Refining the Genetic Portrait of Portuguese Roma Through X-Chromosomal Markers Va ˆ nia Pereira, 1,2,3 * Leonor Gusma ˜ o, 1 Cristina Valente, 1,2 Rui Pereira, 1 Joa ˜ o Carneiro, 1,2 Iva Gomes, 1 Niels Morling, 3 Anto ´ nio Amorim, 1,2 and Maria Joa ˜ o Prata 1,2 1 IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto 4200-465, Portugal 2 Faculty of Sciences, University of Porto, Porto 4169-007, Portugal 3 Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenha- gen, Copenhagen DK-2100, Denmark KEY WORDS gypsies; indels; Short Tandem Repeats; linkage disequilibrium ABSTRACT Due to differences in transmission between X-chromosomal and autosomal DNA, the com- parison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non- Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic di- versity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromo- some in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differen- tiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using com- bined information from the X chromosome and auto- somes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with impor- tant contributions from both males and females. We provide evidence that a sex-biased admixture with Euro- peans is probably associated with the founding of the Portuguese Gypsies. Am J Phys Anthropol 148:389–394, 2012. V V C 2012 Wiley Periodicals, Inc. Recent studies have shown that the comparison between patterns of diversity on X-linked and autosomal markers can provide important insights into the history of human populations by allowing the distinction between male and female demographic contributions (Hammer et al., 2008; Emery et al., 2010; Keinan and Reich, 2010; Labuda et al., 2010). The approach relies on the distinct transmission properties of autosomes and the X chromosome, excluding pseudoautosomal regions (subsequently in this work, references to the X chromo- some, will specify only its X-specific part). Since males have only one copy of the X chromosome whereas females have two, the effective number of X chromo- somes in a population is three quarters that of the auto- somes, assuming both genders contributed equally to each generation. The recombination rates of the X chro- mosome are lower than those of the autosomes because recombination on the X chromosome occurs only in females. As a result, the relative magnitude of linkage disequilibrium (LD) on the X chromosome is larger than that observed on autosomes. This property explains the pronounced block-like pattern on the X chromosome in which different chromosomal regions are informative for distinct genetic histories (Schaffner, 2004). Together, the X chromosome’s lower recombination rate and its smaller effective size imply that the effects of selection, genetic drift and substructure in a given population are expected to be more pronounced on this chromosome than on autosomes. Furthermore, X-chromosome diversity is dis- proportionately influenced by female demography, mak- ing the X chromosome notably useful for detecting subtle differences in sex-specific demographic processes (Schaffner, 2004; Hammer et al. 2008; Casto et al., 2010; Keinan and Reich, 2010), that would otherwise remain undisclosed. Most often, the study of gender-biased demographic events has been addressed through the recruitment of information from Y-chromosomal and mitochondrial Present address of Iva Gomes: Institute of Legal Medicine, Uni- versity Hospital, University of Cologne, Cologne, Germany *Correspondence to: Va ˆnia Pereira; IPATIMUP - Rua Dr. Roberto Frias, s/n 4200-465 Porto, Portugal. E-mail: vpereira@ipatimup.pt Additional Supporting Information may be found in the online version of this article. Grant sponsor: Portuguese Foundation for Science and Technology (FCT); Grant numbers: SFRH/BD/70881/2010 (VP) and SFRH/BD/ 63343/2009 (CV). Grant sponsor: Ellen and Aage Andersen’s Foun- dation. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is par- tially supported by FCT. Received 6 October 2011; accepted 27 February 2012 DOI 10.1002/ajpa.22061 Published online 11 May 2012 in Wiley Online Library (wileyonlinelibrary.com). V V C 2012 WILEY PERIODICALS, INC. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 148:389–394 (2012)