doi: 10.1111/j.1469-1809.2007.00421.x A Perspective on the History of the Iberian Gypsies Provided by Phylogeographic Analysis of Y-Chromosome Lineages A. Gusm ˜ ao 1 , L. Gusm ˜ ao 1, * , V. Gomes 1 , C. Alves 1 , F. Calafell 2 , A. Amorim 1,3 and M. J. Prata 1,3 1 Ipatimup, Instituto de Patologia e Imunologia da Universidade do Porto. R. Dr. Roberto Frias, s/n. 4200-465 Porto. Portugal 2 Unitat de Biologia Evolutiva, Departament de Ci` encies Experimentals i de la Salut, Universitat Pompeu Fabra. 08003 Barcelona, Catalonia, Spain 3 Faculty of Sciences, University of Porto, Pr. Gomes Teixeira, 4099-002 Porto. Portugal Summary The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; ∼ 17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; ∼ 31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; ∼ 10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; ∼ 37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe. Keywords: Portuguese Gypsies, Gypsy diaspora, Roma, Y-chromosome lineages, Y-SNP haplogroups, Y-STR haplo- types Introduction Portugal is the westernmost region reached by the Gypsy diaspora after the Roma people arrived in Europe 600– 700 years ago (Li´ egeois, 1989; Fraser, 1998; Kendrick & Puxon, 1998). The establishment of Gypsy groups in Por- tugal is recorded since the second half of the 15th century and at present they are estimated to amount to 30–50 thou- sand individuals. The Portuguese Gypsies are likely to be a branch of the group that crossed the Pyrenees as early as the first quarter of the 15th century and rapidly spread throughout Spain and Portugal. Contrary to many other Roma, the Iberian Gypsies, known as Gitanos in Spain and Ciganos in Portugal, are non-Romani-speakers. Af- ∗ Corresponding Author: Leonor Gusm˜ ao, Ipatimup Rua Dr. Roberto Frias, s/n 4200-465 Porto, Portugal. Tel: +351 22 5570700; Fax: +351 22 5570799; E-mail address: lgusmao@ipatimup.pt ter entering Iberia they progressively lost the original lan- guage, and while nowadays many Gitanos still speak Calo, which is basically Spanish with a large amount of Romani loan words, the Ciganos from Portugal speak Portuguese with the Calo just being a reminiscent reference language (Fraser, 1998). The Roma in Portugal, as indeed the Roma elsewhere, are a transnational genetic isolate which fulfil the prop- erties that make genetic isolates an interesting resource in genetic epidemiology; namely, they have reduced genetic diversity and increased linkage disequilibrium (Gonz´ alez- Neira et al. personal communication). The Roma therefore present a particular genetic disease spectrum, with some prevalent diseases almost absent, others specific to Gypsies, and others with private Roma mutations (for a review, see Kalaydjieva et al. 2001b). Presently in Portugal, Gypsy communities are spread all over the country and represent indeed a conspicuous component of the Portuguese social C  2008 The Authors Journal compilation C  2008 University College London Annals of Human Genetics (2008) 72,215–227 215