28.4: Gene Flow on the Indian Subcontinent

Genetic evidence suggests that modern populations on the Indian subcontinent descended from two different ancestral populations that mingled 4,000 years ago. SNP array data was collected from about 500 different people from 73 Indian groups with different language families [? ]. A principle component analysis plot reveals that the the Dravidian/Indo-European language groups and the Austro-Asiatic language groups are in two different clusters, which suggests they have different lineages. Within the Dravidian/Indo-European language groups, there is a gradient of relatedness to West Eurasian groups.

The same mosaic technique used in the African/European intermixing study was used to estimate the date of mixture. The Indian population is a mixture of a Central Asian/European group and another group most closely related to the people of the Andaman Islands. The chunk size of the DNA belonging to each group suggests a mixture about 100 generations old, or 2,000 to 4,000 years ago. Many groups have this mixed heritage, but mixture stops after the creation of the caste system.

Knowledge of the heritage of genes can predict diseases. For example, a South Asian mutation in myosin binding protein C causes a seven-fold increase in heart failure Many ethnic groups are endogamous and have a low genetic diversity, resulting in a higher prevelance of recessive diseases.

Past surveys in India have studied such aspects as anthropometric variation, mtDNA, and the Y chromosome. The anthropometric study looked at significant differences in physical characteristics between groups separated by geography and ethnicity. The results showed variation much higher than that of Europe. The mtDNA study was a survey of maternal lineage and the results suggested that there was a single Indian tree such that age of lineage could be inferred by the number of mutations. The data also showed that Indian populations were separated from non-Indian populations at least 40,000 years ago. Finally, the Y chromosome study looked at paternal lineage and showed a more recent similarity to Middle Eastern men and dependencies on geography and caste. This data conflicts with the mtDNA results. One possible ex- planation is that there was a more recent male migration. Either way, the genetic studies done in India have served to show its genetic complexity. The high genetic variation, dissimilarity with other samples, and diculty of obtaining more samples lead to India being left out of HapMap, the 1000 Genomes Project, and the HGDP.

In David Reich and collaborators study of India, 25 Indian groups were chosen to represent various geographies, language roots, and ethnicities. The raw data included five samples for each of the twenty five groups. Even though this number seems small, the number of SNPs from each sample has a lot of information. Approximately five hundred thousand markers were genotyped per individual. Looking at the data to emerge from the study, if Principal Components Analysis is used on data from West Eurasians and Asians, and if the Indian populations are compared using the same components, the India Cline emerges. This shows a gradient of similarity that might indicate a staggered divergence of Indian populations and European populations.

Almost All Mainland Indian Groups are Mixed

Further analysis of the India Cline phenomenon produces interesting results. For instance, some Pakistani sub-populations have ancestry that also falls along the Indian Cline. Populations can be projected onto the principal components of other populations: South Asians projected onto Chinese and European principal components produces a linear effect (the India Cline), while Europeans projected onto South Asian and Chinese principal components does not. One interpretation is that Indian ancestry shows more variability than the other groups. A similar variability assessment appears when comparing African to non-African populations. Two tree hypotheses emerge from this analysis:

1. there were serial founder events in India's history or

2. there was gene flow between ancestral populations.

The authors developed a formal four population test to test ancestry hypotheses in the presence of admixture or other confounding effects. The test takes a proposed tree topology and sums over all SNPs of (Pp1 Pp2)(Pp3 Pp4), where P values are frequencies for the four populations. If the proposed tree is correct, the correlation will be 0 and the populations in question form a clade. This method is resistant to several problems that limit other models. A complete model can be built to fit history. The topology information from the admixture graphs can be augmented with Fst values through a fitting procedure. This method makes no assumptions about population split times, expansion and contractions, and duration of gene flow, resulting in a more robust estimation procedure.

Figure 28.2: Populations can be projected onto the principal components of other populations: South Asians projected onto Chinese and European principal components produces a linear effect (the India Cline), while Europeans projected onto South Asian and Chinese principal components does not.

Furthermore, estimating the mixture proportions using the 4 population statistic gives error estimates for each of the groups on the tree. Complicated history does not factor into this calculation, as long as the topology as determined by the 4-population test is valid.

These tests and the cline analysis allowed the authors to determine the relative strength of Ancestral North Indian and Ancestral South Indian ancestry in each representative population sample. They found

Figure 28.3: An admixture graph that fits Indian history

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that high Ancestral North Indian ancestry is correlated with traditionally higher caste and certain language groupings. Furthermore, Ancestral North Indian (ANI) and South Indian (ASI) ancestry is as different from Chinese as European.

Population structure in India is different from Europe

Population structure in India is much less correlated with geography than in Europe. Even correcting populations for language, geographic, and social status differences, the F_st value is 0.007, about 7 times that of the most divergent populations in Europe. An open question is whether this could be due to missing (largely India-specific) SNPs on the genotyping arrays. This is because the set of targeted SNPs were identified primarily from the HapMap project, which did not include Indian sources.

Most Indian genetic variation does not arise from events outside India. Additionally, consanguineous marriages cannot explain the signal. Many serial founder events, perhaps tied to the castes or precursor groups, could contribute. Analyzing a single group at a time, it becomes apparent that castes and subcastes have a lot of endogamy. The autocorrelation of allele sharing between pairs of samples within a group is used to determine whether a founder event occurred and its relative age. There are segments of DNA from a founder, many indicating events more than 1000 years old. In most groups there is evidence for a strong, ancient founder event and subsequent endogamy. This stands in contrast to the population structure in most of Europe or Africa, where more population mixing occurs (less endogamy).

These serial founder events and their resulting structure have important medical implications. The strong founder events followed by endogamy and some mixing have lead to groups that have strong propensities for various recessive diseases. This structure means that Indian groups have a collection of prevalent diseases, similar to those already known in other groups, such as Ashkenazi Jews or Finns. Unique variation within India means that linkages to disease alleles prevalent in India might not be discoverable using only non-Indian data sources. A small number of samples are needed from each group, and more groups, to better map these recessive diseases. These maps can then be used to better predict disease patterns in India.

28.4.3 Discussion

Overall, strong founder events followed by endogamy have given India more substructure than Europe. All surveyed tribal and caste groups show a strong mixing of ANI and ASI ancestry, varying between 35% and 75% ANI identity. Estimating the time and mechanism of the ANI-ASI mixture is currently a high priority. Additionally, future studies will determine whether and how new techniques like the 4-population test and admixture graphs can be applied to other populations.