The genetics of Bene Israel from India reveals both substantial Jewish and Indian ancestry

Abstract

The Bene Israel Jewish community from West India is a unique population whose history before the 18 th 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 F ST , 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.

Familial migration of the Neolithic contrasts massive male migration during Bronze Age in Europe inferred from ancient X chromosomes

“…As a first line of evidence for the sex-specific relationships between the two sets of migrating and admixed populations, AF-CE and SP-BA, we compared genetic differentiation on the X versus autosomes ( Table 1). We followed the method of (27,28), computing the statistic Q, which measures relative genetic drift between the X and autosomes,…”

“…We compare genetic differentiation of the autosomes and the X chromosome between the migrating and admixed populations for each migration event: Anatolian farmers (AF) to early Neolithic Central Europeans (CE) and Pontic Steppe pastoralists (SP) to late Neolithic and Bronze Age Central Europeans (BA). We compute the statistic Q (27,28), which is an estimator of the ratio of effective population size of the X chromosome to that of the autosomes based on !" (Materials and Methods).…”