Copyright © 2008 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 82, Issue 4, 873-882, 28 March 2008
doi:10.1016/j.ajhg.2008.01.020
Article
Pierre A. Zalloua1, Yali Xue2, Jade Khalife1, Nadine Makhoul1, Labib Debiane1, Daniel E. Platt3, Ajay K. Royyuru3, Rene J. Herrera4, David F. Soria Hernanz5, Jason Blue-Smith5, R. Spencer Wells5, David Comas6, Jaume Bertranpetit6, Chris Tyler-Smith2,
,
, The Genographic Consortium7
1 The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon
2 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK
3 Bioinformatics and Pattern Discovery, IBM T. J. Watson Research Center, Yorktown Hgts, NY 10598, USA
4 Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
5 The Genographic Project, National Geographic Society, Washington, DC 20036, USA
6 Unitat de Biologia Evolutiva, Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
Corresponding authorAbstract
Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography. We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J∗(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture. We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11th–13th centuries CE introduced western European lineages into Lebanese Christians.
| Phylogenetic and Familial Estimates of Mitochondrial Substitution Rates: Study of Control Region Mutations in Deep-Rooting Pedigrees The American Journal of Human Genetics, Volume 69, Issue 5, 1 November 2001, Pages 1113-1126 Evelyne Heyer, Ewa Zietkiewicz, Andrzej Rochowski, Vania Yotova, Jack Puymirat and Damian Labuda Abstract We studied mutations in the mtDNA control region (CR) using deep-rooting French-Canadian pedigrees. In 508 maternal transmissions, we observed four substitutions (0.0079 per generation per 673 bp, 95% CI 0.0023–0.186). Combined with other familial studies, our results add up to 18 substitutions in 1,729 transmissions (0.0104), confirming earlier findings of much greater mutation rates in families than those based on phylogenetic comparisons. Only 12 of these mutations occurred at independent sites, whereas three positions mutated twice each, suggesting that pedigree studies preferentially reveal a fraction of highly mutable sites. Fitting the data through use of a nonuniform rate model predicts the presence of 40 (95% CI 27–54) such fast sites in the whole CR, characterized by the mutation rate of 274 per site per million generations (95% CI 138–410). The corresponding values for hypervariable regions I (HVI; 1,729 transmissions) and II (HVII; 1,956 transmissions), are 19 and 22 fast sites, with rates of 224 and 274, respectively. Because of the high probability of recurrent mutations, such sites are expected to be of no or little informativity for the evaluation of mutational distances at the phylogenetic time scale. The analysis of substitution density in the alignment of 973 HVI and 650 HVII unrelated European sequences reveals that the bulk of the sites mutate at relatively moderate and slow rates. Assuming a star-like phylogeny and an average time depth of 250 generations, we estimate the rates for HVI and HVII at 23 and 24 for the moderate sites and 1.3 and 1.0 for the slow sites. The fast, moderate, and slow sites, at the ratio of 1:2:13, respectively, describe the mutation-rate heterogeneity in the CR. Our results reconcile the controversial rate estimates in the phylogenetic and familial studies; the fast sites prevail in the latter, whereas the slow and moderate sites dominate the phylogenetic-rate estimations. Abstract | | |
| Genes, Demography, and Life Span: The Contribution of Demographic Data in Genetic Studies on Aging and Longevity The American Journal of Human Genetics, Volume 65, Issue 4, 1 October 1999, Pages 1178-1193 A.I. Yashin, G. De Benedictis, J.W. Vaupel, Q. Tan, K.F. Andreev, I.A. Iachine, M. Bonafe, M. DeLuca, S. Valensin, L. Carotenuto and C. Franceschi Abstract Summary:
In population studies on aging, the data on genetic markers are often collected for individuals from different age groups. The purpose of such studies is to identify, by comparison of the frequencies of selected genotypes, “longevity” or “frailty” genes in the oldest and in younger groups of individuals. To address questions about more-complicated aspects of genetic influence on longevity, additional information must be used. In this article, we show that the use of demographic information, together with data on genetic markers, allows us to calculate hazard rates, relative risks, and survival functions for respective genes or genotypes. New methods of combining genetic and demographic information are discussed. These methods are tested on simulated data and then are applied to the analysis of data on genetic markers for two haplogroups of human mtDNA. The approaches suggested in this article provide a powerful tool for analyzing the influence of candidate genes on longevity and survival. We also show how factors such as changes in the initial frequencies of candidate genes in subsequent cohorts, or secular trends in cohort mortality, may influence the results of an analysis. Abstract | | |