The genetic history of Cochin Jews from India

Yedael Y. Waldman, Arjun Biddanda, Maya Dubrovsky, Christopher L. Campbell, Carole Oddoux, Eitan Friedman, Gil Atzmon, Eran Halperin, Harry Ostrer, Alon Keinan

Research output: Contribution to journalArticlepeer-review


Cochin Jews form a small and unique community on the Malabar coast in southwest India. While the arrival time of any putative Jewish ancestors of the community has been speculated to have taken place as far back as biblical times (King Solomon’s era), a Jewish community in the Malabar coast has been documented only since the 9th century CE. Here, we explore the genetic history of Cochin Jews by collecting and genotyping 21 community members and combining the data with that of 707 individuals from 72 other Indian, Jewish, and Pakistani populations, together with additional individuals from worldwide populations. We applied comprehensive genome-wide analyses based on principal component analysis, FST, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing, allele sharing autocorrelation decay and contrasting the X chromosome with the autosomes. We find that, as reported by several previous studies, the genetics of Cochin Jews resembles that of local Indian populations. However, we also identify considerable Jewish genetic ancestry that is not present in any other Indian or Pakistani populations (with the exception of the Jewish Bene Israel, which we characterized previously). Combined, Cochin Jews have both Jewish and Indian ancestry. Specifically, we detect a significant recent Jewish gene flow into this community 13–22 generations (~470–730 years) ago, with contributions from Yemenite, Sephardi, and Middle-Eastern Jews, in accordance with historical records. Genetic analyses also point to high endogamy and a recent population bottleneck in this population, which might explain the increased prevalence of some recessive diseases in Cochin Jews.

Original languageEnglish
Pages (from-to)1127-1143
Number of pages17
JournalHuman Genetics
Issue number10
StatePublished - 1 Oct 2016

Bibliographical note

Funding Information:
We thank all the individuals who contributed DNA for this study. We thank David Reich and Priya Moorjani for providing us with the Indian data set. We also thank members of the Keinan and Halperin labs for helpful discussions. This work was supported by the National Institutes of Health (Grants R01HG006849 and R01GM108805 to AK), the Ellison Medical Foundation and the Edward Mallinckrodt, Jr. Foundation (AK), the Israeli Science Foundation (Grant 1425/13 to EH and YYW), the United States-Israel Binational Science Foundation (Grant 2012304 to EH and YYW), the German-Israeli Foundation (Grant 1094-33.2/2010 to EH and YYW), and Len Blavatnik and the Blavatnik Family Foundation (to YYW). EH is a faculty fellow of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.

Publisher Copyright:
© 2016, The Author(s).

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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