Genetics and archaeogenetics of South Asia

Genetics and Archaeogenetics of South Asia: An Overview

Key Points

• South Asians are a genetically diverse population with ancestry from both West Eurasian and East Eurasian populations.
• The majority of South Asian genetic diversity originated in the Indian subcontinent.
• The genetic makeup of modern South Asians can be described as a combination of:
  • West Eurasian ancestry: related to ancient and modern people in Europe and West Asia
  • Diverse East Eurasian ancestries: including an indigenous South Asian component (AASI), East Asian ancestry, and Southeast Asian ancestry
• The AASI ancestry is closely related to the Andamanese people and other indigenous populations of Southeast Asia.
• The West Eurasian ancestry forms the major source of the South Asian genetic makeup and combined with varying degrees of AASI ancestry, formed the Indus Periphery Cline around 5400-3700 BCE, which constitutes the main ancestral heritage of most modern South Asian groups.
• Around the 2nd millennium BCE, the Indus Periphery ancestry mixed with an incoming mostly male-mediated Yamnaya-Steppe component (archaeogenetically dubbed the Western Steppe Herders) to form the Ancestral North Indians (ANI).
• The ANI ancestry contributed to the formation of Ancestral South Indians (ASI) by admixture with hunter-gatherers having higher proportions of AASI-related ancestry.
• The ANI-ASI gradient, as demonstrated by the higher proportion of ANI in traditionally upper caste and Indo-European speakers, resulted from the admixture between the ANI and the ASI after 2000 BCE at various proportions, and is termed as the Indian Cline.
• East Asian ancestry forms the major ancestry among Tibeto-Burmese and Khasian speakers, and is generally restricted to the Himalayan foothills and Northeast India, with substantial presence also in Munda-speaking groups, as well as in some populations of northern, central and eastern South Asia.

Background

Genetic Diversity: - South Asian subpopulations show genetic unity across various regions, with the ancestral nodes of mtDNA types originating in the subcontinent. - Mitochondrial DNA (mtDNA) studies suggest that haplogroups M and R are common in South Asia, while Y chromosome studies show varied conclusions. - Autosomal DNA studies indicate that South Asians have a combination of West Eurasian and diverse East Eurasian ancestries.

Indigenous Ancestral South Indian (AASI) Ancestry: - The proposed AASI ancestry is hypothesized to represent the ancestry of the very first hunter-gatherers and peoples of the Indian subcontinent. - AASI is distinct from West Eurasian groups and has a closer genetic affinity with Ancient East Eurasians (such as Andamanese Onge or East Asian peoples). - Genetic data shows that the main West Eurasian geneflow event happened during the Neolithic period or already during the Holocene (pre-Neolithic period).

West Eurasian Ancestry: - The West Eurasian ancestry, which is closely related to Neolithic Iranian plateau lineages, forms the major source of the South Asian gene pool. - Paired with varying degrees of AASI admixture, the Ancient Iranian lineage gave rise to the Indus Periphery Cline, which is characteristic for modern South Asians and central in the South Asian genetic heritage. - The ANI-ASI gradient, also termed the Indian Cline, is based on the proximity to West Eurasian populations, with groups harboring higher ANI-ancestry being closer to West Eurasians as compared to populations harboring higher ASI-ancestry.

East Asian Ancestry: - An East Asian-related ancestry component forms the major ancestry among Tibeto-Burmese and Khasi speakers in the Himalayan foothills and Northeast India, and is also found in substantial presence in Mundari-speaking groups.

Mitochondrial DNA (mtDNA) Variation

• The most frequent mtDNA haplogroups in South Asia are M, R and U (where U is a descendant of R).
• Haplogroup M represents more than 60% of South Asian MtDNA and is considered as a cluster of the proto-Asian maternal lineages.
• Haplogroup R is also widely represented and accounts for the other 40% of South Asian MtDNA.
• Haplogroup U is a sub-haplogroup of macrohaplogroup R and is frequent in European populations as well as among South Asians.

Y Chromosome Variation

• The major South Asian Y-chromosome DNA haplogroups are H, J2, L, R1a1, R2, which are commonly found among other West Eurasian populations.
• Haplogroup H is found at a high frequency in South Asia and is considered to represent the major paternal lineage.
• Haplogroup J2 is present in South Asia mostly as J2a-M410 and J2b-M102, since neolithic times (9500 YBP).
• Haplogroup L shows time of neolithic expansion and is present in the Indian population at an overall frequency of c. 7-15%.
• Haplogroup R1a1 has been observed often with high frequency in a number of demographic groups in South Asia, as well as with highest STR diversity, which led some to see it as the locus of origin.
• Haplogroup R2 is found in South Asia at a frequency of around 10-15% in India and Sri Lanka and 7-8% in Pakistan.
• Haplogroup O is very common among the Austroasiatic and Tibeto-Burmese speaking populations of South Asia respectively.