title: The genetic history of Cochin Jews from India.
abstract: 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, F ST, 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.
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.|Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
authors.forename: Yedael Y
authors.initials: YY
authors.lastname: Waldman
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Arjun
authors.initials: A
authors.lastname: Biddanda
authors.affiliation: Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, 52621, Ramat Gan, Israel.|Sackler School of Medicine, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
authors.forename: Maya
authors.initials: M
authors.lastname: Dubrovsky
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Campbell
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
authors.forename: Carole
authors.initials: C
authors.lastname: Oddoux
authors.affiliation: Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, 52621, Ramat Gan, Israel.|Sackler School of Medicine, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
authors.forename: Eitan
authors.initials: E
authors.lastname: Friedman
authors.affiliation: Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.|Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.|Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.
authors.forename: Gil
authors.initials: G
authors.lastname: Atzmon
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.|The Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.|International Computer Science Institute, Berkeley, CA, 94704, USA.
authors.forename: Eran
authors.initials: E
authors.lastname: Halperin
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.|Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
authors.forename: Harry
authors.initials: H
authors.lastname: Ostrer
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA. alon.keinan@cornell.edu.
authors.forename: Alon
authors.initials: A
authors.lastname: Keinan
mesh_terms: D000483:Alleles; D044466:Asian People / Q000235:genetics; D005828:Genetics, Population; D015894:Genome, Human; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007194:India; D007557:Israel; D007585:Jews / Q000235:genetics*; D015810:Linkage Disequilibrium