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The Habbani Yemeni Jews were a religious isolate in Yemen for centuries. Since a bottleneck in the late eighteenth century the population, composed of six patrilineages, has steadily grown. Isonymy analysis of Habbani genealogies reveals a significant increase in lineage endogamy by the early twentieth century, suggesting that microdifferentiation of Habbani population genetic structure along the patrilineages was occurring. We examine reflectance data from a “parental” generation of 159 individuals studied by Hulse in the 1960s and reflectance data from an “offspring” generation of 243 individuals studied by Towne in the 1980s. A greater amount of interlineage skin color differences is found in the offspring generation than in the parental generation. This finding is consistent with what is known of the evolution of Habbani population genetic structure.