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      X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

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          Abstract

          Background

          Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome.

          Results

          A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea.

          A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area.

          Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza.

          Conclusion

          Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.

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          Most cited references51

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          Association mapping in structured populations.

          J. Pritchard, M. Stephens, N. Rosenberg … (2000)
          The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations.
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            Patterns of linkage disequilibrium in the human genome.

            Kristin Ardlie, Leonid Kruglyak, Mark Seielstad (2002)
            Particular alleles at neighbouring loci tend to be co-inherited. For tightly linked loci, this might lead to associations between alleles in the population a property known as linkage disequilibrium (LD). LD has recently become the focus of intense study in the hope that it might facilitate the mapping of complex disease loci through whole-genome association studies. This approach depends crucially on the patterns of LD in the human genome. In this review, we draw on empirical studies in humans and Drosophila, as well as simulation studies, to assess the current state of knowledge about patterns of LD, and consider the implications for the use of LD as a mapping tool.
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              Prospects for whole-genome linkage disequilibrium mapping of common disease genes.

              L Kruglyak (1999)
              Recently, attention has focused on the use of whole-genome linkage disequilibrium (LD) studies to map common disease genes. Such studies would employ a dense map of single nucleotide polymorphisms (SNPs) to detect association between a marker and disease. Construction of SNP maps is currently underway. An essential issue yet to be settled is the required marker density of such maps. Here, I use population simulations to estimate the extent of LD surrounding common gene variants in the general human population as well as in isolated populations. Two main conclusions emerge from these investigations. First, a useful level of LD is unlikely to extend beyond an average distance of roughly 3 kb in the general population, which implies that approximately 500,000 SNPs will be required for whole-genome studies. Second, the extent of LD is similar in isolated populations unless the founding bottleneck is very narrow or the frequency of the variant is low (<5%).
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                Author and article information

                Journal
                Journal ID (nlm-ta): BMC Evol Biol
                Title: BMC Evolutionary Biology
                Publisher: BioMed Central
                ISSN (Electronic): 1471-2148
                Publication date Collection: 2008
                Publication date (Electronic): 29 February 2008
                Volume: 8
                Page: 75
                Affiliations
                [1 ]Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
                [2 ]Instituto Nacional de Toxicología y Ciencias Forenses, Delegación de Canarias, Tenerife, Spain
                [3 ]Sezione di Genetica Forense, SIMEF (Studio Indagini Mediche E Forensi), Reggio Calabria, Italy
                [4 ]Institut Universitaire de Médecine Légale, Lausanne, Switzerland
                [5 ]Service de Médecine Légale, Hôpital Farhat Hached, Sousse, Tunisia
                [6 ]Institut Universitari d'Investigacions en Ciències de la Salut i Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
                Article
                Publisher ID: 1471-2148-8-75
                DOI: 10.1186/1471-2148-8-75
                PMC ID: 2315647
                PubMed ID: 18312628
                SO-VID: 568cc364-f8a5-4a5b-8b97-771273a74f00
                Copyright © Copyright © 2008 Tomas et al; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 27 August 2007
                Date accepted : 29 February 2008
                Categories
                Subject: Research Article

                ScienceOpen disciplines: Evolutionary Biology
                Data availability:
                ScienceOpen disciplines: Evolutionary Biology

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