The Largest Ever DNA Survey of Asian Indian Heritage Reveals Two Genetically Distinct Founders

The largest ever DNA survey of Indian heritage has revealed that the population of India was founded by just two ancient groups that are as genetically distinct from each other as they are from other Asians, according to a Nature Magazine, and also reported in a Sept. 25, 2009 article at The Indian News. Read the August 2009 article, "Reconstructing Indian population history: Article : Nature."

International genetics did the DNA study to find out who were the founding mothers and fathers of ancient and modern India. The results will help scientists to better understand the health and ancestry issues surrounding the very diverse population of India.

The study shows that most Indian populations are genetic admixtures of two ancient but genetically divergent groups, which each contributed around 40-60 percent of the DNA to most present-day Indians, Nature magazine reported Wednesday.

One ancestral lineage - genetically similar to Middle Eastern, Central Asian and European populations - was higher in upper-caste individuals and speakers of Indo-European languages such as Hindi, the researchers found.

The other lineage was not close to any group outside the Indian subcontinent, and was most common in people indigenous to the Andaman islands, says the study conducted by a team led by David Reich of the Broad Institute in Cambridge, Massachusetts, and Lalji Singh of the Centre for Cellular and Molecular Biology in Hyderabad, India.

Nature said that although India makes up around one-sixth of the world's population, it has been "sorely under-represented" in genetic DNA studies such as genome-wide studies of human genetic variation.

The Indian Genome Variation database (IGVDB), launched in 2003 to fill the gap, has so far studied only 420 DNA-letter differences, called single nucleotide polymorphisms (SNPs), in 75 genes.

In sharp contrast, the study reported by Nature has looked at more than 560,000 SNPs across the genomes of 132 Indian individuals from 25 diverse ethnic and tribal groups dotted all over India.

The researchers also found that Indian populations are much more highly socially subdivided than European populations. For example, European ancestry is mostly carved up by geography. And Indian segregation was in the ancient past driven largely by caste.

In India, you have people living in the same city for thousands of years without marrying one another and mixing their genes.

The authors of the study said the new genetic evidence refutes the claim that the Indian caste structure was a modern invention of British colonialism.

How many thousands of years did the caste system go back, preventing large scale intermixing of the two distinct gene types? It's controversial to anthropologists to say that genetics shows up as a result of the caste system. Many anthropologists won't accept that theory. It's also controversial to say people married only within their caste for thousands of years, but that's what the two distinct genetic types are pointing to.

The study also suggests that Indian populations, although currently huge in number, were founded by relatively small bands of individuals - a finding that has clinical implications. The goal is to use the genetic studies to help health issues such as recessive gene diseases that may be different in each separate population.

The two diverse genetically populations can be mapped genetically. If the recessive genes for diseases are very different in the two different populations, scientists can study what's needed for health. But there are today more than two populations. It's a diverse society with people migrating into India from many countries in the past.

According to the study's abstract, "Reconstructing Indian Population History," has been underrepresented in genome-wide surveys of human variation. Scientists analyzed 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, scientists showed that ANI ancestry ranges from 39-71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. (For example, Hindi is an Indo-European language as is the ancient Sanskrit.)

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 (gene) 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. The scientists predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically.

References

1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
2. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
3. Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
4. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
5. These authors contributed equally to this work.