1
|
Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| |
Collapse
|
2
|
Currat M, Poloni ES, Sanchez-Mazas A. Human genetic differentiation across the Strait of Gibraltar. BMC Evol Biol 2010; 10:237. [PMID: 20682051 PMCID: PMC3020631 DOI: 10.1186/1471-2148-10-237] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 08/03/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The Strait of Gibraltar is a crucial area in the settlement history of modern humans because it represents a possible connection between Africa and Europe. So far, genetic data were inconclusive about the fact that this strait constitutes a barrier to gene flow, as previous results were highly variable depending on the genetic locus studied. The present study evaluates the impact of the Gibraltar region in reducing gene flow between populations from North-Western Africa and South-Western Europe, by comparing formally various genetic loci. First, we compute several statistics of population differentiation. Then, we use an original simulation approach in order to infer the most probable evolutionary scenario for the settlement of the area, taking into account the effects of both demography and natural selection at some loci. RESULTS We show that the genetic patterns observed today in the region of the Strait of Gibraltar may reflect an ancient population genetic structure which has not been completely erased by more recent events such as Neolithic migrations. Moreover, the differences observed among the loci (i.e. a strong genetic boundary revealed by the Y-chromosome polymorphism and, at the other extreme, no genetic differentiation revealed by HLA-DRB1 variation) across the strait suggest specific evolutionary histories like sex-mediated migration and natural selection. By considering a model of balancing selection for HLA-DRB1, we here estimate a coefficient of selection of 2.2% for this locus (although weaker in Europe than in Africa), which is in line with what was estimated from synonymous versus non-synonymous substitution rates. Selection at this marker thus appears strong enough to leave a signature not only at the DNA level, but also at the population level where drift and migration processes were certainly relevant. CONCLUSIONS Our multi-loci approach using both descriptive analyses and Bayesian inferences lead to better characterize the role of the Strait of Gibraltar in the evolution of modern humans. We show that gene flow across the Strait of Gibraltar occurred at relatively high rates since pre-Neolithic times and that natural selection and sex-bias migrations distorted the demographic signal at some specific loci of our genome.
Collapse
Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Anthropology, University of Geneva, Geneva, Switzerland.
| | | | | |
Collapse
|
4
|
Ennafaa H, Cabrera VM, Abu-Amero KK, González AM, Amor MB, Bouhaha R, Dzimiri N, Elgaaïed AB, Larruga JM. Mitochondrial DNA haplogroup H structure in North Africa. BMC Genet 2009; 10:8. [PMID: 19243582 PMCID: PMC2657161 DOI: 10.1186/1471-2156-10-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Strait of Gibraltar separating the Iberian Peninsula from North Africa is thought to be a stronger barrier to gene flow for male than for female lineages. However, the recent subdivision of the haplogroup H at mitochondrial DNA (mtDNA) level has revealed greater genetic differentiation among geographic regions than previously detected. The dissection of the mtDNA haplogroup H in North Africa, and its comparison with the Iberian Peninsula and Near-East profiles would help clarify the relative affinities among these regions. RESULTS Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 +/- 2 ky) and H3 (11 +/- 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis. CONCLUSION The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographical rather than cultural barriers. It also shows that the historical Arabian role on the region had more a cultural than a demic effect. Whole mtDNA sequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this new information, it seems that the Strait of Gibraltar barrier affected both male and female gene flow in a similar fashion.
Collapse
Affiliation(s)
- Hajer Ennafaa
- Laboratory of Genetics, Immunology and Human Pathology at the Faculty of Sciences of Tunis, Faculty of Sciences of Tunis, University El Manar I, Tunis, Tunisia.
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, Makrelouf M, Pascali VL, Novelletto A, Tyler-Smith C. A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 2004; 75:338-45. [PMID: 15202071 PMCID: PMC1216069 DOI: 10.1086/423147] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Accepted: 06/07/2004] [Indexed: 11/04/2022] Open
Abstract
We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East.
Collapse
Affiliation(s)
- Barbara Arredi
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Estella S. Poloni
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Silvia Paracchini
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Tatiana Zerjal
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Dahmani M. Fathallah
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Mohamed Makrelouf
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Vincenzo L. Pascali
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Andrea Novelletto
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Chris Tyler-Smith
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| |
Collapse
|
7
|
Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM. Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genet 2003; 4:15. [PMID: 14563219 PMCID: PMC270091 DOI: 10.1186/1471-2156-4-15] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2003] [Accepted: 10/16/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND World-wide phylogeographic distribution of human complete mitochondrial DNA sequences suggested a West Asian origin for the autochthonous North African lineage U6. We report here a more detailed analysis of this lineage, unraveling successive expansions that affected not only Africa but neighboring regions such as the Near East, the Iberian Peninsula and the Canary Islands. RESULTS Divergence times, geographic origin and expansions of the U6 mitochondrial DNA clade, have been deduced from the analysis of 14 complete U6 sequences, and 56 different haplotypes, characterized by hypervariable segment sequences and RFLPs. CONCLUSIONS The most probable origin of the proto-U6 lineage was the Near East. Around 30,000 years ago it spread to North Africa where it represents a signature of regional continuity. Subgroup U6a reflects the first African expansion from the Maghrib returning to the east in Paleolithic times. Derivative clade U6a1 signals a posterior movement from East Africa back to the Maghrib and the Near East. This migration coincides with the probable Afroasiatic linguistic expansion. U6b and U6c clades, restricted to West Africa, had more localized expansions. U6b probably reached the Iberian Peninsula during the Capsian diffusion in North Africa. Two autochthonous derivatives of these clades (U6b1 and U6c1) indicate the arrival of North African settlers to the Canarian Archipelago in prehistoric times, most probably due to the Saharan desiccation. The absence of these Canarian lineages nowadays in Africa suggests important demographic movements in the western area of this Continent.
Collapse
Affiliation(s)
- Nicole Maca-Meyer
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, Tenerife, SPAIN
| | - Ana M González
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, Tenerife, SPAIN
| | - José Pestano
- Laboratorio de Genética, Facultad de Medicina, Universidad de Las Palmas de Gran Canaria, Gran Canaria, SPAIN
| | - Carlos Flores
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, Tenerife, SPAIN
| | - José M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, Tenerife, SPAIN
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, Tenerife, SPAIN
| |
Collapse
|