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Ziętkiewicz E, Yotova V, Gehl D, Wambach T, Arrieta I, Batzer M, Cole DEC, Hechtman P, Kaplan F, Modiano D, Moisan JP, Michalski R, Labuda D. Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity. Am J Hum Genet 2003; 73:994-1015. [PMID: 14513410 PMCID: PMC1180505 DOI: 10.1086/378777] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2003] [Accepted: 07/23/2003] [Indexed: 11/03/2022] Open
Abstract
Although Africa has played a central role in human evolutionary history, certain studies have suggested that not all contemporary human genetic diversity is of recent African origin. We investigated 35 simple polymorphic sites and one T(n) microsatellite in an 8-kb segment of the dystrophin gene. We found 86 haplotypes in 1,343 chromosomes from around the world. Although a classical out-of-Africa topology was observed in trees based on the variant frequencies, the tree of haplotype sequences reveals three lineages accounting for present-day diversity. The proportion of new recombinants and the diversity of the T(n) microsatellite were used to estimate the age of haplotype lineages and the time of colonization events. The lineage that underwent the great expansion originated in Africa prior to the Upper Paleolithic (27,000-56,000 years ago). A second group, of structurally distinct haplotypes that occupy a central position on the tree, has never left Africa. The third lineage is represented by the haplotype that lies closest to the root, is virtually absent in Africa, and appears older than the recent out-of-Africa expansion. We propose that this lineage could have left Africa before the expansion (as early as 160,000 years ago) and admixed, outside of Africa, with the expanding lineage. Contemporary human diversity, although dominated by the recently expanded African lineage, thus represents a mosaic of different contributions.
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Affiliation(s)
- Ewa Ziętkiewicz
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Vania Yotova
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Dominik Gehl
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Tina Wambach
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Isabel Arrieta
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Mark Batzer
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - David E. C. Cole
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Peter Hechtman
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Feige Kaplan
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - David Modiano
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Jean-Paul Moisan
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Roman Michalski
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
| | - Damian Labuda
- Centre de Recherche de l’Hôpital Sainte-Justine and Département de Pédiatrie, Université de Montréal, and Departments of Human Genetics and Pediatrics, McGill University, Montréal; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; Departamento Biologia Animal y Genetica, Universidad del Pais Vasco, Bilbao, Spain; Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; Fondazione Pasteur Cenci-Bolognetti, Istituto di Parassitologia, Universita “La Sapienza,” Rome; Centre Hospitalier Régional et Universitaire, Nantes, France; and Prince Albert Parkland Health Region, Victoria Hospital, Prince Albert, Canada
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Heyer E, Zietkiewicz E, Rochowski A, Yotova V, Puymirat J, Labuda D. Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. Am J Hum Genet 2001; 69:1113-26. [PMID: 11582570 PMCID: PMC1274355 DOI: 10.1086/324024] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2001] [Accepted: 08/23/2001] [Indexed: 11/03/2022] Open
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.
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Affiliation(s)
- Evelyne Heyer
- Laboratoire d’Anthropologie Biologique (CNRS/Paris VII/MNHN), Musée de l’Homme, Paris; Centre de Recherche, Hôpital Sainte-Justine, and Département de Pédiatrie, Université de Montréal, Montréal; Instytut Genetyki Czlowieka, PAN, Poznan, Poland; and Centre de recherche du CHUL, Sainte-Foy, Québec, Canada
| | - Ewa Zietkiewicz
- Laboratoire d’Anthropologie Biologique (CNRS/Paris VII/MNHN), Musée de l’Homme, Paris; Centre de Recherche, Hôpital Sainte-Justine, and Département de Pédiatrie, Université de Montréal, Montréal; Instytut Genetyki Czlowieka, PAN, Poznan, Poland; and Centre de recherche du CHUL, Sainte-Foy, Québec, Canada
| | - Andrzej Rochowski
- Laboratoire d’Anthropologie Biologique (CNRS/Paris VII/MNHN), Musée de l’Homme, Paris; Centre de Recherche, Hôpital Sainte-Justine, and Département de Pédiatrie, Université de Montréal, Montréal; Instytut Genetyki Czlowieka, PAN, Poznan, Poland; and Centre de recherche du CHUL, Sainte-Foy, Québec, Canada
| | - Vania Yotova
- Laboratoire d’Anthropologie Biologique (CNRS/Paris VII/MNHN), Musée de l’Homme, Paris; Centre de Recherche, Hôpital Sainte-Justine, and Département de Pédiatrie, Université de Montréal, Montréal; Instytut Genetyki Czlowieka, PAN, Poznan, Poland; and Centre de recherche du CHUL, Sainte-Foy, Québec, Canada
| | - Jack Puymirat
- Laboratoire d’Anthropologie Biologique (CNRS/Paris VII/MNHN), Musée de l’Homme, Paris; Centre de Recherche, Hôpital Sainte-Justine, and Département de Pédiatrie, Université de Montréal, Montréal; Instytut Genetyki Czlowieka, PAN, Poznan, Poland; and Centre de recherche du CHUL, Sainte-Foy, Québec, Canada
| | - Damian Labuda
- Laboratoire d’Anthropologie Biologique (CNRS/Paris VII/MNHN), Musée de l’Homme, Paris; Centre de Recherche, Hôpital Sainte-Justine, and Département de Pédiatrie, Université de Montréal, Montréal; Instytut Genetyki Czlowieka, PAN, Poznan, Poland; and Centre de recherche du CHUL, Sainte-Foy, Québec, Canada
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