R1ans still at large (or, the story of India)

Ten ago, in the pre-ancient DNA "Dark Ages" a big debate raged on about the origin of R1a  men in India. The stage had been set even earlier, by the pioneering Eurasian heartland paper which was the first (to my memory) to link M17 with steppe migrations and Indo-Iranians. Yet, there was pushback as the distribution of M17 was better described, and people started using Y-STRs to try to date and place phylogeographically its migrations.

The two poles of the debate were the "Out-of-India", which relied primarily on Y-STR based time estimates that seemed very old (even Paleolithic, if one used the wrong mutation rate) in India, and the "Into-India" which thought that the R1a distribution pointed to its being brought into India by the Indo-Aryans in the conventional ~3,500BC time frame of the "Aryan Invasion Theory" (AIT).

AIT has been much maligned because it has been received as a Western colonialist imposition on Indian history: a way to claim that Indian civilization was not native but European in origin. Europeans were certainly guilty of misusing AIT: for British colonials it represented a precedent for their colonization of India; for German National Socialists it was evidence for the greatness of the Aryan race and its past expansions eastward. It also played into internal Indian politics, espoused by some as a means of furthering their superiority as either descendants of "Aryan conquerors" or as oppressed victims of the same.

Of course, a misuse of a theory does not mean it is wrong, and if a new preprint based on ancient and modern DNA is correct, it means that AIT was basically correct: Indo-Aryans did come to India in the Late Bronze Age, via the steppe, and ultimately from central Europe.

The opposing Out-of-India theory is all but dead, although failed theories often have a long half-life, especially if they are espoused for psycho-political reasons. I would argue that Out-of-India was dead for thousands of years before it was conceived, since even in Homer's time it was known that "India" was not "one thing" but was peopled by Indians in the north and "Eastern Ethiopians" in the south (which differed from their western "actual" Ethiopians of Africa by their possession of straight rather than curly hair). These were the "Ancestral North Indians" and "Ancestral South Indians" that modern science has revealed. Out-of-India is little more than a nationalistic myth functioning as an antidote to this basic dichotomy, a way to imbue India's diverse citizens with a myth of common origins.

Yet, proponents of AIT (who have a non-trivial overlap with R1an enthusiasts) are also scratching their heads because of the 27 ancient South Asian males from South Asia studied in the preprint there is exactly one R1a, who also happened to live after the time of the Buddha and not during the Bronze Age.

Both OIT enthusiasts (who expected copious and abundant R1a in India and its environs since the Paleolithic) and AIT/R1an enthusiasts (who expected to see it come in c. 3,500BC) are bound to be disappointed.

Perhaps the R1a Indo-Aryans did come to South Asia in a conventional AIT time frame and they haven't been sampled. Or, maybe they were, indeed, there, but were not R1ans. Or, maybe both sides missed the bigger story which is that the Indo-Aryans (so closely associated with India today) were simply not there as early as people have thought. 

bioRxiv: doi: https://doi.org/10.1101/292581

The Genomic Formation of South and Central Asia

Vagheesh M Narasimhan, Nick J Patterson et al.

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

Link

Jewish and Indian ancestry in the Bene Israel

PLoS ONE 11(3): e0152056. doi:10.1371/journal.pone.0152056

The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry
Yedael Y. Waldman , Arjun Biddanda , Natalie R. Davidson, Paul Billing-Ross, Maya Dubrovsky, Christopher L. Campbell, Carole Oddoux, Eitan Friedman, Gil Atzmon, Eran Halperin, Harry Ostrer, Alon Keinan

The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19–33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.

Link

Denisovan ancestry in Oceanians (and some in South Asians)

Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.03.037

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

Sriram Sankararaman et al.

Some present-day humans derive up to ∼5% [ 1 ] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [ 2 ]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [ 3 ]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Link

History of extant populations of India

The five components they speak of are ANI, ASI, AAA (Ancestral Austro-Asiatic), ATB (Ancestral Tibeto-Burman), and a distinct fifth ancestry in the Andaman archipelago.

The differentiation of the four main components seems clear enough on the figure (left). The big question is how and in what order the different components got into India. I would wager that ASI was first and I modify my New Year's wish to ask for some ancient DNA from India too.

An interesting bit from the paper:

...that the practice of endogamy was established almost simultaneously, possibly by decree of the rulers, in upper-caste populations of all geographical regions, about 70 generations before present, probably during the reign (319–550 CE) of the ardent Hindu Gupta rulers

How plausible is that to anyone familiar with Indian history?

PNAS doi: 10.1073/pnas.1513197113

Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure

Analabha Basu, Neeta Sarkar-Roya, and Partha P. Majumder

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform.

Link

Kalash origins

This is an open access paper.

AJHG http://dx.doi.org/10.1016/j.ajhg.2015.03.012

The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection

Qasim Ayub et al.

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.

Link

168 South Asian Genomes

PLoS ONE 9(8): e102645. doi:10.1371/journal.pone.0102645

The South Asian Genome

John C. Chambers et al.

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

Link

Near Eastern roots of South Asian Neolithic

The table of dates for different sites might prove useful (pdf).

PLoS ONE 9(5): e95714. doi:10.1371/journal.pone.0095714

The Near-Eastern Roots of the Neolithic in South Asia

Kavita Gangal et al.

The Fertile Crescent in the Near East is one of the independent origins of the Neolithic, the source from which farming and pottery-making spread across Europe from 9,000 to 6,000 years ago at an average rate of about 1 km/yr. There is also strong evidence for causal connections between the Near-Eastern Neolithic and that further east, up to the Indus Valley. The Neolithic in South Asia has been far less explored than its European counterpart, especially in terms of absolute (14C) dating; hence, there were no previous attempts to assess quantitatively its spread in Asia. We combine the available 14C data with the archaeological evidence for early Neolithic sites in South Asia to analyze the spatio-temporal continuity of the Neolithic dispersal from the Near East through the Middle East and to the Indian subcontinent. We reveal an approximately linear dependence between the age and the geodesic distance from the Near East, suggesting a systematic (but not necessarily uniform) spread at an average speed of about 0.65 km/yr.

Link

Origins of the Tharu

European Journal of Human Genetics advance online publication 26 March 2014; doi: 10.1038/ejhg.2014.36

Unravelling the distinct strains of Tharu ancestry

Gyaneshwer Chaubey et al.

The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43.

Link

4.2 kiloyear event and the demise of Indus Valley megacities

From the paper:

The 4.2 ka aridification event is regarded as one of the most severe climatic changes in the Holocene, and affected several Early Bronze Age populations from the Aegean to the ancient Near East (Cullen et al., 2000; Weiss and Brad- ley, 2001). This study demonstrates that the cli- mate changes at that time extended to the plains of northwestern India. The Kotla Dahar record alone cannot fully explain the role of climate change in the cultural evolution of the Indus civilization. The Indus settlements spanned a diverse range of environmental and ecological zones (Wright, 2010; Petrie, 2013); therefore, correlation of evidence for climate change and the decline of Indus urbanism requires a comprehensive assessment of the relationship between settlement and climate across a sub- stantial area (Weiss and Bradley, 2001; Petrie, 2013). The impact of the abrupt climate event in India and West Asia records, and that observed at Kotla Dahar, on settled life in the Indus region warrants further investigation.

Plato (or rather the Egyptian priest speaking through Plato) may have been the first one to note the differential survival of people as a result of natural catastrophes. It is hard to imagine that such an extreme event would not unbalance agricultural economies leading to famine and also endanger the supply systems on which early cities were based. The failure of cities would in turn lead to a failure of governing elites centered on them and a power vacuum which new elites (armed with bronze weapons at this time) might take advantage of. Climate may have ended the Bronze Age civilization itself 1000 years later.

Geology doi: 10.1130/G35236.1

Abrupt weakening of the summer monsoon in northwest India ∼4100 yr ago

Yama Dixit et al.

Climate change has been suggested as a possible cause for the decline of urban centers of the Indus Civilization ∼4000 yr ago, but extant paleoclimatic evidence has been derived from locations well outside the distribution of Indus settlements. Here we report an oxygen isotope record of gastropod aragonite (δ18Oa) from Holocene sediments of paleolake Kotla Dahar (Haryana, India), which is adjacent to Indus settlements and documents Indian summer monsoon (ISM) variability for the past 6.5 k.y. A 4‰ increase in δ18Oa occurred at ca. 4.1 ka marking a peak in the evaporation/precipitation ratio in the lake catchment related to weakening of the ISM. Although dating uncertainty exists in both climate and archaeological records, the drought event 4.1 ka on the northwestern Indian plains is within the radiocarbon age range for the beginning of Indus de-urbanization, suggesting that climate may have played a role in the Indus cultural transformation.

Link

Europeans and South Asians share by descent SLC24A5 light skin allele

The age estimate for this allele is quite old but with a huge 95% confidence interval. Hopefully ancient DNA can illuminate the trajectory of the allele's frequency through time and space.

Razib has more.

PLoS Genet 9(11): e1003912. doi:10.1371/journal.pgen.1003912

The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent

Chandana Basu Mallick et al.

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.

Link

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

Major admixture in India took place ~4.2-1.9 thousand years ago (Moorjani et al. 2013)

A new paper on the topic of Indian population history has just appeared in the American Journal of Human Genetics. In previous work it was determined that Indians trace their ancestry to two major groups, Ancestral North Indians (ANI) (= West Eurasians of some kind), and Ancestral South Indians (ASI) (= distant relatives of Andaman Islanders, existing today only in admixed form). The new paper demonstrates that admixture between these two groups took place ~4.2-1.9 thousand years ago.

The authors caution about this evidence of admixture:

It is also important to emphasize what our study has not shown. Although we have documented evidence for mixture in India between about 1,900 and 4,200 years BP, this does not imply migration from West Eurasia into India during this time. On the contrary, a recent study that searched for West Eurasian groups most closely related to the ANI ancestors of Indians failed to find any evidence for shared ancestry between the ANI and groups in West Eurasia within the past 12,500 years3 (although it is possible that with further sampling and new methods such relatedness might be detected). An alternative possibility that is also consistent with our data is that the ANI and ASI were both living in or near South Asia for a substantial period prior to their mixture. Such a pattern has been documented elsewhere; for example, ancient DNA studies of northern Europeans have shown that Neolithic farmers originating in Western Asia migrated to Europe about 7,500 years BP but did not mix with local hunter gatherers until thousands of years later to form the present-day populations of northern Europe.15, 16, 44 and 45

This is of course true, because admixture postdates migration and it is conceivable that the West Eurasian groups might not have admixed with ASI populations immediately after their arrival into South Asia. On the other hand, a long period of co-existence without admixture would be against much of human history (e.g., the reverse movement of the Roma into Europe, who picked up European admixture despite strong social pressure against it by both European and Roma communities, or the absorption of most Native Americans by incoming European, and later African, populations in post-Columbian times). It is difficult to imagine really long reproductive isolation between neighboring peoples.

Such reproductive isolation would require a cultural shift from a long period of endogamy (ANI migration, followed by ANI/ASI co-existence without admixture) to exogamy ~4.2-1.9kya (to explain the thoroughness of blending that left no group untouched), and then back to fairly strict exogamy (within the modern caste system). It might be simpler to postulate only one cultural shift (migration with admixture soon thereafter, with later introduction of endogamy which greatly diminished the admixture.

The authors cite the evidence from neolithic Sweden which does, indeed, suggest that the neolithic farmers this far north were "southern European" genetically and had not (yet) mixed with contemporary hunter-gatherers, as they must have done eventually. But, perhaps farmers and hunters could avoid each other during first contact, when Europe was sparsely populated. It is not clear whether the same could be said for India ~4 thousand years ago with the Indus Valley Civilization providing evidence for a large indigenous population that any intrusive group would have encountered. In any case, the problem of when the West Eurasian element arrived in India will probably be solved by relating it to events elsewhere in Eurasia, and, in particular, to the ultimate source of the "Ancestral North Indians".

It is also possible that some of the ANI-ASI admixture might actually pre-date migration. At present it's anyone's guess where the original limes between the west Eurasian and ASI worlds were. There is some mtDNA haplogroup M in Iran and Central Asia, which is otherwise rare in west Eurasia, so it is not inconceivable that ASI may have once extended outside the Indian subcontinent: the fact that it is concentrated today in southern India (hence its name) may indicate only the area of this element's maximum survival, rather than the extent of its original distribution. In any case, all mixture must have taken place somewhere in the vicinity of India.

A second interesting finding of the paper is that admixture dates in Indo-European groups are later than in Dravidian groups. This is demonstrated quite clearly in the rolloff figure on the left. Moreover, it does not seem that the admixture times for Indo-Europeans coincide with the appearance of the Indo-Aryans, presumably during the 2nd millennium BC: they are much later. I believe that this is fairly convincing evidence that north India has been affected by subsequent population movements from central Asia of "Indo-Scythian"-related populations, for which there is ample historical evidence. So, the difference in dates might be explained by secondary (later) admixture with other West Eurasians after the arrival of Indo-Aryans. Interestingly, the paper does not reject simple ANI-ASI admixture "often from tribal and traditionally lower-caste groups," while finding evidence for multiple layers of ANI ancestry  in several other populations.

My own analysis of Dodecad Project South Indian Brahmins arrived at a date of 4.1ky, and of North Indian Brahmins, a date of 2.3ky, which seems to be in good agreement with these results.

The authors also report that "we find that Georgians along with other Caucasus groups are consistent with sharing the most genetic drift with ANI". I had made a post on the differential relationship of ANI to Caucasus populations which seems to agree with this, and, of course, in various ADMIXTURE analyses, the component which I've labeled "West Asian" tends to be the major west Eurasian element in south Asia.

Here are the estimated admixture proportions/times from the paper:

Sadly, the warm and moist climate of India, and the adoption of cremation have probably destroyed any hope of studying much of its recent history with ancient DNA. On the other hand, the caste system has probably "fossilized" old socio-linguistic groups, allowing us to tell much by studying their differences and correlating them with groups outside India.

Coverage elsewhere: Gene Expression, HarappaDNA
Related podcast on BBC.

AJHG doi:10.1016/j.ajhg.2013.07.006

Genetic Evidence for Recent Population Mixture in India

Priya Moorjani et al.

Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.

Link

Y chromosomes in Lingayat and Vokkaliga Dravidians from SW India

From the paper:

The virtual absence of Z283 subclades, namely Z280 and M458, and the total representation of R1a1a-derived samples by the Z93 marker in our dataset support an earlier observation that the M198 chromosome likely differentiated in the region between Eastern Europe and South Asia (Pamjav et al., 2012), and subsequently expanded in opposite directions. However, it will require additional R1a1a* samples from different populations across Eurasia to comprehensively evaluate the geographic origins, distribution and ethno-linguistic associations of the individual M198-derived lineages (Pamjav et al., 2012).

This study extends the results of Pamjav et al. 2012 which found only Z93 within R1a1 in mainland Indian populations. The authors estimate 12.8ky as the age of R-Z93 in the Lingayat, but since this uses the evolutionary mutation rate it should actually be divided by a factor of 3.6 which translates into ~1,500BC. So, it seems quite likely that R-Z93 moved from Central->South Asia during the Bronze Age, both on account of its age and the fact that it is a subset of Central Asian diversity. Haplogroup R2 with a nominal age of ~22ky in the Lingayat seems more like a Neolithic lineage.

Also of interest:

Another haplogroup that is associated with the spread of agriculture from the Fertile Crescent and Anatolia regions is J2-M172 (Cinnioğlu et al., 2004 and Semino et al., 2004). According to Sahoo et al. (2006), only J2 lineages, originating from West Asia rather than Central Asia, represent an external contribution to the Indian paternal gene pool. In particular, subclade J2a-M410 is believed to have entered through the northwestern corridor and subsequently diffused to the south and east (Sahoo et al., 2006 and Thangaraj et al., 2010). This haplogroup is present exclusively in the Lingayat (6.93%), except for one individual from Vokkaliga, suggesting gene flow from West Asia (Sahoo et al., 2006 and Thangaraj et al., 2010). Interestingly, four J2b2-M241 Lingayat males displayed a null allele at DYS458 and failed to produce the AMGY PCR amplicon while their X homolog (AMGX) amplified successfully. Comparison of Y-STR haplotypes of the affected males from the present study with those from the literature (Cadenas et al., 2006), demonstrated a high level of allele sharing, implying shared paternal lineages or a recent common ancestry for these groups of individuals.

According to the paper the Lingayat are a community that originally attracted members from across the caste system, while the Vokkaliga are involved in farming. An uneven distribution of haplogroup J2a has been previously observed, so I guess this paper adds to this evidence.

Gene Available online 7 May 2013

Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India

Shilpa Chennakrishnaiah et al.

Previous studies have shown that India's vast coastal rim played an important role in the dispersal of modern humans out of Africa but the Karnataka state, which is located on the southwest coast of India, remains poorly characterized genetically. In the present study, two Dravidian populations, namely Lingayat (N = 101) and Vokkaliga (N = 102), who represent the two major communities of the Karnataka state, were examined using high-resolution analyses of Y-chromosome single nucleotide polymorphisms (Y-SNPs) and seventeen short tandem repeat (Y-STR) loci. Our results revealed that the majority of the Lingayat and Vokkaliga paternal gene pools are composed of four Y-chromosomal haplogroups (H, L, F* and R2) that are frequent in the Indian subcontinent. The high level of L1-M76 chromosomes in the Vokkaligas suggests an agricultural expansion in the region, while the predominance of R1a1a1b2-Z93 and J2a-M410 lineages in the Lingayat indicates gene flow from neighboring south Indian populations and West Asia, respectively. Lingayat (0.9981) also exhibits a relatively high haplotype diversity compared to Vokkaliga (0.9901), supporting the historical record that the Lingayat originated from multiple source populations. In addition, we detected ancient lineages such as F*-M213, H*-M69 and C*-M216 that may be indicative of genetic signatures of the earliest settlers who reached India after their migration out of Africa.

Link

A Middle Paleolithic link between North Africa and the Thar desert

One more piece of evidence against the idea that modern humans expanded Out-of-Africa because of the technological/behavioral revolution evidenced during the Upper Paleolithic/Late Stone Age.

And, one more piece of evidence against the idea that early modern humans in Eurasia died out and were replaced wholesale circa 50-60 thousand years ago from a fresh OoA impulse. It would have been possible to suppose such a thing if the evidence for MP African influence was minor or geographically localized, but much more difficult when it extends over a wide region.

Of course, the attribution of the Katoati assemblages to modern humans is done indirectly by linking them to MSA sites of the Sahara, but the proliferation of real archaeological sites (see map) that can be linked to OoA makes it difficult to adopt the idea of an archaeologically invisible late OoA that (somehow) replaced all previous inhabitants.

Quaternary Science Reviews Available online 5 July 2013

Middle Palaeolithic occupation in the Thar Desert during the Upper Pleistocene: the signature of a modern human exit out of Africa?

James Blinkhorn et al.

The Thar Desert marks the transition from the Saharo-Arabian deserts to the Oriental biogeographical zone and is therefore an important location in understanding hominin occupation and dispersal during the Upper Pleistocene. Here, we report the discovery of stratified Middle Palaeolithic assemblages at Katoati in the north-eastern Thar Desert, dating to Marine Isotope Stages (MIS) 5 and the MIS 4–3 boundary, during periods of enhanced humidity. Hominins procured cobbles from gravels at the site as evidenced by early stages of stone tool reduction, with a component of more formalised point production. The MIS 5c assemblages at Katoati represent the earliest securely dated Middle Palaeolithic occupation of South Asia. Distinctive artefacts identified in both MIS 5 and MIS 4–3 boundary horizons match technological entities observed in Middle Palaeolithic assemblages in South Asia, Arabia and Middle Stone Age sites in the Sahara. The evidence from Katoati is consistent with arguments for the dispersal of Homo sapiens populations from Africa across southern Asia using Middle Palaeolithic technologies.

Link

Continuity of microblade technology in India since 45ka

An interesting new paper extends continuity of microblade technologies in India to ~45ka, and hence makes it probable that these were introduced by AMH together with the UP colonization of the rest of Eurasia.

I am not sure that the authors' suggestion that early modern humans were "tropically adapted" is certain. Personally, my idea du jour is to derive them from the Saharo-Arabian belt. In any case, as an advocate of "early OOA" (in the sense of pre-UP/LSA), it makes sense to me that modern humans in Eurasia would be initially climate-limited and at a disadvantage vis a vis archaic Eurasians inhabiting regions for which they were maladapted. In my opinion, it was the technological revolution of ~50ka being responsible for the extension of their range at the expense of other Eurasians.

PLoS ONE 8(7): e69280. doi:10.1371/journal.pone.0069280

Continuity of Microblade Technology in the Indian Subcontinent Since 45 ka: Implications for the Dispersal of Modern Humans

Sheila Mishra et al.

We extend the continuity of microblade technology in the Indian Subcontinent to 45 ka, on the basis of optical dating of microblade assemblages from the site of Mehtakheri, (22° 13' 44″ N Lat 76° 01' 36″ E Long) in Madhya Pradesh, India. Microblade technology in the Indian Subcontinent is continuously present from its first appearance until the Iron Age (~3 ka), making its association with modern humans undisputed. It has been suggested that microblade technology in the Indian Subcontinent was developed locally by modern humans after 35 ka. The dates reported here from Mehtakheri show this inference to be untenable and suggest alternatively that this technology arrived in the Indian Subcontinent with the earliest modern humans. It also shows that modern humans in Indian Subcontinent and SE Asia were associated with differing technologies and this calls into question the “southern dispersal” route of modern humans from Africa through India to SE Asia and then to Australia. We suggest that modern humans dispersed from Africa in two stages coinciding with the warmer interglacial conditions of MIS 5 and MIS 3. Competitive interactions between African modern humans and Indian archaics who shared an adaptation to tropical environments differed from that between modern humans and archaics like Neanderthals and Denisovans, who were adapted to temperate environments. Thus, while modern humans expanded into temperate regions during warmer climates, their expansion into tropical regions, like the Indian Subcontinent, in competition with similarly adapted populations, occurred during arid climates. Thus modern humans probably entered the Indian Subcontinent during the arid climate of MIS 4 coinciding with their disappearance from the Middle East and Northern Africa. The out of phase expansion of modern humans into tropical versus temperate regions has been one of the factors affecting the dispersal of modern humans from Africa during the period 200–40 ka.

Link

Prince William's Indian matrilineage?

William has a hint of Indian in his DNA, find British researchers

Researchers have sourced William’s Indian ancestry to Eliza Kewark, his great-great-great-great-great grandmother, who was assumed to be Armenian, but now has been revealed as an Indian by genetic research.

...

“Through genealogy we traced two living direct descendants of Eliza and by reading the sequence of their mtDNA, we showed not only that they matched, but also that it belongs to a haplogroup called R30b, thus determining Eliza Kewark’s haplogroup,” the research team revealed.

The haplogroup, which is a group of related ancestral lineages, in this case was revealed to be rare and found only in South Asia. Other related branches of R30a and R30* are also entirely South Asian.

“This confirms therefore that the mtDNA of Eliza Kewark of Surat was of Indian heritage. R30b is rare even in India, where roughly 0.3 per cent of people carry this lineage,” the researchers revealed.

Chaubey et al. (2008) is an article that touches upon the subject of R30b.

Personally, I wouldn't be so quick in discounting the traditional genealogical story. A lineage that occurs at a frequency of 0.3% will almost certainly be missed in any small sample if it occurs at similar trace frequencies in other populations.

mtDNA from Nepal and Tibet (Gayden et al. 2013)

Am J Phys Anthropol. 2013 Jun;151(2):169-82. doi: 10.1002/ajpa.22240. Epub 2013 Apr 12.

The Himalayas: Barrier and conduit for gene flow.

Gayden T, Perez A, Persad PJ, Bukhari A, Chennakrishnaiah S, Simms T, Maloney T, Rodriguez K, Herrera RJ.

Abstract

The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia.

Link

ESHG 2013 abstracts

A couple of weeks before the ESHG 2013 conference, here are a few abstracts that caught my eye. Feel free to point to more interesting presentations in the comments section.

• J16.05 - Checking the hypothesis of a Balkan origin of the Armenians
• P17.5 - Y chromosome haplogroup analysis to estimate genetic origin of Balts
• J16.27 - Armenian Highland as a transition corridor for the spread of Neolithic agriculturists
• J16.14 - In Search of the Origin of Haplogroup J1-P58
• J16.03 - Y-chromosome haplogroup analysis in the Besermyan ethnic group
• P17.4 - Mitochondrial DNA Analysis of the Southeast European Genetic Variation Reveals a New, Local Subbranching in Hg X2
• P16.085 - Population diversity and history of the Indian subcontinent: Uncovering the deeper mosaic of sub-structuring and the intricate network of dispersals
• J16.43 - Ancient mtDNA diversity in Bulgaria
• P16.072 - Mitochondrial DNA diversity in medieval and modern Romanian population
• P16.012 - Frequency analysis of the CCR5-Delta32 allele in medieval and modern Romanian population
• J16.78 - The gene pool of Argyn in the context of generic structure of Kazakhs according to data on SNP-Y-Chromosome markers.

Y chromosomes and mtDNA from the Maldives

Of interest from the paper:

The haplogroup J(M304) Y chromosomes are all in subgroup J2(M172). 

... 

However, Eaaswarkhanth et al. (2010) report that Muslims and non-Muslims in India largely have the same Y-haplogroup frequency distribution, except that in Muslims low frequencies of Y-E1b1b1a(M78), Y-J(M304)(xJ2(M172)), and Y-G(M201) are found that are absent in non-Muslims (Eaaswarkhanth et al., 2010). In our Maldivian sample, none of those Y-haplogroups were found.

AJPA DOI: 10.1002/ajpa.22256

Indian ocean crossroads: Human genetic origin and population structure in the maldives

Jeroen Pijpe et al.

The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago. Am J Phys Anthropol 000:000–000, 2013. © 2013 Wiley Periodicals, Inc.

Link

Connections between Indus Valley and Mesopotamia

Of interest from the paper:

Based on this distribution of values, it would appear from our preliminary analysis that almost half of the individuals sampled from the Harappa cemetery have isotope values outside the local baseline (0.7158-0.7189). Most of these individuals have values below the Harappa range. In addition, there are at least three non-local individuals with higher values, including one with an extremely isotope ratio that cannot be from the Harappa region. A more detailed discussion of the Harappa samples will be presented in a future publication on the Harappa cemetery, but it is clear that many of what appear to be local individuals at Harappa are females and they are associated in burial with nearby males who are clearly not local. These preliminary patterns require further testing before major conclusions can be proposed, but it does suggest that they represent a unique population of people from multiple regions of the Indus valley or beyond.

Journal of Archaeological Science
Volume 40, Issue 5, May 2013, Pages 2286–2297

A new approach to tracking connections between the Indus Valley and Mesopotamia: initial results of strontium isotope analyses from Harappa and Ur

J. Mark Kenoyer et al.

Exchange and interaction between early state-level societies in Mesopotamia and the Indus Valley during the 3rd millennium BC has been documented for some time. The study of this interaction has been dominated by the analysis of artifacts such as carnelian beads and marine shell, along with limited textual evidence. With the aid of strontium, carbon, and oxygen isotopes, it is now possible to develop more direct means for determining the presence of non-local people in both regions. This preliminary study of tooth enamel from individuals buried at Harappa and at the Royal Cemetery of Ur, indicates that it should be feasible to identify Harappans in Mesopotamia. It is also possible to examine the mobility of individuals from communities within the greater Indus Valley region.

Link