Friday, December 31, 2010

Happy New Year!

A break from genetic anthropology and a bit of hockey history . . .


USSR vs Canada 1972 (Link)

Valeri Kharlamov (Link)

Phil Esposito (Link)

Wednesday, December 29, 2010

Assyrians and the ADMIXTURE Southwest Asian Component Revisited

Last month, I wrote a series of articles in which I tried to date the expansion of the ADMIXTURE Southwest Asian component.

Assyrians,
Demic Diffusion Model:  Bounded and Unbounded,
Estimating a First Arrival Date for Southwest Asian peoples in the Fertile Crescent

In writing these articles, I was under the assumption that the Southwest Asian component emerged in the Arabian peninsula and moved northward.  I had used Assyrians as a timestamp of a Northern Fertile Crescent population that had not changed in the last 3500 years, but had absorbed the Southwest Asian component during the Bronze Age. From this assumption, I then tried to date the introduction of the Southwest Asian component into the northern Fertile Crescent.

As discussed in yesterday's post, it is clear that the J1e y-chromosome haplogroup, which is spatially correlated with the ADMIXTURE Southwest Asian component, originated in the Zagros Mountains with an expansion time of 16.2 kya (SD 6.4 kya).  Clearly, Assyrians, as a Zagros descended people, have not acquired the J1e haplogroup during the Bronze Age!

The distribution of the J1 haplogroup is deceptive in that its area of greatest frequency on the Arabian peninsula is not distributed about its region of origin.   That's certainly a warning about making assumptions about origin from spatial frequency distributions.

My original curiosity about the Southwest Asian component stemmed from looking at ADMIXTURE results for European populations.  The Southwest Asian component does not appear in Northern European countries while Mediterranean populations possess it in small proportions (See Dodecad K10 ADMIXTURE result.)  Even more curiously, all European populations, with the exception of French Basques and Sardinians, have a proportion of the West Asian component. 

One question I asked myself is "Why does the West Asian component, but not the Southwest Asian component, appear in Northern European populations?"

In these November articles, I assumed that the Southwest Asian component had been confined on the Arabian peninsula at the time of the early expansions into Europe.   As it turns out, the Southwest Asian component and the J1e y-haplogroup have been distributed, along with the West Asian component, throughout the Fertile Crescent and the Arabian peninsula for at least 9,000 years (Chiaroni, et al).

The El-Sibai et al paper

lends a possible answer to the absence of the J1 haplogroup in Europe as well as to why ADMIXTURE detects two separate components in West Asia: "We sought, through STR network analysis, to assess whether or not the observed geographic distribution of each haplogroup was reflected in geographic variations of STR haplotype distributions. The J1 and J2 (Fig. 5A) sister clades depicted a clear non-uniform geographic distribution of STR haplotypes and few instances of haplotype sharing across geographic regions. Consistent with previous analyses, coastal Levantine regions were well represented in the J2 network. The J1 network was dominated by inland Levantine samples (mainly Jordan and inland Lebanon and Syria)." This suggests populations correlated with the J2 y-chromosome haplogroup as a source of the West Asian component in Europe. J1 y-chromosome correlated populations remained inland and separate from their coastal J2 cousins.

This separation in the J1 and J2 correlated populations may have existed over millenia. Early Holocene J2 (and other coastal agriculturalist populations) could have travelled from West Asia to Europe, bringing with them the West Asian component, but not the Southwest Asian component. Eventually, the Neolithic wave of advance across Europe carried the West Asian component as far north as Scandinavia. Meanwhile, back in the Bronze Age Levant, the J1 and J2 populations once again came into contact with each other. From the Bronze Age onward, these J1/J2 populations established themselves throughout the Mediterranean. This would account for the Southwest Asian component that appears in Mediterranean populations such as Tuscans and Greeks.

For simplicity, I've ignored the contribution of other West Asian haplogroups to Europeans such as y-chromosome haplogroup G.

My apologies for this error. I hope that the above is a more plausible explanation for the distribution of the J1 haplogroup and the Southwest Asian component.

Tuesday, December 28, 2010

The Origin of Y-chromosome Haplogroup J1: Another Lake, Other Rivers

What a surprising story the J1e haplogroup tells.  Thanks to the work of Chiaroni et al (1), Sengupta et al (2005)  and El-Sibai et al (2), we have detailed spatial frequency distribution maps of the J1 and J2 y-chromosome haplogroups.  Chiaroni et al, with their detailed samplings of the Lake Van and Greater Zab River areas, also pinpoint the region of greatest J1e and J1* variance spatial distribution.  Table 1 of the Chiaroni paper describes expansion times, mean YSTR variance and archaeological correlates for all of their sampled populations.  Three populations are boldface standouts:  Alawites of coastal Syria with a mean J1e YSTR variance of 0.37 and an expansion time of 16.1 kya (SD 4.5 kya), Assyrians (Northern Syria, Northern Iraq, Lake Van and Urmia in Iran) with a mean J1e YSTR variance of 0.43 and an expansion time of 16.2 kya (SD 6.4 kya) and J1* Turks with a J1* expansion time of 20 kya (SD 7.5 kya).

Figure 1 results in the paper are vivid:

"(a) Red symbols indicate the geographical locations of 36 populations analyzed. (b) Interpolated spatial contours of annual precipitation (mm) distribution. (c) Interpolated J1* frequency spatial distribution. (d) Interpolated J1e frequency spatial distribution. (e) Interpolated J1e mean haplotype variance spatial distribution. (f) Construed trajectories of J1e lineage spread episodes. In red are delineated the initial Holocene migrations from the Taurus/Zagros Mountains to the Arabian Peninsula. Shown with black arrows are the subsequent expansions of Arabic populations in Arabia beginning in the Bronze Age."

Figure 1c and 1e are highly suggestive of a J1*-J1e origin in the Lake Van region of Turkey.  It is notable that Lake Van lies at the nexus of the Aras and Tigris Rivers which I have described in previous posts Rivers, Lakes and Mountains and Northern Fertile Crescent Hunter Gatherers.  According to Figure 1f, the expansion trajectory of J1e between 11 and 8 kya is threefold:  southwestward to what appears to be the Orontes River in Syria, southward to the Arabian peninsula and southeastward along the Greater Zab and Tigris Rivers.

Lake Van and the Greater Zab River present a beautiful if windswept picture.  No doubt, the climate during the Mesolithic period was even colder and dryer in this region than it is today.  The Mesolithic ancestors of J1 must have been an inventive and resourceful people to have survived:

The Akhtamar Island in Lake Van with the 10th century Armenian Cathedral of the Holy Cross

As Table 1 notes, the J1e ancestors of the Assyrians of Lake Van and the Greater Zab River, as well as J1* Turks of Lake Van, originate from a common ancestor some 16 kya.  Zagros archaeological results for this period, known as the Zarzian, are at the cutting edge of current research and are giving us some idea of the lifestyle of these Mesolithic people (references 3, 4 and 5).  A map illustrates the region of the Zarzian Mesolithic:

Geometric Kebaran 16,000BC-12,500BC calibrated (Radiocarbon Context Database (Link))

I will note also that the Zarzian Mesolithic region shows a surprising correspondence with the LBK Derenberg graveyard genetic analysis (Haak et al):

Figure 3A and 3B
"Mapped genetic distances are illustrated between 55 modern Western Eurasian populations and the total of 42 Neolithic LBK samples (A) or the single graveyard of Derenburg (B). Black dots denote the location of modern-day populations used in the analysis. The coloring indicates the degree of similarity of the modern local population(s) with the Neolithic sample set: short distances (greatest similarity) are marked by dark green and long distances (greatest dissimilarity) by orange, with fainter colors in between the extremes. Note that green intervals are scaled by genetic distance values of 0.02, with increasingly larger intervals towards the “orange” end of the scale."

This leads me to wonder if further analysis of  the Derenburg LBK y-DNA would yield J1* and J1e y-chromosome haplogroups.  The Assyrians sampled in the Chiaroni paper showed the highest J1e variance but also have a G y-chromozome haplogroup correlation which corresponds with the y-chromosome results at Derenburg.

Other results emerge from the Chiaroni et al and El-Sibai et al papers.  A clear split appears in the expansion pattern between the J1 and J2 y-haplogroups:  The J1 expansion is associated with pastoralism;  J2 demonstrates a coastal agriculture expansion pattern.

In keeping with my post on The Bedouin, both papers also support the notion of an expansion of J1e onto the Arabian peninsula, followed by an exodus from the Central Arabian peninsula approximately 6000 years ago with the cessation of Indian Ocean Monsoon induced rains.



References

(1)  Chiaroni et al;  The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations (Link)

(2)  El-Sibai et al;  Geographical Structure of the Y-chromosome Genetic Landscape of the Levant:  A coastal-inland contrast (Link)

(3)  The Central Zagros Archaeological Project Biblographic Reference List (Link)

(4)  Solecki, Ralph S.; Rose L. Solecki, Anagnostis Agelarakis; The Proto Neolithic Grave at Shanidar Cave (Book), Texas A&M University Anthropology Series

(5) Peasnall, B; Iranian Mesolithic in Encyclopedia of Prehistory:  South and Southwest Asia, Volume 8, University of Pennsylvania Museum Near East Section, pp. 205-214.
(Link)

Monday, December 27, 2010

Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast

El-Sibai et al
(Link)

Results:  "The J1 and J2 (Fig. 5A) sister clades depicted a clear non-uniform geographic distribution of STR haplotypes and few instances of haplotype sharing across geographic regions. Consistent with previous analyses, coastal Levantine regions were well represented in the J2 network. Some evidence of sharing with Jordan was also apparent. The J1 network was dominated by inland Levantine samples (mainly Jordan and inland Lebanon and Syria). The R1b network showed much less geographic correlation, possibly because most of the R1b chromosomes have entered the region recently (Fig. 5B). In fact, without extra-Levantine representation of R1b to establish context, it is difficult to identify where these R1bs originated. Finally, E1b1b showed a clear demarcation between the Levantine STR haplotypes and North African STR haplotypes, with a lower diversity among North African STR haplotypes than among Levantine STR haplotypes (Fig. 5C). 91 STR haplotypes belonged to the E1b1b1 haplogroup within the Levantine population compared to 60 STR haplotypes within the North African population (Table S6)."

J1-M267 Y lineage marks climate-driven pre-historical human displacements

Tofanelli et al

Abstract:  "The present day distribution of Y chromosomes bearing the haplogroup J1 M267*G variant has been associated with different episodes of human demographic history, the main one being the diffusion of Islam since the Early Middle Ages. To better understand the modes and timing of J1 dispersals, we reconstructed the genealogical relationships among 282 M267*G chromosomes from 29 populations typed at 20 YSTRs and 6 SNPs. Phylogenetic analyses depicted a new genetic background consistent with climate-driven demographic dynamics occurring during two key phases of human pre-history: (1) the spatial expansion of hunter gatherers in response to the end of the late Pleistocene cooling phases and (2) the displacement of groups of foragers/herders following the mid-Holocene rainfall retreats across the Sahara and Arabia. Furthermore, J1 STR motifs previously used to trace Arab or Jewish ancestries were shown unsuitable as diagnostic markers for ethnicity."

Thursday, December 23, 2010

Neolithic Expansion into Coastal West India

A close reading of the recent Thangaraj paper, referenced below, indicates that there are primarily two West Asian y-haplogroups that entered the Indian subcontinent by a western coastal route during the Neolithic:  J2a4 and L1.  It notes that the R1a y-haplogroup is not strongly associated with this coastal Neolithic expansion. The described J2a4 and L1 Neolithic expansion is consistent with the findings of Sengupta et al

Neither the Thangaraj paper or the Sengupta paper support the notion of a single Iron Age expansion of Indo-Aryans.  The Thangaraj paper specifically suggests an approximate age of paternal gene flow from West Asia of approximately 10,000 years.

These results are consistent with earlier posts on the y-haplogroup distribution maps for J2 and L.

Eurogenes ADMIXTURE K=10 results run on the Eurogenes dataset help to illustrate the process of West Asian admixture into the South Indian genetic background:
The distribution of ADMIXTURE components across Georgians, Armenians, Assyrians, Iranians, Sindhis and Gujaratis indicates a diffusion process between West Asia and Western Coastal India.

The fact that there is a very low contribution to Sindhis and Gujaratis from the Southwest Asian component is consistent with the Thangaraj assertion that the age of J2 and L paternal gene flow into India occured approximately 10,000 years ago.  The Southwest Asian component is associated with the J1 y-haplogroup.  The J1 y-haplogroup has a pre-Holocene expansion time in the Zagros Mountains, but its rapid growth is associated with the J1 expansion into the Arabian peninsula in the last 9000 years.

Reference:

The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations
Thangaraj et al
(Link)

Results and Discussion:

"The Y chromosome analysis identified nine major haplogroups in Maharashtra populations (Table 2), of which South Asian specific haplogroup H is most frequent in caste and tribal populations. Second most frequent haplogroup is hg R1a present in caste as well as tribal populations. Some of the studies considered hg H as a tribal and hg R1a as caste specific marker previously [12], [24], [25]. In contrast to them, the present study supports the occurrence of these haplogroups in both caste and tribal populations of India [11], [15]. The discrepancy of frequency distribution of these haplogroups in caste and tribal populations can be explained by their different population sizes where evolutionary forces act in a different way and diverse social customs that involve practicing endogamy at different levels [18]."

"Near Eastern specific hg J2 is also significantly present in both of the studied populations (Table 2 and Table S2). This haplogroup thought to be associated with the intrusion from Near East during Neolithic agricultural expansion [14]. Further dissection of this hg revealed most of the samples to be derived for marker M410 (hg. J2a). The further genotyping of M410 derived samples remained ancestral to M67 marker (hg. J2a4). The worldwide phylogeographic distribution of hg J2a suggests its entry in Indian subcontinent through northwestern corridor and an abrupt drop further south due to Western Ghat mountain ranges (Fig. 3). The rooted Y-STR network of different Y chromosomal haplogroups provided a diverse haplotype distribution in Maharashtra populations (Fig. 4)."

"By using the Y-STR data from both of the populations, we have calculated the variance and coalescent ages for different haplogroups (Table 4). The age of microsatellites variation in all of the major haplogroups ranges from 7–35 KYA (Table 4). The South Asian specific haplogroups F*, H1a and R2 show pre-Neolithic, while hg L1 shows Neolithic expansion time. The age of haplogroup R1a ranges from 10–17 KYA which is consistent with previous large scale study on this haplogroup [38]. The network analysis of R1a with other Indian populations failed to provide any regional or linguistic clustering (Fig. S2)."

"In conclusion, our results on Maharashtra populations are consistent with other Indian populations suggest that the tribal as well as caste populations of Indian subcontinent practice a strict endogamy even though they live in a close proximity and share the ritual and social customs. The mtDNA results dissected and increased the clarity of South Asian mtDNA phylogeny. The colonization of western part of Western Ghat is facilitated mainly through migration of populations via western coast rather than mainland where Western Ghat-Vindhya mountains and Narmada-Tapti rivers worked as a natural barrier. Our data is in congruent with the other observations that Indian populations including Maharashtra state are largely derived from Paleolithic ancient settlers, however, a more recent (~10 Ky older) detectable paternal gene flow from west Asia is well reflected in present genetic study."

Tuesday, December 21, 2010

Ossetians

South Ossetian woman and boy (Link)

Map of the Caucasus Region

In the continuing investigation into candidate mtDNA and yDNA members of the ADMIXTURE K10 West Asian component, Ossetia is interesting in that its population has a high incidence of y haplogroups G and R1b (Myres et al).   Its mtDNA demonstrates continuity with surrounding Caucasus regions.  South Ossetia lies within the country of Georgia which is notable for its pronounced West Asian component which would suggest that both its mtDNA and yDNA distributions are correlated with the ADMIXTURE West Asian component.

An important 2004 paper examines the population composition of Ossetians and relates this to the linguistic and geographic structure in the region:

Genetic Evidence Concerning the Origins of South and North Ossetians
Nasidze, et al
(Link)

Summary: "Ossetians are a unique group in the Caucasus, in that they are the only ethnic group found on both the north and south slopes of the Caucasus, and moreover they speak an Indo-European language in contrast to their Caucasian-speaking neighbours. We analyzed mtDNA HV1 sequences, Y chromosome binary genetic markers, and Y chromosome short tandem repeat (Y-STR) variability in three North Ossetian groups and compared these data to published data for two additional North Ossetian groups and for South Ossetians. The mtDNA data suggest a common origin for North and South Ossetians, whereas the Y-haplogroup data indicate that North Ossetians are more similar to other North Caucasian groups, and South Ossetians are more similar to other South Caucasian groups, than to each other. Also, with respect to mtDNA, Ossetians are significantly more similar to Iranian groups than to Caucasian groups. We suggest that a common origin of Ossetians from Iran, followed by subsequent male-mediated migrations from their Caucasian neighbours, is the most likely explanation for these results. Thus, genetic studies of such complex and multiple migrations as the Ossetians can provide additional insights into the circumstances surrounding such migrations."

Y Chromosome STRs:  "Since haplogroup G(M201) has an unusually high frequency in North Ossetian (average frequency = 0.57) compared with other groups from the Caucasus (average frequency = 0.21), we typed 9 Y-STR loci in individuals with this Y-SNP haplogroup to determine if this elevated frequency indicates a bottleneck effect.We compared the results with the same set of loci on the same Y-SNP background typed in other groups from the Caucasus (Nasidze et al. 2003). Haplotype diversity(M201) is significantly reduced in Ossetians (0.722± 0.071) compared± 0.005). A median network of Y-STR haplotypes on the background∗(M201) revealed two clearly separated clusters (Figure 3). One of them almost exclusively contains haplotypes found in the Digora group. The second cluster contains the remaining North Ossetian groups, suggesting either different sources of introduction of haplogroup G∗(M201) or isolation and genetic drift in the Digora group."

Comparison of mtDNA and Y-Chromosome Data: "The geographic and linguistic structure of Ossetians, other Caucasus groups, and European, West and Central Asian groups, as assessed by mtDNA and Y chromosome variation, was investigated by the AMOVA procedure (Table 4). As is typically seen in human populations, the within-populations proportion of the variance was much higher for mtDNA (about 96% than for the Y chromosome (about 76-77%). For both the mtDNA and the Y-SNP data, the geographic classification of populations gave a slightly better fit to the genetic data (in terms of higher among-group variance and lower among-populations-within-groups variance) than did linguistic classifications (Table 4). Further classifying the Caucasian groups into South and North groups did not significantly improve the fit of either classification to the data (Table 4)."

Discussion:

"North and South Ossetians are the only ethnic group found on both slopes of the Caucasus Mountains. They speak a language which belongs to the Iranian branch of the Indo-European language family; hence, Ossetians are a linguistic isolate, surrounded by Caucasian speaking populations. By surveying mtDNA and Ychromosome variation in Ossetians, we sought answers to several questions concerning the origins and genetic relationships of Ossetians. First, are North and South Ossetians more genetically similar to each other, or to their geographic neighbours (i.e., Caucasian-speaking populations in the North and South Caucasus, respectively)? The results are somewhat different for mtDNA vs. the Y-chromosome. North and South Ossetians do cluster somewhat in the MDS plot based on mtDNA (Fig. 2A), which may indicate a common origin. However, for the Y-chromosome, North Ossetians are more similar to other North Caucasian populations, and South Ossetians to other South Caucasian populations, than to each other. The SAMOVA analysis also identifies a boundary between South Ossetians and other groups for the Y chromosome, but not for mtDNA. Thus, there is no indication in the Y-chromosome of a particularly close genetic relationship between N. Ossetians and S. Ossetians. If they did have a common origin in the past, it has apparently become obscured by subsequent gene flow with their geographic neighbours on the same sides of the Caucasus Mountains.

"Putting together the archaeological and genetic data, and assuming a common origin of South and North Ossetians (which is supported by the mtDNA data), a plausible scenario is that “alteration” of the initial Ossetian Y-chromosome gene pool took place in North Ossetians via other North Caucasus groups. This assumption is enforced by the fact that the genetic distances between North Ossetians and South Caucasus groups are similar to those between North Ossetians and South Ossetians, but the genetic distances between North Ossetians and other North Caucasus groups are much smaller. Moreover, there are differences in genetic structures based on Y chromosome and mtDNA, as the correlation between Fst distances among pairs of Caucasus groups based on mtDNA and Y-haplogroups was not statistically significant. The different patterns observed between South and North Ossetians for the Y chromosome may also have been reinforced by the traditional patrilocal social structure of this population, leading to a higher degree of differentiation for the Y chromosome than for mtDNA.

"The Ossetians speak an Iranian language; is this because they are directly descended from the Alani (an Iranian-speaking group), or is it rather that genetically the Ossetians resemble their geographic neighbours in the Caucasus, and hence replaced their ancestral Caucasian language with an Iranian language, after contact with the Alani (or another group)? Average pairwise Fst values are smaller between Ossetians and Iranians than between Ossetians and Caucasians for both mtDNA and the Y chromosome, significantly so for mtDNA, which suggests an Iranian origin of Ossetians. Subsequent and largely male-mediated migrations between Ossetians and neighbouring groups in the North and South Caucasus, respectively, would explain the greater similarity between Ossetians and Caucasians for the Ychromosome, as discussed previously.

"In conclusion, the genetic results are supported by the archaeological record, in that they reflect a common Iranian origin of South and North Ossetians, as well as a genetic footprint of ancient migrations in the North Caucasus that mostly involved male individuals. Thus, genetic studies of such complex and multiple migrations as the Ossetians can provide additional insights into the circumstances surrounding such migrations."

Monday, December 20, 2010

Lunar Eclipse in North America Tonight

 
For those of us in North America, there's a lunar eclipse tonight.  (Link)
Happy first day of Winter to all!

Sunday, December 19, 2010

A Possible Source of the Daghestan ADMIXTURE Component

L Haplogroup Distribution

Dienekes posts today on an unusual distribution of an ADMIXTURE component he calls the Daghestan component.  Based on its hap map distribution, it is possible that this component is correlated with the L Y-DNA Haplogroup.

A recent paper discusses Daghestan:

Caciagli, L et al; The key role of patrilineal inheritance in shaping the genetic variation of Dagestan highlanders (Link)

ISOGG Y-DNA Haplogroup L and its Subclades - 2010 (Link)

Fertile Crescent Pre-Holocene Expansion of Haplogroup J


Distribution of J2a 
Sengupta, S.et al., 2006

Dienekes covered the Sengupta paper, which discusses the distribution of J2 and other West Asian y-haplogroups, back in 2005.  In light of ADMIXTURE results, it is helpful to revisit this paper (Sengupta et al 2006).  From this paper, two major branches of J2, J2a and J2b, are described on the phylogenic tree:


Based on the distribution and diversity of the J2b branch of the tree, it is likely of a Central or South Asian provenance, as discussed in Senguta et al.

Sengupta notes that many y-haplogroups in India appear to be of a pre-Neolithic origin. Regarding the eastward expansion of J2, he has this to say:

"One interpretation of the presence of J2a-M410 chromosomes in North Africa and Eurasia is that it reflects the demographic spread of Neolithic farmers. This is consistent with previous interpretations of M172-associated HGs (Semino et al. 2000; King and Underhill 2002). Figure 3 [above] demonstrates the eastward expansion of J2a-M410 to Iraq, Iran, and Central Asia coincident with painted pottery and ceramic figurines, well documented in the Neolithic archeological record (Cauvin 2000). Near the Indus Valley, the Neolithic site of Mehrgarh, estimated to have been founded 7 KYA (Kenoyer 1998), displays the presence of these types of material culture correlated with the spread J2a-M410 in Pakistan. Although the association of agriculture with J2a-M410 is recognized, the spread of agriculture may not be the only explanation for the spread of this HG. Despite an apparent exogenous frequency spread pattern of HG J2a toward North and Central India from the west (fig. 3), it is premature to attribute the spread to a simplistic demic expansion of early agriculturalists and pastoralists from the Middle East. It reflects the overall net process of spread that may contain numerous as-yet-unrevealed movements embedded within the general pattern. It may also reflect a combination of elements of earlier prehistoric Holocene epi-Paleolithic peoples from the Middle East, subsequent Bronze Age Harappans of uncertain provenance, and succeeding Iron Age Indo-Aryans from Central Asia (Kennedy 2000). Although the overall age of J2a Y-microsatellite variation (table 11) exceeds the appearance of agriculture in the Indus Valley (6 KYA), the current lack of informative subdivision within HG J2a in southwestern Asia prevents analysis of such potential layers, which are currently more evident in Anatolia, southeastern Europe, and the Mediterranean. In these regions, HGs J2a1b-M67(xM92) and J2a1b1-M92 have spatial and temporal characteristics consistent with the spread of early farmers and Bronze Age cultures (Di Giacomo et al. 2004). Besides the notable absence of J2a1b-M67(xM92) and J2a1b1-M92 in southwestern Asia, HGs J1-M267 and G-M201 that, respectively, occur at 9% and 10.9% in Turkey (Cinnioglu et al. 2004), 33.1% and 2.2% in Iraq (Al-Zahery et al. 2003), and 3.4% and 6% in Pakistan are also virtually absent in India, indicating differential influences from the Middle East in southeastern Europe and southwestern Asia. Similarly, the presence of HG E lineages, thought to possibly be associated with the spread of agriculturalists in southeastern Europe (Hammer et al. 1998; Semino et al. 2004), are absent in India except in specific populations known to have recent African heritage (Thangaraj et al. 1999). Until the paraphyletic J2a-M410* with DYS413 short-alleles chromosomes are better resolved molecularly in southeastern European, western Asian, and southwestern Asian regions, the magnitude of the contribution of agriculturalists within this HG remains uncertain. The mean variance for J2b2-M241 chromosomes is highest in southwestern Asia(0.33), in contrast with Turkey (0.24) (Cinnioglu et al. 2004) and the Balkans (Pericic et al. 2005). Further, the mean expansion time of J2b2 in India is 13.8KYA, clearly earlier than the appearance of agriculture."

A pre-Holocene expansion of J in the Fertile Crescent is consistent with both the Sengupta findings and the recent suggested early Holocene southward expansion of J1 from the Taurus-Zagros region (Charioni et al).

From ISOGG: "Y-DNA haplogroup J evolved in the ancient Near East and was carried into North Africa, Europe, Central Asia, Pakistan and India. J2 lineages originated in the area known as the Fertile Crescent. The main spread of J2 into the Mediterranean area is thought to have coincided with the expansion of agricultural peoples during the Neolithic period. The timing of the demographic events that brought J2 to Central Asia, Pakistan, and India is not yet known."

References:

(1) Cinnioglu, C (2004); Excavating y-chromosome haplotype strata in Anatolia.  (Link)

(2) Regueiro, M (2006); Iran: Tricontinental Nexus for Y-Chromosome Driven Migration.  (Link)

(3)  Sengupta, S (2006); Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. (Link)

(4) ISOGG Y-DNA Haplogroup J and its Subclades - 2010 (Link)

J1 Hap Map


In my recent The Bedouin post, I discuss the southward expansion of J1e.  A hap map of the distribution of J1 is illuminating.  This map is taken from the wiki page for Y-DNA maps which unfortunately does not reference its source.

The map describes not only the position of J1 in the Arabian peninsula, but also suggests a back migration into Africa.

The high concentration of J1 north of the Caucasus along the Caspian Sea is a surprise and a topic for further investigation.

Friday, December 17, 2010

Saudi and Bedouin mt-DNA

Bedouin Girl, Artist: Heba Amin (Link, Link)

Eurasian and African mitocondrial DNA influences in the Saudi population

Khaled K Abu-Amero, Ana M González, Jose M Larruga, Thomas M Bosley, and Vicente M Cabrera
(Link)

Conclusion:  "The 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."

The paper also contains mt-DNA results for a number of other Mid East populations, including the Bedouin.  I have summarized the autosomal results from Behar, then added mtDNA and yDNA results from Abu-Amero et al and Mohammed et al in the following tables.

Key to Admixture autosomal components:
WAs - West Asian
CAs - Central Asian
SEur - Southern European
NEAs - North East Asian
SWAs - South West Asian
EAs - East Asian
NEur - Northern European
WAfr - West African
EAfr - East African
SAs - South East Asian

Behar et al      
autosomal    
                WAs   CAs  SEur   NEAs  SWAs EAs  NEur   WAfr   EAfr   SAs
Saudis:      0.22    0     0.14   0       0.54   0     0.01    0.03   0.03  0.02
Bed:          0.15    0.01 0.12   0       0.6    0     0.01    0.07   0.05  0

Mohammed et al      
y-DNA        
                   J1           R1a1    E3b3        G2         R1b3
Bed:             0.84        0.067    0.06        0.034     0.013
                   SWAs                               WAs
                   (1)                                   (1)

Abu-Amero et al      
mt-DNA     
                   L               M              N                 R
Saudis:         0.07        0.07        0.1           0.75
Bed:             0.07        0.1         0.12          0.69
                   Afr          C&SAs     WAs          SWAs

Approximate geographic position is listed for the mtDNA and y-DNA haplogroups based on Battaglia et al and Mohammed et al.  Working from these results would indicate that y-DNA haplogroup J1 and mtDNA haplogroup R correlate strongly with the Southwest Asian component.  It is notable that mtDNA R is downstream from Northern Fertile Crescent mtDNA N.  Candidates for the West Asian component are y-DNA G2 and mtDNA N.  Minor ADMIXTURE components withing the Central Asian, West African, East African and South Asian populations are likely associated with L and M mtDNA.

Reference:
(1)  Battaglia, Vincenza; Fornarino, Simona; Al-Zahery, Nadia; Olivieri, Anna; Pala, Maria; Myres, Natalie M; King, Roy J; Rootsi, Siiri et al. (24 December 2008). "Y-chromosomal evidence of the cultural diffusion of agriculture in southeast Europe". European Journal of Human Genetics 17: 820.  (Link)

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

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

Monday, December 13, 2010

Slowdown of the Neolithic Transition in the Levant?

Overlooking the Sea of Galilee         

Based on extensive archaeological work, the 2008 Zeder paper on early domestication (see previous post) gives some estimates of where and when domestication of goats, sheep, cattle and pigs occurred as well as dates for the arrival in other Fertile Crescent areas.  A map in the paper illustrates the location of domestication as being on the Taurus-Zagros Arc:

  (Link)

From the points of domestication, domesticated goats, sheep, cattle and pigs were brought southward into the Southern Levant. 

Of particular interest are the dates for the introduction of domesticated goats.  Travelling from the westernmost tip of goat domestication on the upper Tigris River 11,000 years ago, it takes 1,400 years to reach the northern tip of the Levantine Corridor.  However, goat domestication then travels simultaneously from the area of the Natufian site Abu Hureira to the Southern Levant.

From the archaeological record, we know that the Late Natufian culture, with their distinctive exposed semi-subterranean houses, moved northward into the Syro-Arabian desert, reaching Abu Hureira, starting approximately 14,500 years before present:  "The climatic improvement after 14,500 B.P. seems to have been responsible for the presence of more stable occupations in the steppic and desertic belts.  Groups moved into areas that were previously uninhabited, from the Mediterranean steppe into the margins of the Syro-Arabian desert.  Others came from the Nile valley, creating an interesting social mosaic."(link, p. 161)  The "Syro-Arabian desert in the east accommodated only small Natufian occupations due to both their lower carrying capacity and the presence of other groups of foragers who exploited this vast region." (Ibid. p. 162). 

Abu Hureira at the northern end of the Levantine Corridor

One possible explanation for the rapid transmission of goats from the area of Abu Hureira to the Southern Levant is that the Natufian culture adopted goat domestication from others in Abu Hureira and then immediately carried it southward. 

For the domestication of sheep, cattle and pigs, the Zeder 2008 paper describes dates for the region of origin and destination in the southern Levant.  From these, it is possible to estimate speeds for the dispersal of these livestock breeds.   Since there are only two points for sheep, cattle and pigs, it isn't possible to know if the dispersal sped up or slowed down during the trip.

From the Isern and Fort paper, we have a rough idea of the speed of advance of European Neolithic farmers as a function of the population density in the area of advance. 

This raises the question as to whether there was a similar slowdown with the Neolithic expansion southward into the southern Levant.  We know that today the ADMIXTURE population components "West Asian", "Southern European" and "Southwest Asian" are distributed in an approximate normal distribution, indicating the phenomena of absolute density regulation and space competition. (link)  However, a lot can happen in 10,000 years, so we cannot directly infer that Neolithic Fertile Crescent populations experienced space competition.

It is not difficult to plot the speed of the advance for goats, sheep, pigs and cattle from the point of domestication to the southern Levant.  In the case of goats, the distance used is from the westernmost point of domestication in the Zagros to Abu Hureira.  The other distances are calculated from the point of domestication to Jericho.  These speeds (horizontal lines) are plotted with the c(m1) and c(m4) functions derived for the European Neolithic advance (Isern and For), to obtain c/cmax and c:

Note that values for cmax, D, a and T are replicated from Isern and Fort.

Goats and sheep seem to be the slowest travelers at about 0.3 km/year  Pigs are a little faster and cattle are veritable race horses, travelling at 0.4 km/year. 

Considering that Levant shepherds traversed mostly open woodland and steppe, these speeds seem very slow indeed.  What's more, we know that since sheep and goats were the first to reach the Levantine Corridor, they were on the leading edge of the Neolithic advance.  If there was already a population in the Levant such as Natufian hunters, it would be the leading edge of the front that would be the slowest.  That appears to be the case for sheep.  Pigs and cattle, who arrive 500 to 1000 years after sheep, are faster.

It is also notable that the Levant livestock speeds intersect the European m4 test function at approximately the distance actually travelled by Fertile Crescent shepherds and farmers from the point of domestication to Jericho:  about 700 kilometers.

The goat data lend to the idea that Natufian Hunter-Gatherers adopted goat shepherding in the area of Abu Hureira 9600 years ago and very quickly introduced it in the Southern Levant. 

Because we don't have a midpoint date and position for domestication of sheep, pigs and cattle, it is more difficult to infer whether it was Natufians or Northern Fertile Crescent farmers who brought sheep, pigs and cattle southward.  It does seem that the southward advance was slow going, especially for the first wave of sheep herders, suggesting some kind of resistance. 

Thursday, December 9, 2010

Migration Paths: Dienekes' Clusters Galore Scatter Plot Results

Taking a slight diversion from ADMIXTURE and the Fertile Crescent discussion, I'd like to mention Dienekes' Scatter Plot Results (link) for human populations.  Dienekes uses a method he calls Clusters Galore with MCLUST software to dimensionalize populations according to SNP cluster groupings.  It works by carving through SNP data sets to look for SNP cluster groupings.  So far, I haven't seen any ADMIXTURE-like results with linear combinations of components in this method.  I believe that's because the cluster search algorithm results in a non-linear weighting.  However, MCLUST can handle much larger data sets than ADMIXTURE and is computationally much faster.  That permits a world view approach, without having to carefully group and balance datasets.

With this approach, you can very quickly see that certain populations or demes are grouped on certain dimensions, even those that are geographically very far apart.  Some of the demes such as those in  Europe form huge scatter plot blobs.  China and neighboring countries make up another blob.  Other groupings are more interesting, like the long arms of a galaxy or strings of dandylion seeds blowing in the wind.  They clearly represent the long arms of ancient human migrations.

I sat down the other day and tried to describe some of these migration paths and give them some names.  I was able to pick out many of the familiar migratory paths that have appeared in discussions about the peopling of Siberia, Southeast Asia and the Americas.  After looking at the first three plots (the first six dimensions) I could see that already, paths described in one plot were overlapping with other plots.  The ordering of the populations may be jumbled up a bit, but you can see that certain populations are grouped in particular migratory paths.  You can also see that the migratory paths sometimes intersect.

I only looked at the first six dimensions and did not do an exhaustive job.  Still, it is appears to be a very powerful technique to pick out long range migration paths in human populations.

Here's my list:

Dimension 1 versus 2:

A:  French Basques-Chuvash-Athabask-Aleut-West Greenland-Selkup-Yukagir-East Greenland-Ket-Maya-Chukchi-Pima-Columbians-Karitiana-Surui
(North Asian Steppe:  Northern Europe-Russia-Bering Straight-Alberta Corridor-Arizona-Central America-Columbia-Amazon)

B:  Lesgins-Adygei-Kalash-Uzbeks-Hazara
(Central Asian Steppe:  Caucasus to Pakistan)

C:  Altai-Mongol-Koryak-Tuva-Nganassan-Buryat-Oroqen-Daur-Hezhen-Han Chinese-Miaozu
(Central Asian Steppe:  Altai to Siberia)

E:  Lezgins-Adygei-Kalash-Pathan-Burusho-Gujarati-Malayan
(Caucasus-Persian Gulf-India-Coastal root to Malaysia)

F: Bantu SE-Mandenka-Bantu NE-Maasai-Ethiopians-Moroccans-Mozabites-Egyptians-Bedouin-Jordanians 
(Trans African-Nile-Red Sea)


Dimension 3 versus 4:

G. Miaozu-Dai-Lahu-Cambodians-Malay_Singapore
(Southeast Asian-to Malay Peninsula)

H. Iranians-Brahui-Burusho-Pathan-Kalash-Sindhi-Gujarati
(Iran to India)

Dimension 5 versus 6:

J. Cambodians-Dai-Maya-Pima–Columbians-Surui-Karitiana
(Pacific Rim Coastal:  Southeast Asia-China-Bering Straight-Pacific Coast, intersecting A at Pima)

K. Lithuanians-Finns-Chuvash-Chukchi-L
(See A, North Asian Steppe)

L. Yakut-Selkup-Ket-Koryak-Nganassan
(See B, Central Asian Steppe)

M. Mongola-Uzbeks-Daur-Hezhen-Mongol-Oroqen-Altai-Buryat-Tuva-L
(See B, Central Asian Steppe)