Afghan mega-paper (Di Cristofaro et al.)

The admixture results nicely presented on a map:

The authors note that none of the ancestral components peaks in Central Asia, concluding that this region has been a destination rather than a source of population movements. I certainly agree that Central Asia has a lot of recent history affecting it from virtually all directions. On the other hand, we should be cautious about interpreting geographical clines in terms of directionality of population movement; a good example is Sardinia which often emerges as a "focus" of Mediterranean ancestry, but this does not mean that it is the origin of such ancestry. It would certainly be interesting to remove the layers of more recent ancestry from Central Asia to see what was there before the last few thousand years.

The PCA based on autosomal data:

The Y-chromosome haplogroup data can be found in Figure S7. The authors comment:

94% of the chromosomes are distributed within the following 9 main haplogroups: R-M207 (34%), J-M304 (16%), C-M130 (15%), L-M20 (6%), G-M201 (6%), Q-M242 (6%), N-M231 (4%), O-M175 (4%) and E-M96 (3%). Within the core haplogroups observed in the Afghan populations, there are sub-haplogroups that provide more refined insights into the underlying structure of the Y-chromosome gene pool. One of the important sub-haplogroups includes the C3b2b1-M401 lineage that is amplified in Hazara, Kyrgyz and Mongol populations. Haplogroup G2c-M377 reaches 14.7% in Pashtun, consistent with previous results [31], whereas it is virtually absent from all other populations. J2a1-Page55 is found in 23% of Iranians, 13% of the Hazara from the Hindu Kush, 11% of the Tajik and Uzbek from the Hindu Kush, 10% of Pakistanis, 4% of the Turkmen from the Hindu Kush, 3% of the Pashtun and 2% of the Kyrgyz and Mongol populations. Concerning haplogroup L, L1c-M357 is significantly higher in Burusho and Kalash (15% and 25%) than in other populations. L1a-M76 is most frequent in Balochi (20%), and is found at lower levels in Kyrgyz, Pashtun, Tajik, Uzbek and Turkmen populations. Q1a2-M25 lineage is characteristic of Turkmen (31%), significantly higher than all other populations. Haplogroup R1a1a-M198/M17 is characterized by its absence or very low frequency in Iranian, Mongol and Hazara populations and its high frequency in Pashtun and Kyrgyz populations.

PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748

Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge

Julie Di Cristofaro et al.

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

Link

Archaeometallurgy in the Mediterranean

Continuing a discussion on metallurgical innovation which I began here.

Some interesting excerpts from a book chapter:

Tin bronze first appeared in Mesopotamia and Anatolia during the third millennium B.C., or Early Bronze Age (Pare 2000a:6–7). In the Mediterranean,the transition from arsenical to tin bronze took place during the course of the Middle Bronze Age (late third to early second millennium B.C.in the eastern Mediter-ranean, somewhat later in the west). The implication (Renfrew 1972:313–319) that tin bronze was an independent development in the northeast Aegean is contradicted by lead isotope analyses which show that most copper or bronze objects from sites such as Troy, Poliochni, and Kastri were not produced from local ores (Muhly and Pernicka 1992; Pernicka 1998:140–141). Exactly what caused the transition from arsenical to tin bronze is not well understood: as an alloy, tin bronze is not mechanically superior to arsenical copper (Pernicka 1998:135–136).Unlike arsenic, moreover, tin is not widely available as a mineral, and new trade networks would have been required to enable its distribution. However, it may have been easier to control the quality of tin bronze, and the production of tin bronze would have overcome the problem of working with toxic arsenic fumes (Charles 1978:30;Pare 2000a:7).

Given the limited number of tin deposits in the region, the source(s) of tin usedin the prehistoric eastern Mediterranean has always been a highly controversial issue. The suggestion that Afghanistan served as a prime source of tin for Bronze Age eastern Mediterranean societies is based in part on the existence of its rich tin resources (Muhly and Pernicka 1992:315;Weeks 1999:60–61).Muhly (1999:21) recently argued that Afghanistan or central Asia provided the tin that supplied the bronze industries of Mesopotamia, Anatolia, and the eastern Mediterranean, including Cyprus. Cuneiform documents from the early second millennium B.C., moreover, point to a trade network that brought tin from the east to the early states of Anatolia and Mesopotamia (Maddin et al.1977:41:Weeks 1999),and thence to the Mediterranean. Weisgerber and Cierny (2002,with fuller references) now maintain that prehistoric tin mining (second millennium B.C.), attested at the sites of Karnab (Uzbekhistan) and Musciston (Tajikistan), provided an important source of tin for Anatolia and Mesopotamia, if not for the Mediterranean. In contrast, Yener and Vandiver (1993) have argued that (very limited) tin deposits in the Taurus Mountains of southern Turkey were exploited during the Early Bronze Age. Their argument has been challenged by several scholars (e.g.,Muhly 1993;Weisgerberand Chierny 2002:180–181;papers in Journal of Mediterranean Archaeology 5[1995]) who maintain that the archaeological evidence is unclear,and far too limited to demonstrate anything beyond local use. Even if tin from the Taurus were mined during the Early Bronze Age, it now seems more likely that central Asia provided at least some of the tin used during the Middle-Late Bronze Ages,when tin bronze was far more widely produced, traded, and consumed in the Mediterranean. 

... 

By the Late Neolithic period (ca.4800–3100 B.C.), most people living in the Mediterranean region produced their own food, lived the year round in sedentary communities and increasingly were involved in intricate social and economic exchanges. By the beginning of the Bronze Age, certain alliances, special-interest groups, or even individual local leaders came to control access to raw materials in demand: obsidian, precious or semi-precious stones, metals such as gold, silver, copper, and tin, and a range of more perishable goods. From about 3000 B.C.onward – corresponding to the Chalcolithic period (Argaric culture) in Spain, the Final Neolithic in Italy, and the Early Bronze Age in the Aegean and eastern Mediterranean – the production and trade in metals increasingly became a key factor in promoting social change (Giardino 2000b;Knapp 1990a;Levy et al.2002;Manning 1994;Ruiz Taboada and Montero Ruiz 1999).  

...  

Technological innovations may be seen as progressive by managers and elites, but for the people who mined ores or smelted metals they were also potentially disruptive, forming the backdrop for social change as well as social abuse (Heskel andLamberg-Karlovsky 1980:260–261;Stollner 2003:427–429). Miners and metal-smiths often use ideology as a means to maintain, resist,or change their power base within society. Because elites who control and organize metallurgical produc-tion often use material culture to restructure relations of power (Gamble 1986:39), we may also expect such transformations to be visible in the archaeological record. 

...  

Consequently, there is little room to doubt that innovations in technology had deep-seated and long-lasting social and ecological effects, placing constraints as well as conferring benefits on Bronze Age mining and metallurgical production. In social terms, whereas the intensified production of copper employing an advanced technology did not preclude a strong sense of local community, such factors served to increase social distinctions between those at the top of the control structure and those at the bottom (Hardesty 1988:102,116;Knapp 1986b;2003). 

...  

The trade in metals during the Chalcolithic period was carried out on a very limited scale, and most metals were certainly consumed in the same area where they were produced (cf.Gale 1991). During the Early Bronze Age (third millennium B.C.), technological innovations like the longboat and sail facilitated the bulk transport of raw materials or manufactured goods on a much larger scale than ever before (Broodbank 1989). 

... 

Metals and metallurgy wielded an immense impact on Mediterranean Bronze Age societies, clearly evident in all the fundamental changes seen in the archaeological record from the end of the Chalcolithic period (Copper Age) onward. During the Bronze Age,innovations in maritime transport and the earliest cultivation of olives and vines stimulated the economy of the Mediterranean region and spurred some of its inhabitants to produce metals, take part in maritime trade, manufacture distinctive artifacts, and build domestic and public structures that represented the earliest towns and ceremonial complexes in the Mediterranean. The advent and spread of metallurgy promoted greater social distinctions,as certain individuals or groups acquired new wealth and prestige items. Because tin had to be imported in order to produce bronze, long-distance trade was stimulated. Duringthe second millennium B.C., gold, silver, copper, and tin came to represent what Sherratt (2000:83) has termed “convertible”value, both in an economic sense and in the literal sense that they could be consumed, stored, redistributed, or recycled in diverse forms and for various symbolic or ideological ends.Such documentary evidence as exists, exclusively in the eastern Mediterranean, is frequently preoccupied with these self-same metals (Liverani 1990:205–223,247–266;Moran,inKnapp 1996:21–25).

A remarkable series of social and economic changes thus were linked closely to all the innovative developments in extractive and metallurgical technologies,and tothe increasingly widespread and intensified production and distribution of metalsand metal objects. These changes include but are not limited to: (1) the proliferation of settlements and the emergence of town centers;(2) the development and expansion in interregional trade;(3) the growth of palatial regimes and city-state kingdoms,with their attendant writing systems (notably in the eastern Mediterranean);(4) the development and refinement of craft specialization and the spread of an iconographic koine;(5) the elaboration of mortuary rituals and burials with large quantities of precious metal goods;(6) the widespread occurrence of metal hoards and the related trade in recycled and scrap metal. The circulation of goods, ideas, and ideologies across geographic,cultural,and economic boundaries represents a social transaction,one that entangled producers, distributors, and consumers in wider relations of alliance and dependence, patronage and privilege, prestige and debt (Thomas 1991:123–124). Certain occupational identities came to be focused around metallurgical production and trade, and Cyprus even gave its name to the island’s most prominent product: copper ore (Muhly 1973:174–175).The coming of the Age of Iron, subsequent to all the developments discussed in this study, itself relied on extractive and smelting technologies developed during theBronze Age,together with the use of carburization, all of which are linked directly(albeit over the millennia) to the dramatic social and economic changes that ushered in the Industrial Revolution and the beginnings of the modern era.If it is indeed the case that “metals make the world go round” (Pare 2000b),nowhere can this slogan be better and more widely illustrated than in the prehistoric Bronze Age of the Mediterranean.

Archaeometallurgy in the Mediterranean: The Social Context of Mining, Technology, and Trade

Vasiliki Kassianidou and A.Bernard Knapp

Link

Another look at the Y chromosomes of Afghanistan

Good things come in pairs, so a little after the recent publication of a paper on the Y chromosomes of Afghanistan, there is yet another paper on the same topic. There is some quite useful information in the open access supplementary material, including a table of haplogroup R-M198 and R-M198*(xM458) frequencies in a wide range of human populations.

Unfortunately, this paper too was probably written before the current developments in the R1a world, and did not take advantage of the newer discovered SNPs. Hopefully the DNA samples can be eventually tested  in more phylogenetic detail.

European Journal of Human Genetics advance online publication 18 April 2012; doi: 10.1038/ejhg.2012.59

Afghanistan from a Y-chromosome perspective

Harlette Lacau et al.

Abstract

Central Asia has served as a corridor for human migrations providing trading routes since ancient times. It has functioned as a conduit connecting Europe and the Middle East with South Asia and far Eastern civilizations. Therefore, the study of populations in this region is essential for a comprehensive understanding of early human dispersal on the Eurasian continent. Although Y- chromosome distributions in Central Asia have been widely surveyed, present-day Afghanistan remains poorly characterized genetically. The present study addresses this lacuna by analyzing 190 Pathan males from Afghanistan using high-resolution Y-chromosome binary markers. In addition, haplotype diversity for its most common lineages (haplogroups R1a1a*-M198 and L3-M357) was estimated using a set of 15 Y-specific STR loci. The observed haplogroup distribution suggests some degree of genetic isolation of the northern population, likely due to the Hindu Kush mountain range separating it from the southern Afghans who have had greater contact with neighboring Pathans from Pakistan and migrations from the Indian subcontinent. Our study demonstrates genetic similarities between Pathans from Afghanistan and Pakistan, both of which are characterized by the predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype. Furthermore, the high frequencies of R1a1a-M198 and the presence of G2c-M377 chromosomes in Pathans might represent phylogenetic signals from Khazars, a common link between Pathans and Ashkenazi groups, whereas the absence of E1b1b1a2-V13 lineage does not support their professed Greek ancestry.

Link

A rare look at the Y chromosomes of Afghanistan

I often bemoan the fact that some of the regions of the world that are most interesting to the student of prehistory (e.g., Mesopotamia and the Iranian Plateau) seem to also be the ones with more than their fair share of political trouble, hindering efforts to study them with the newest set of tools. Afghanistan is certainly one case that hasn't been quite the most welcoming of places in recent decades.

The country is transitional between the Iranic speaking world of Iran and the Indo-Aryan speaking world of South Asia, as well as between the Indo-Iranian world and the (mostly) Turkic-speaking world of Central Asia. Hence, the absence of data for that country has been acutely felt for all those who are trying to understand "what happened" in Eurasia.

The appearance of a new paper by the Genographic Project is a welcome sight, and a good example of what is best about this Project. I haven't been exactly a fan of the Genographic's interpretation of their own data, but kudos to them for getting them in the first place.

From the paper:

Pashtuns are the largest ethnic group in Afghanistan, accounting for about 42 percent of the population, with Tajiks (27%), Hazaras (9%), Uzbeks (9%), Aimaqs (4%), Turkmen people (3%), Baluch (2%), and other groups (4%) making up the remainder [6]. In the present study, eight ethnic groups were examined, with a focus on the largest four groups: - The Pashtuns, traditionally lived a seminomadic lifestyle, they reside mainly in southern and eastern Afghanistan and in western Pakistan. They speak Pashto which is a member of the Eastern Iranian languages. - The Tajiks are a Persian-speaking ethnic group which are closely related to the Persians of Iran. In Afghanistan, they are the largest Tajik population outside their homeland to the north in Tajikistan. - The Hazara population speaks Persian with some Mongolian words. They believe they are descendants of Genghis Khan's army that invaded during the twelfth century. - The Uzbeks are a Turkic speaking group that have been living a sedentary farming lifestyle in Northern Afghanistan.

The main features of the Y-chromosome gene pool:

Genotyping revealed 32 halpogroups present in Afghanistan's ethnic groups among our samples. Haplogroups R1a1a-M17, C3-M217, J2-M172, and L-M20 were the most frequent when Afghan ethnic groups were pooled, together comprising >66% of the chromosomes. Absolute and relative haplogroup frequencies are tabulated in Table S4.

-The PCA analysis (left) showcases wonderfully the correspondence between different haplogroups and the three main regions of the Near East (green), South Asia (yellow), and Central Asia (purple).

It is a real shame that the newer markers available within the most prominent R-M17 haplogroup were not tested:

The prevailing Y-chromosome lineage in Pashtun and Tajik (R1a1a-M17), has the highest observed diversity among populations of the Indus Valley [46]. R1a1a-M17 diversity declines toward the Pontic-Caspian steppe where the mid-Holocene R1a1a7-M458 sublineage is dominant [46]. R1a1a7-M458 was absent in Afghanistan, suggesting that R1a1a-M17 does not support, as previously thought [47], expansions from the Pontic Steppe [3], bringing the Indo-European languages to Central Asia and India.

Nonetheless, I can't really disagree with the dismissal of the R-M17/Indo-European theory. R-M17 is simply too populous in South Asia to be the genetic legacy of "Indo-Europeans": (i) under an elite-dominance model, its frequency is way too high (compared to well-attested examples of elite dominance, e.g., Hungary or Turkey where the genetic legacy of the elite element is in the minority), (ii) under a folk migration model, it is difficult to understand why a hypothetical migrating Indo-European people would have such an overwhelming influence in the region while at the same time hardly influencing at all other densely occupied agricultural landscapes of the Eurasian steppe periphery; moreover, no autosomal signal corresponding to a migration from eastern Europe to South Asia really exists -the main cline of variation links South with West Asia, not Europe- and the small signal that does exist does not really correspond to observed levels of R-M17.

From the paper:

The E1b1b1-M35 lineages in some Pakistani Pashtun were previously traced to a Greek origin brought by Alexander's invasions [48]. However, RM network of E1b1b1-M35 found that Afghanistan's lineages are correlated with Middle Easterners and Iranians but not with populations from the Balkans.

Greek populations are not homogeneous in their haplogroup E frequencies, so it would be useful to consider the possibility that the lack of this frequent Southeastern European haplogroup in South Asia may not reflect a complete lack of Greek influence in this region, but rather, an influence from a structured ancient Greek population.

Looking at the Y-haplogroup composition:

A few points of interest:

• The clear link between C/N/O with Central Asia
• A clear difference between Persian and Pashto speakers in terms of inverse J2a/R1a frequences
• The paucity of J1 chromosomes (only 1 Tajik) testifies to the absence of relatively recent Middle Eastern influences associated with the spread of Islam; consistent with the absence of the autosomal "Southwest Asian" component in South/Central Asia.
• Paucity of R1b, except in a couple Uzbeks and a Tajik; I have argued before that R1a had an early distribution in the arc of flatlands north and east of the Caspian, while R1b a complementary distribution in the smaller arc of the highlands west and south of it, out of which the Tocharians may have originated.
• The small Nurestani sample comprises of J2a, R1a, and R2; these are linguistic relatives of the Kalash of Pakistan who -unlike the latter- were converted to Islam in the 19th century.

I would say that the evidence is pretty clear that the earliest Iranians may have included haplogroups R1a and J2, although I would not wager on their relative proportions and overall contribution to modern Iranian-speaking populations. For whatever reason, it seems that Kurds and Persians ended up with a J2-over-R1a advantage, while Pathans and (plausibly) Turkified Central Asian former Iranian speakers with the reverse. Nonetheless, the occurrence of both haplogroups in most Iranian groups, as well as in most Indo-Aryan ones is quite telling. It is unfortunate that the relationships between these Y chromosomes (still J2a*! six years after Sengupta et al.) and their West Eurasian brethren was not further pursued.

Hopefully, the data can be re-used down the road once the phylogeny of different haplogroups (and R1a in particular) is better understood. As I've stated before on this blog, I take Y-STR based age estimates with a huge grain of salt, so I would not put much faith in any of the ones presented in this paper.

Related: Firasat et al. (2006), Y-chromosomes of Afghanistan, Lashgary et al. (2011), Regueiro et al. (2006).

PLoS ONE doi:10.1371/journal.pone.0034288


Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events

Marc Haber et al.

Abstract


Afghanistan has held a strategic position throughout history. It has been inhabited since the Paleolithic and later became a crossroad for expanding civilizations and empires. Afghanistan's location, history, and diverse ethnic groups present a unique opportunity to explore how nations and ethnic groups emerged, and how major cultural evolutions and technological developments in human history have influenced modern population structures. In this study we have analyzed, for the first time, the four major ethnic groups in present-day Afghanistan: Hazara, Pashtun, Tajik, and Uzbek, using 52 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y-chromosome. A total of 204 Afghan samples were investigated along with more than 8,500 samples from surrounding populations important to Afghanistan's history through migrations and conquests, including Iranians, Greeks, Indians, Middle Easterners, East Europeans, and East Asians. Our results suggest that all current Afghans largely share a heritage derived from a common unstructured ancestral population that could have emerged during the Neolithic revolution and the formation of the first farming communities. Our results also indicate that inter-Afghan differentiation started during the Bronze Age, probably driven by the formation of the first civilizations in the region. Later migrations and invasions into the region have been assimilated differentially among the ethnic groups, increasing inter-population genetic differences, and giving the Afghans a unique genetic diversity in Central Asia.

Link

Y chromosomes from Afghanistan

Someone from dna-forums was kind enough to send me the haplogroup estimates for this collection of haplotypes; the modal haplogroup in both North and South Afghanistan seems to be R1a with estimates ages that are consistent with those of the Underhill et al. study. (in "evolutionary mutation rate" years/25 years per genration: 12ky south, 7.8ky north, corresponding to 4.7/3ky using germline rate, correction factor, and 31.5 years/generation). I repeat what I wrote in the forum:

While I don't put much faith in Y-STR estimates due to the huge confidence intervals associated with them once all sources of uncertainty are factored in, these are comparable to the Underhill ones, and they seem to establish that (a) Afghanistan is not really remarkable in terms of Y-STR variation, (B) R1a (or at least the likely R1a1a forming the bulk of these) is a Neolithic-to-Bronze Age phenomenon, and (c) if the North/South difference is real, then it fits well with the highest estimated age in India-Pakistan-Nepal and a diminution towards Central Asia.

It would be great to see a study of Afghans with a detailed suite of Y-SNP markers to see how they fit in the Eurasian landscape. Hopefully a combination of more phylogenetic resolution and ancient DNA will help us better understand the ancient distribution and dispersals of the R1a haplogroup.

Somewhat related: some thoughts on Indo-Iranians.

Legal Medicine Volume 13, Issue 2, Pages 103-108 (March 2011)

Y-STR profiling in two Afghanistan populations

Harlette Lacauab et al.

Abstract

Afghanistan’s unique geostrategic position in Eurasia has historically attracted commerce, conflict and conquest to the region. It was also an important stop along the Silk Road, connecting the far eastern civilizations with the western world. Nevertheless, limited genetic studies have been performed in Afghan populations. In this study, 17 Y-chromosomal short tandem repeat (Y-STR) loci were typed to evaluate their forensic and population genetic applications in 189 unrelated Afghan males geographically partitioned along the Hindu Kush Mountain range into north (N=44) and south (N=145) populations. North Afghanistan (0.9734, 0.9905) exhibits higher haplotype diversity than south Afghanistan (0.9408, 0.9813) at both the minimal 9-loci and 17-loci Yfiler haplotypes, respectively. The overall haplotype diversity for both Afghan populations at 17 Y-STR loci is 0.9850 and the corresponding value for the minimal 9-loci haplotypes is 0.9487. A query using of the most frequent Afghan Yfiler haplotype (7.98%) against the worldwide Y-STR haplotype reference database (YHRD) returned no profile match, indicating a high power of discrimination with 17 Y-STR loci. A median-joining network based on 15 Y-STR loci displays limited haplotype sharing between the two Afghan populations, possibly due to the Hindu Kush Mountain range serving as a natural barrier to gene flow between the two regions.

Link