements including Acacia, Prosopis and Tamarix (Parker et al., 2004).  The evidence for a rich cover of grasslands supports the archaeological evidence for Neolithic herding between the mountains, desert and coast during the period of maximum monsoonal rainfall (Uerpmann, 2002)(Reference 2).

"Lacustrine and speleothem records suggest the IOM weakened and retreated southwards around 5.9kya (Neff et al, 2001; Uerpmann, 2002; Parker et al., 2004, 2006a).  The retreat of the IOM led to the cessation of the Hoti cave speleothem, which records a large reduction in precipitation immediately prior to this date (Neff et al, 2001).  The lakes of the central Rub' al Khali also ceased to exist beyond this point (McClure, 1976).  The reduction in precipitation led to a lowering of the lake level at Awafi, unlike central Rub'al Khali lakes, which did not dry up completely.  For the lake to have persisted, it is suggested that westerly winter rainfall must have existed in the Gulf region to have maintained the lake.  Change in precipitation from IOM to westerly sources is marked by a sharp change from C3 to drier adapted C4 grasslands across the dune field (Parker et al, 2004).  A similar pattern of winter rainfall was postulated in the Nafud in western Arabia (Schultz and Whitney, 1986).  The archaeological record indicates that the Arabian Bifacial Type/Ubaid period came to an abrupt end in eastern Arabian and the Oman peninsula at 5.8ka and no evidence of human presence exists to the area for ~1,000 years (Uerpmann, 2002).  This period has been described as the 'Dark Millennium' in the Arabian Gulf region because of the lack of known archaeological sites (Vogt, 1994, Uerpman, 2002).  In contrast to the sites on the Arabian Gulf [or Persian Gulf], those on the Omani coast continued into the 4th millenium and persisted during the dry period (Uerpmann, 2002).  It has been suggested that climatic deterioration caused dramatic changes in semi-desert nomadism, subsistence, and settlement patterns around 5.8ka.  The number of known sites suggests that the population shrank considerably at this time and became concentrated in the few parts of Arabia which offered greater ecological diversity (Uerpmann and Uerpmann, 1996; Parker et al, 2004)."

Thus there was a population expansion into the Arabian peninsula starting 9,000 years ago which took advantage of an increasing period of rain.  It was then subjected to a bottleneck as the rain subsided 5,800 years ago.

Today, 65% of Yemen-Saudi and 38.5% of Palestinian men carry the J1e haplotype.(Link)  According to Charioni et al, it is distributed throughout the Arabian Peninsula among Arab speakers.  Among the Bedouin of Kuwait, 84% of sampled individuals were J1(Mohammed et al, Reference 3).  The remaining y-chromosome haplogroups are:  R1a1 (6.75%); E3b3 (6%); G2 (3.4%); R1b3 (1.35%).  Other samples indicate K2, E3b1, Q* and R2.  (See Table 3 in reference 3.)

Unfortunately, the Mohammed paper doesn't indicate whether the J1 they report is J1e.  However, the Chiaroni paper seems to indicate that it is.

The very high incidence of J1e in the Bedouin population points to the origin of the ADMIXTURE Southwest Asian component that appears for the Behar et al data set.  Revisiting the Fertile Crescent plot from the post Eurogenes K10 Middle East Admixture Results, the Bedouin, with their >60% Southwest Asian component, sit distinctly on the right of the plot:


Given the 84% incidence of J1 among the Bedouin of Kuwait in combination with the 60% incidence of the Southwest Asian component for Bedouins (Behar et al data set), it is very likely that they are strongly correlated.  If the Chiaroni paper is correct, the origin of J1 is in the Taurus-Zagros Arc. Thus, it is likely that the origin of the Southwest Asian component is also in the Taurus-Zagros Arc.  Its expansion southward is associated with the expansion of nomadic pastoralists advancing into the Indian Ocean Monsoon rainy period in the Arabian peninsula between 9,000 to 6,000 years ago.  From the plot, it is notable that more than 90% of the autosomal genetic makeup of Bedouins and Saudis are likely of a Taurus-Zagros origin.

There has been much debate surrounding demographic processes in the Arabian pensinsula.  To illustrate, I quote a comment from the superlative text The Evolution of Human Populations in Arabia (See Reference 1 and 2):

"At all events, it is unlikely to have been an event and much likelier to have been a process which may initially have involved hunters and gatherers coming from the south, soon followed by aceramic herders from the northwest using some variant of PPNB-related lithic technology.  How and where they met and mixed and how they sorted out their subsistence economies is a fascinating topic for future research." (Uerpmann et al 2009, Reference 2).

ADMIXTURE analysis of the Behar et al data set offers a partial answer to the demographic process on the Arabian peninsula:  "Aceramic herders from the northwest" compose more than 90% of the genetic make up of Saudis and the Bedouin.

The effect of climate during the 'Dark Millenium' may account for the variability in Y-STR diversity sited in the Charioni et al paper: 

"The timing and geographical distribution of J1e is representative of a demic expansion of agriculturalists and herder–hunters from the Pre-Pottery Neolithic B to the late Neolithic era. The higher variances observed in Oman, Yemen and Ethiopia suggest either sampling variability and/or demographic complexity associated with multiple founders and multiple migrations." 

The demographic complexity cited in Oman, Yemen and Ethiopia could be a result of the wetter climate in southern coastal Oman and the Yemen/Ethiopia region during the 'Dark Millenium'.  Populations in UAE and Qatar were likely not so lucky and were subjected to a bottlenecking effect.

The northern and southern split in proto-Semitic mentioned by the 2009 paper "Bronze Age origin of Semitic languages" 6000 years ago is also coincident with the 'Dark Millenium' and the depopulation of the central Arabian peninsula.  Nomadic populations of this region probably struggled to make an exit north or south during this sudden dry period.  The diversity of semitic languages in Ethiopia is suggestive of one route of exit.

Further analysis of the phylogenic relationship of the J1 Y-chromosome across Fertile Crescent populations will be necessary to definitively say that the J1 haplogroup and the Southwest Asian component originate on the Taurus-Zagros Arc.  However, the combined picture of domestication, climate, archaeological evidence, linguistic data, y-chromosome data and ADMIXTURE autosomal data would indicate a Northern Fertile Crescent nomadic pastoralist origin for both in the early Holocene.

References:

(1) Parker, A. G. (2009) Pleistocene climate change from Arabia - developing a framework for hominin dispersal over the last 350kyr:  Late Quaternary Climate Change in Arabia:  lacustrine records from MIS 9-1.  In Petraglia, M., and Rose, J. (eds).  The Evolution of Human Populations in Arabia. Vertebrate Paleobiology adn Paleoanthropology. Dordrecht:  Springer Science, pp. 39-49. (Link)

(2) Uerpmann, H-P; Potts, D.T.; Uerpmann, M; (2009) Holocene (Re-)Occupation of Eastern Arabia.  In Petraglia, M., and Rose, J. (eds).  The Evolution of Human Populations in Arabia. Vertebrate Paleobiology adn Paleoanthropology. Dordrecht:  Springer Science, p. 205. (Link)

(3) Mohammed, T; Xue, Y; Evison, M; Tyler-Smith, C; Genetic structure of nomadic Bedouin from Kuwait (Link

4 comments:

  1. In Dienekes' latest K=15 ADMIXTURE run he identified a cluster named 'Red sea' which peaked in Ethiopian_Jews, followed by Bedouins. It has similar frequencies as the K=10 'Southwest Asian' cluster. Doesn't this perhaps indicate that the SW Asian cluster could be partially Northeast African and partially West Asian?

    URL: http://dienekes.blogspot.com/2010/12/human-genetic-variation-first.html

    ReplyDelete
  2. Hi Perahu,

    The Eurogenes K10 Run I am using for the Fertile Crescent Analysis, as well as Dienekes' K10 Eurasian runs from October (http://dienekes.blogspot.com/2010/10/more-detailed-analysis-of-eurasian.html) correspond, approximately, to his current K=9, 10, 11, and 12 ADMIXTURE runs.

    At these K value, results seem to correlate with root branches of haplogroups: J1 and J2, for instance. At higher values of K, we may be looking at components and combinations of components that are further down the phylogenic trees.

    I've indicated in my post that J1 is a "candidate" for the SW Asian component. I haven't run the appropriate correlation statistics, so keep this in mind.

    Based on the distribution of Dienekes' latest admixture run at K=15, the component 1 that you mention may be an effect of the E haplogroup. It's notable that it appears in the Maasai which have a high incidence of E.

    Note that Greeks and Assyrians show a minor K15, component 1 contribution.

    Here's the map for E:

    http://en.wikipedia.org/wiki/File:Haplogrupo_E-ADN-Y.GIF

    and the wiki page:

    http://en.wikipedia.org/wiki/Haplogroup_E_(Y-DNA)

    K15, component 1 may be associated with a subclade of y-DNA E. It may also be associated with mtDNA M or L. Multiple sources are possible.

    A more geographically precise sampling of Southwest African and Red Sea populations with sub clade analysis would be necessary to be more certain of the source of K=15, component 1.

    In any case, I suspect that E is at least partly grouping in the South European component in my K10 runs, so I can't classify it as either South European or Southwest Asian.

    ReplyDelete
  3. You're welcome. Good question.

    ReplyDelete

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