Genetic History of India

Tamil Bride in Antique Kundan Sets

The proto-Dravidian people may have arrived from the Fertile Crescent, which explains the presence of the bull-leaping tradition shared with ancient Mesopotamians and the Minoans, who were the first Europeans to have literate civilisation. The proto-Elamo-Dravidian language originated in the Elam province in southwestern Iran, and spread eastwards to the Indus Valley and the Indian sub-continent. The proto-Dravidian people were preceded by the Tibeto-Burman language speakers, who live in six of the seven states of Northeastern India. Tibeto-Burman languages are currently spoken in Tibet and western China and the Tibeto-Burman language speakers were most likely to be the original inhabitants of the Indian sub-continent.




Although Paleolithic and Mesolithic people left their mark in the Iranian Plateau, major human population developments with possible genetic implications occurred here during the Neolithic period and later [1], [10], [11]. The Middle Eastern region spanning from Zagros Mountains and northern Mesopotamia to Southeast Anatolia, called Fertile Crescent, is broadly accepted to be the place where agriculture first arose [1]. Important agricultural developments occurred in the eastern horn of the Fertile Crescent, notably in Elam (southwestern Iran), connecting Mesopotamia and the Iranian Plateau [12]. The highly urban Elamite civilization had close contacts with Mesopotamians but exhibited an extensive differentiation from the rest of the Fertile Crescent populations, including a language that is thought to belong to the Dravidian family [3], [13]. Another major innovation, that most likely emerged later than agriculture, was the domestication of animals, which is thought to have led to dramatic population expansions in Eurasia [1], [14], [15]. Starting about 5000 years (ky) before present, pastoral nomadism developed in the grasslands of Central Asia, as well as in southeastern Europe, opening up the possibility of rapid movements of large population groups [16]. The spread of these new technologies has been associated with the dispersal of Dravidian and Indo-European languages in southern Asia [17], [18]. It is hypothesized that the proto-Elamo-Dravidian language, most likely originated in the Elam province in southwestern Iran, spread eastwards with the movement of farmers to the Indus Valley and the Indian sub-continent [13], [19].

Between the third and second millennia BCE the Iranian Plateau became exposed to incursions of pastoral nomads from the Central Asian steppes, who brought the Indo-Iranian language of the Indo-European family, which eventually replaced Dravidian languages, perhaps by an elite-dominance model [13], [17], [20].


Figure 1. MDS plot based on Fst statistics calculated from complete mtDNA sequences for population samples from Iran, Anatolia, Caucasus, and Europe.

In order to visualize the relationships between Iranians studied and other populations of the Caucasus, Anatolia and Europe based on complete mtDNA sequence data, MDS plot was constructed from the pairwise Fst values (Table S3). The results show that Persians and Qashqais are close to each other and to Armenians, whereas Azeris from Iran are located nearby Georgians. It is worth pointing out the position of Azeris from the Caucasus region, who despite their supposed common origin with Iranian Azeris, cluster quite separately and occupy an intermediate position between the Azeris/Georgians and Turks/Iranians grouping (Figure 1). Interestingly, the results of our MDS analysis do not combine the populations studied according to their geographic and/or linguistic affinity. Therefore, Turkic-speaking Qashqais, Azeris, and Turks are located quite distantly from each other on the plot, even though association between the latter two groups has been recently revealed based on complete mtDNA sequences [40]. All populations from the Caucasus region (Armenians, Azeris, and Georgians) are scattered on the plot though their genetic proximity has been demonstrated by Schönberg et al. [40]. Similarly, Iranians from Tehran province [40] and Persians studied here are clearly separated from each other.

The genetic structure of Iranians in comparison with the populations from the Caucasus, Anatolia and Europe was investigated by AMOVA (Table S4). As expected, before grouping, the majority of variability was due to within population component (98.5% for Iranian populations only and 98.12% for the complete data set). After grouping, neither geographic nor linguistic classification gave a good fit to the genetic data. A slightly higher degree of geographic rather than linguistic correlation with the genetic structuring of the examined populations emerges only when the geographically and genetically distant population of Buryats from Inner Mongolia region of China was added to the studied data set, thus underlining the importance of geographic distance. It should be noted that correlation between geographical proximity and genetic relationships of populations has been shown previously based on HVS1 variability data for Indo-European and Semitic-speaking groups of southwestern Iran [56], [57]. Moreover, a slightly better fit of geographic rather than linguistic classification of populations to the complete mtDNA sequence data has been demonstrated recently for Iranian, Anatolian and Caucasus region populations [40].


Figure 2. BSP indicating the median of the hypothetical effective population size through time based on complete mtDNA genome data for Persians, Qashqais and Azeris.

The haplogroup assignment for each individual according to the nomenclature of Phylotree.org [43] (Build 15) is given in Table S4. A total of 212 different sub-haplogroups or paragroups (unclassified lineages within a clade) were identified, which fall into 75 principal haplogroups. The vast majority of the mtDNAs clustered into macrohaplogroups M, N, and R, but a limited number was found to belong to the sub-Saharan haplogroups L2a, L3d, L3e, L3f and L5c (Figure S2). Two haplogroups, H91 and HV18, are defined here for the first time, whereas others (marked red in Table S1 and Figure S2) represent newly identified sub-clades. Moreover, for some previously known haplogroups we redefined diagnostic markers that allow a better definition of the haplogroup topology within the tree.

Haplogroup frequencies for Azeris, Persians, Qashqais and the entire Iranian mtDNA data set are presented in Table 2. All Iranian populations studied here are characterized by the same most prominent western Eurasian mtDNA haplogroups, H, J, T and U; however, the frequency distribution of these lineages varies between different populations. All the three populations show similar frequencies of haplogroup U (22.7%, 24.3%, and 22.3%, respectively), but the frequencies of haplogroups H and J are more pronounced in Qashqais (28.6% and 15.2%, respectively) than in Persians (16.6% and 6.1%, respectively) and Azeris (22.7% and 4.6%, respectively). In contrast, haplogroup T dominates in Azeris (18.2%) and Persians (11.6%), being found only in 4.5% in Qashqais. Another notable difference between Azeris and two other populations studied is the higher frequency of haplogroups X2 (9.1% versus 2.8% in Persians and 2.7% in Qashqais) and N1a3 (9.1% versus 0.6% in Persians), and the absence of haplogroups U and H diversification, which may be merely the result of smaller sample size. There are also distinguished differences between the Persians and Qashqais with respect to the distribution of some sub-haplogroups, including H13 (2.8% versus 6.3%), T2 (7.2% versus 1.8%), U3 (2.8% versus 8%), and U7 (7.2% versus 2.7%) (Table 2).


Table 2. Mitochondrial haplogroup frequencies (%) in Iranian populations.

It is known that some of the mtDNA lineages are either autochthonous to Iran or underwent a major expansion in this region [11]. Among them is haplogroup R2, which is concentrated in southern Pakistan and in India, and is present at low frequencies in the most of adjacent regions, including the Near East, the Caucasus, the Iranian Plateau, the Arabian Peninsula, and Central Asia [11], [25], [37]. The extensive sequencing of complete mtDNAs from a large part of the Iranian Plateau led us to the identification of several highly divergent Qashqai lineages within the entire haplogroup R2 and revealed a new Persian-specific sub-clade within haplogroup R2a. The reconstructed complete mtDNA phylogeny based on fifteen published and nine new Iranian R2 sequences is shown in Figure 3 and includes age estimates obtained from complete genome and synonymous mutations. As can be seen, haplogroup R2 has a likely pre-LGM/Late Glacial time depth, characterized by an overall coalescence time estimate of 21–31 kya, and it probably originated in the southern region of Iran and split early into three branches. The first sub-clade, R2a, dates to ∼15–20 kya and includes several branches found mostly in southern Arabians (R2a1, R2a2, R2a3) and Persians (R2a4), as well as single mtDNAs from South Asia, the Near East and Europe. Two other mtDNA lineages, which are named here as R2b and R2c, restricted to Qashqais from southern Iran and potentially could have split before the main R2a sub-clade (sample size does not allow dating).


Figure 3. Maximum-parsimony phylogenetic tree of complete mtDNA sequences belonging to haplogroup R2.

Overall, the complete mtDNA sequence analysis revealed an extremely high level of genetic diversity in the Iranian populations studied which is comparable to the other groups from the South Caucasus, Anatolia and Europe. The results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia/Caucasus and Iran region pointing to strong genetic affinity of Indo-European speaking Persians and Turkic-speaking Qashqais, thus suggesting their origin from a common maternal ancestral gene pool. The pronounced influence of the South Caucasus populations on the maternal diversity of Iranian Azeris is also evident from the MDS analysis results.

Our results confirms that populations from Iran, Anatolia, the Caucasus and the Arabian Peninsula display a common set of maternal lineages although considerable regional differences in haplogroup frequencies exist [11], [29]. Meanwhile, some haplogroups previously defined as South Asian (such as R2 and HV2) could be considered as having Southwest Asian origin, taking into account the relatively high frequency and diversity of those haplogroups in Iran. Although R2 is a very rare haplogroup, the phylogeographic analysis indicates that it is present mostly in southern Arabia, while it has been suggested that the unrepresented Near East can be considered as a possible place of origin for R2 [37]. Meanwhile, our data indicate that haplogroup R2 has a likely pre-LGM/LGM time depth, with a coalescence time estimate of 21–31 kya, and it probably originated in southern Iran, although the neighboring Gulf Oasis region cannot be excluded, taking into account the close genetic affinity between Persians and Arabians proposed by Terreros et al. [26]. One should note also that the age estimate for the extremely rare haplogroup N3, which is specific for Iranian populations, is close to the LGM time, as it has been dated to 13–24 kya.

dx.doi.org/10.1371/journal.pone.0080673

India has been underrepresented in genome-wide surveys of human variation. We analyse 25 diverse groups in India to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39-71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry. Allele frequency differences between groups in India are larger than in Europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy. We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically.

We warn that ‘models’ in population genetics should be treated with caution. Although they provide an important framework for testing historical hypotheses, they are oversimplifications. For example, the true ancestral populations of India were probably not homogeneous as we assume in our model, but instead were probably formed by clusters of related groups that mixed at different times. However, modelling them as homogeneous fits the data and seems to capture meaningful features of history.



The following figure illustrates the general model which looms in the background of this paper: Note that the Andaman Islanders, the Onge, aren’t really the ancestors of Indians on the mainland. Rather, they’re a branch of the ancient population which presumably first settled South Asia, and close to the ASI. Who were the ASI? Since they aren’t really around, we can only generate conjectures and inferences. In this paper the ANI are actually represented in some ways by Europeans, even though presumably the assumption is that both these are daughter populations of another group. Though not pushed very hard, they do mention proto-Indo-Europeans as the candidate for the ANI.



This should not surprise, previous work shows that South Asians distribute along an axis away from Europeans. One of the points in the paper is that there is both geographic and caste stratification. I added some labels, but I thought drilling-down was probably useful. I don’t know all these groups off the top of my head, and I assume few of readers do either. So I zoomed in:



I think some of the shortcomings with a sample size on the order of the low hundreds is rather clear. They couldn’t even use all their samples, or some of the samples were not relevant to the question on hand. The Siddis are an Indian-African mix which emerged during the period of Muslim domination when that group imported black slaves. The Tibeto-Burman groups of Northeast India are interesting, but outliers. The general trends are clear, North Indian groups have more ANI than South Indian groups, and upper caste groups have more ANI than lower caste groups, but that is only with “all things equal.” Note that upper caste South Indian groups clearly have more ANI than lower caste South Indians, but they have a lower proportion than some North Indian lower castes, and are in the range of one North Indian tribal group. Some of the outliers are also interesting; the lower caste individual similar to Austro-Asiatic tribals is from a group which resides in a region with many Austro-Asiatic peoples. Clearly there has been identity switching, so you have aberrations such as one North Indian tribal who clusters with Kashmiri Pandit Brahmins! The Austro-Asiatic group is also interesting, because they speak languages related to those of Southeast Asia. Here is a map of the Austro-Asiatic languages:



We know with near 100% certainty that much of Burma & Thailand were dominated by Mon-Khmer languages before the arrival of the Shan, Bamar (Burmans) and Thai peoples (to mention a few). This is matter of historical record, the rise of modern Burma and Thailand was largely a story of the eclipse of Mon and Khmer societies who transmitted to them much of the Indic character which they have (e.g., the northern populations often arrived as Mahayana Buddhists, but the Mon and Khmer Theravada Buddhism was adopted as the dominant religions in the new states). The position of the Munda languages is more confused, as some posit that they arrived from the east, while others argue that the the Austro-Asiatic languages expanded east from India. This is not going to be resolved in this blog post, but let me note that the genetic data above, which show an “eastern” affinity of the Munda, can be combined to with cultural datum such as the arrival of rice farming from the east and historical records which document the migration of populations from Burma, to construct a plausible east-west narrative. In contrast it seems an almost default position by many that the Austro-Asiatics are the most ancient South Asians, marginalized by Dravidians, and later Indo-Europeans. I would not be surprised if it was actually first Dravidians, then Austro-Asiatics and finally Indo-Europeans. Dravidian are found in every corner of the subcontinent (Brahui in Pakistan, a few groups in Bengal, and scattered through the center) while the Austro-Asiatics exhibit a more restricted northeastern range.



Interestingly, one of the GIH subgroups fall outside the main gradient of Indian groups, suggesting that they harbor substantial ancestry that is not a simple mixture of ASI and ANI. A speculative hypothesisis that some Gujarati groups descend from the founders of the “Gurjara Pratihara” empire, which is thought to have been founded by Central Asian invaders in the 7th century A.D. and to have ruled parts of northwest India from the 7-12th centuries. I. Karve noted that endogamous groups with names like “Gurjar” are now distributed throughout the northwest of the subcontinent, and hypothesized that that they likely trace their names to this invading group.



Next are two charts which shows Indians, Europeans, and Chinese. In the first the PCA was originally constructed with Europeans & Chinese, and the Indians were projected onto it using the variation found in the first two groups. In the second case, Indians and Chinese were used to construct the PCA, and Europeans projected.



What you see is that Europeans are all equally related to Indians, but Indians exhibit a gradient of relationship to Europeans. That is, there is no European group which in particular resembles Indians via the connection with ANI; the distance between all European groups and ANI seems roughly equal. The Indians vary in their relationship to Europeans because they vary in their proportion of ANI.

In the table above there is a reference to the proportion of ANI and ASI in each Indian group. One question you might ask: how do you estimate the proportions of ancestry from groups which you don’t have any information about because they no longer exist? Europeans and the Onge can serve as proxies for the ANI and ASI respectively, but how far does this get you? Well, the methods that they used (they have three) which determine ancestral proportions can be used on populations which exist. So here is a figure which shows how their methods compare when you look at a population where we know something concrete about their ancestral populations because those ancestral populations are still extant, African Americans:



We propose that the high FST among Indian groups could be explained if many groups were founded by a few individuals, followed by limited gene flow. This hypothesis predicts that within groups, pairs of individuals will tend to have substantial stretches of the genome in which they share at least one allele at each SNP. We find signals of excess allele sharing in many groups.

Six Indo-European- and Dravidian speaking groups have evidence of founder events dating tomore than 30 generations ago…including the Vysya at more than 100 generations ago…Strong endogamy must have applied since then (average gene flow less than 1 in 30 per generation) to prevent the genetic signatures of founder events from being erased by gene flow. Some historians have argued that ‘caste’ in modern India is an ‘invention’ of colonialism in the sense that it became more rigid under colonial rule. However, our results indicate thatmany current distinctions among groups are ancient and that strong endogamy must have shaped marriage patterns in India for thousands of years.

Two features of the inferred history are of special interest. First, the ANI and CEU form a clade, and further analysis shows that the Adygei, a Caucasian group, are an outgroup. Many Indian and European groups speak Indo-European languages, whereas the Adygei speak a Northwest Caucasian language. It is tempting to assume that the population ancestral to ANI and CEU spoke ‘Proto-Indo-European’, which has been reconstructed as ancestral to both Sanskrit and European languages, although we cannot be certain without a date for ANI-ASI mixture.


Reich D, Thangaraj K, Patterson N, Price AL, Singh L. 2009. Reconstructing Indian population history. Nature 461:489-494. doi:10.1038/nature08365