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Hamedi B, Feulefack J, Khan A, Sergi C. Association between factor V Leiden mutation and recurrent pregnancy loss in the middle east countries: a Newcastle-Ottawa meta-analysis. Arch Gynecol Obstet 2020; 302:345-354. [PMID: 32472185 DOI: 10.1007/s00404-020-05610-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
PURPOSE Heritable thrombophilia is a category of genetic disorders of the coagulation cascade with the increasing risk of thrombus formation and recurrent pregnancy loss (RPL). Factor V Leiden (FVL) (R506Q) mutation is the most common genetic cause of deep venous thrombosis, but its association with RPL has been inconsistent in studies arising from non-Western countries. The present metanalysis was aimed to determine whether an association exists between FVL and RPL in the Middle East. METHODS We searched PubMed, MEDLINE Web of Science, Scopus, and Embase, evaluating the association between the FVL and RPL. The Middle East countries (Bahrain, Cyprus, Egypt, Iran, Iraq, Israel, Jordan, Kuwait, Lebanon, Oman, Qatar, Saudi Arabia, The State of Palestine, Syria, Turkey, The United Arab Emirates, and Yemen) were evaluated in succession. Raw data were extracted, and 19 case-control studies were included in our final analysis. RESULTS Overall, 2513 cases and 1836 controls in the Middle East showed a prevalence of FVL mutation as 12.6% and 4.9% in patients and controls, respectively. To evaluate the relationship between FVL mutation and RPL, we used Forest plot (random effect model) with the overall random OR of 2.37 (CI 95%: 1.50-3.75). FVL mutation was associated with a higher risk of RPL. In Iran, the OR was 1.90 (95% CI 1.04-3.45), and in Turkey, the OR was 3.01 (95% CI 1.10-8.23). CONCLUSION The results of our study support an association between FVL mutation status and RPL in women of the Middle East countries. It is recommended that specific policies include comprehensive testing for FVL mutation as a standard of care in women of the Middle East region with unexplained RPL.
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Affiliation(s)
- Bahareh Hamedi
- Department of Laboratory Medicine and Pathology, University of Alberta, WMC 5B4.09, 8440 112 ST NW, Edmonton, AB, Canada.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Joseph Feulefack
- Department of Laboratory Medicine and Pathology, University of Alberta, WMC 5B4.09, 8440 112 ST NW, Edmonton, AB, Canada
| | - Aiza Khan
- Department of Laboratory Medicine and Pathology, University of Alberta, WMC 5B4.09, 8440 112 ST NW, Edmonton, AB, Canada
| | - Consolato Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta, WMC 5B4.09, 8440 112 ST NW, Edmonton, AB, Canada. .,Department of Pediatrics, University of Alberta, Stollery Children's Hospital, Edmonton, AB, Canada.
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2
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Wang D, Guo T, Guo Q, Zhang S, Zhang J, Luo J. The Association Between Schizophrenia Risk Variants and Creativity in Healthy Han Chinese Subjects. Front Psychol 2019; 10:2218. [PMID: 31649580 PMCID: PMC6792478 DOI: 10.3389/fpsyg.2019.02218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/17/2019] [Indexed: 11/14/2022] Open
Abstract
Although previous evidence has suggested that there is a genetic link between schizophrenia and creativity, the specific genetic variants that underlie the link are still largely unknown. To further explore the potential genetic link between schizophrenia and creativity, in a sample of 580 healthy Han Chinese subjects, this study aimed to (1) validate the role of Neuregulin 1 (NRG1) rs6994992 (one schizophrenia risk variant that has been previously linked to creativity in the European population) in the relationship between schizophrenia and creativity and (2) explore the associations between 10 other schizophrenia risk variants and creativity. For NRG1 rs6994992, the result validated its association with creativity measures. However, since NRG1 rs6994992 is not a schizophrenia risk variant in the Han Chinese population, the validated association suggested that ethnic difference may exist in the relationship between NRG1 rs6994992, schizophrenia and creativity. For other schizophrenia risk variants, the result only demonstrated a nominal association between ZNF536 rs2053079 and creativity measures which would not survive correction for multiple testing. No association between polygenic risk score for these 10 schizophrenia risk variants and creativity measures was observed. In conclusion, this study provides limited evidence for the associations between these schizophrenia risk variants and creativity in healthy Han Chinese subjects. Future studies are warranted to better understand the potential genetic link between schizophrenia and creativity.
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Affiliation(s)
- Dan Wang
- Beijing Key Laboratory of Learning and Cognition, Department of Psychology, The Collaborative Innovation Center for Capital Education Development, Capital Normal University, Beijing, China
| | - Tingting Guo
- Beijing Gese Technology Co., Ltd., Beijing, China
| | - Qi Guo
- Beijing Key Laboratory of Learning and Cognition, Department of Psychology, The Collaborative Innovation Center for Capital Education Development, Capital Normal University, Beijing, China
| | - Shun Zhang
- Department of Psychology, Shandong Normal University, Jinan, China
| | - Jinghuan Zhang
- Department of Psychology, Shandong Normal University, Jinan, China
| | - Jing Luo
- Beijing Key Laboratory of Learning and Cognition, Department of Psychology, The Collaborative Innovation Center for Capital Education Development, Capital Normal University, Beijing, China
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Williams AC, Hill LJ. Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions? Int J Tryptophan Res 2019; 12:1178646919855944. [PMID: 31258332 PMCID: PMC6585247 DOI: 10.1177/1178646919855944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/28/2022] Open
Abstract
Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
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4
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Benvisto A, Messina F, Finocchio A, Popa L, Stefan M, Stefanescu G, Mironeanu C, Novelletto A, Rapone C, Berti A. A genetic portrait of the South-Eastern Carpathians based on autosomal short tandem repeats loci used in forensics. Am J Hum Biol 2018; 30:e23139. [PMID: 30099799 DOI: 10.1002/ajhb.23139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/02/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES This work aimed to describe the genetic landscape of the Balkan Peninsula, as revealed by STR markers commonly used in forensics and spatial methods specifically developed for genetic data. METHODS We generated and analyzed 16 short tandem repeats (STRs) autosomal genotypes in 287 subjects from ten administrative/geographical regions of Eastern Europe (Romania and the Republic of Moldova). We report estimates of the allele frequencies in these sub-populations, their fixation indexes, and use these results to complement previous spatial analyses of Southern Europe. RESULTS In seven out of ten analyzed regional samples the heterozygosity, averaged across loci, was lower than expected. The average Fis was 0.011. Among the 16 loci, five returned a significant fixation index Fst. The composite Fst across the 16 loci, among the 10 regional samples, was 0.00417, a figure twice as large as that obtained with the same markers across the entire Northern Mediterranean. The first spatial principal component (sPC1) returned the picture of a Central-European pattern of frequencies for the Carpathians, which extended to the Southern boundary of the Balkan Peninsula. However, the 8 alleles extracted by sPC1 returned a picture of a strong reduction of the migration rate in the Carpathian region, mostly between the inner locations. CONCLUSIONS Our results revealed an unexpected heterogeneity in the area. We believe that populations from some regions will require treatment as distinct entities when considered in forensic applications.
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Affiliation(s)
- Alessandro Benvisto
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
| | - Francesco Messina
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Andrea Finocchio
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Luis Popa
- "Grigore Antipa" National Museum of Natural History, Bucharest, 011341, Romania
| | - Mihaela Stefan
- Department of Genetics, University of Bucharest, Bucharest, 76258, Romania
| | | | | | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Cesare Rapone
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
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5
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Messina F, Finocchio A, Akar N, Loutradis A, Michalodimitrakis EI, Brdicka R, Jodice C, Novelletto A. Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients. Ann Hum Biol 2018; 45:77-85. [PMID: 29382282 DOI: 10.1080/03014460.2017.1409365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Tetranucleotide Short Tandem Repeats (STRs) for human identification and common use in forensic cases have recently been used to address the population genetics of the North-Eastern Mediterranean area. However, to gain confidence in the inferences made using STRs, this kind of analysis should be challenged with changes in three main aspects of the data, i.e. the sizes of the samples, their distance across space and the genetic background from which they are drawn. AIM To test the resilience of the gradients previously detected in the North-Eastern Mediterranean to the enlargement of the surveyed area and population set, using revised data. SUBJECTS AND METHODS STR genotype profiles were obtained from a publicly available database (PopAffilietor databank) and a dataset was assembled including >7000 subjects from the Arabian Peninsula to Scandinavia, genotyped at eight loci. Spatial principal component analysis (sPCA) was applied and the frequency maps of the nine alleles which contributed most strongly to sPC1 were examined in detail. RESULTS By far the greatest part of diversity was summarised by a single spatial principal component (sPC1), oriented along a SouthEast-to-NorthWest axis. The alleles with the top 5% squared loadings were TH01(9.3), D19S433(14), TH01(6), D19S433(15.2), FGA(20), FGA(24), D3S1358(14), FGA(21) and D2S1338(19). These results confirm a clinal pattern over the whole range for at least four loci (TH01, D19S433, FGA, D3S1358). CONCLUSIONS Four of the eight STR loci (or even alleles) considered here can reproducibly capture continental arrangements of diversity. This would, in principle, allow for the exploitation of forensic data to clarify important aspects in the formation of local gene pools.
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Affiliation(s)
- Francesco Messina
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
| | - Andrea Finocchio
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
| | - Nejat Akar
- b Pediatrics Department , TOBB-Economy and Technology University Hospital , Ankara , Turkey
| | | | | | - Radim Brdicka
- e Institute of Hematology and Blood Transfusion , Praha , Czech Republic
| | - Carla Jodice
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
| | - Andrea Novelletto
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
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6
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Branco C, Velasco M, Benguigui M, Currat M, Ray N, Arenas M. Consequences of diverse evolutionary processes on american genetic gradients of modern humans. Heredity (Edinb) 2018; 121:548-556. [PMID: 30022169 DOI: 10.1038/s41437-018-0122-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/09/2022] Open
Abstract
European genetic gradients of modern humans were initially interpreted as a consequence of the demic diffusion of expanding Neolithic farmers. However, recent studies showed that these gradients may also be influenced by other evolutionary processes such as population admixture or range contractions. Genetic gradients were observed in the Americas, although their specific evolutionary causes were not investigated. Here we extended the approach used to study genetic gradients in Europe to analyze the influence of diverse evolutionary scenarios on American genetic gradients. Using extensive computer simulations, we evaluated the impact of (i) admixture between expansion waves of modern humans, (ii) the presence of ice-sheets during the last glacial maximum (LGM) and (iii) long-distance dispersal (LDD) events, on the genetic gradients (detected by principal component analysis) of the entire continent, North America and South America. The specific simulation of North and South America showed that genetic gradients are usually orthogonal to the direction of range expansions-either expansions from Bering or posterior re-expansions to recolonize northern regions after ice sheets melting-and we suggest that they result from allele surfing processes. Conversely, our results on the entire continent show a northwest-southeast gradient obtained with any scenario, which we interpreted as a consequence of isolation by distance along the long length of the continent. These findings suggest that distinct genetic gradients can be detected at different regions of the Americas and that subcontinent regions present gradients more sensible to evolutionary and environmental factors (such as LDD and the LGM) than the whole continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Miguel Velasco
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mathias Currat
- Anthropology, Genetics and Peopling History Lab, Department of Genetics & Evolution -Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Nicolas Ray
- EnviroSPACE Lab, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland.,Institute of Global Health, University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain. .,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. .,Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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7
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Zeng TC, Aw AJ, Feldman MW. Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck. Nat Commun 2018; 9:2077. [PMID: 29802241 PMCID: PMC5970157 DOI: 10.1038/s41467-018-04375-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/24/2018] [Indexed: 01/18/2023] Open
Abstract
In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory. A population bottleneck 5000-7000 years ago in human males, but not females, has been inferred across several African, European and Asian populations. Here, Zeng and colleagues synthesize theory and data to suggest that competition among patrilineal kin groups produced the bottleneck pattern.
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Affiliation(s)
- Tian Chen Zeng
- Department of Sociology, Stanford University, Stanford, CA, 94305, USA.,Mathematical and Computational Science Program, Stanford University, Stanford, CA, 94305, USA
| | - Alan J Aw
- Mathematical and Computational Science Program, Stanford University, Stanford, CA, 94305, USA.,Department of Biology, Stanford University, Stanford, CA, USA
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Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: An Allele Frequency Database for Microevolutionary Studies. Evol Bioinform Online 2017. [DOI: 10.1177/117693430500100006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Kei-Hoi Cheung
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Rohit Gadagkar
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Shannon Stein
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Perry L Miller
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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9
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Yardumian A, Shengelia R, Chitanava D, Laliashvili S, Bitadze L, Laliashvili I, Villanea F, Sanders A, Azzam A, Groner V, Edleson K, Vilar MG, Schurr TG. Genetic diversity in Svaneti and its implications for the human settlement of the Highland Caucasus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:837-852. [PMID: 29076141 DOI: 10.1002/ajpa.23324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/19/2017] [Accepted: 09/10/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVES In this study, we characterized genetic diversity in the Svans from northwestern Georgia to better understand the phylogeography of their genetic lineages, determine whether genetic diversity in the highland South Caucasus has been shaped by language or geography, and assess whether Svan genetic diversity was structured by regional residence patterns. MATERIALS AND METHODS We analyzed mtDNA and Y-chromosome variation in 184 individuals from 13 village districts and townlets located throughout the region. For all individuals, we analyzed mtDNA diversity through control region sequencing, and, for males, we analyzed Y-chromosome diversity through SNP and STR genotyping. The resulting data were compared with those for populations from the Caucasus and Middle East. RESULTS We observed significant mtDNA heterogeneity in Svans, with haplogroups U1-U7, H, K, and W6 being common there. By contrast, ∼78% of Svan males belonged to haplogroup G2a, with the remainder falling into four other haplogroups (J2a1, I2, N, and R1a). While showing a distinct genetic profile, Svans also clustered with Caucasus populations speaking languages from different families, suggesting a deep common ancestry for all of them. The mtDNA data were not structured by geography or linguistic affiliation, whereas the NRY data were influenced only by geography. DISCUSSION These patterns of genetic variation confirm a complex set of geographic sources and settlement phases for the Caucasus highlands. Such patterns may also reflect social and cultural practices in the region. The high frequency and antiquity of Y-chromosome haplogroup G2a in this region further points to its emergence there.
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Affiliation(s)
- Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Pennsylvania 19009.,Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ramaz Shengelia
- Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 01747, Georgia
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Fernando Villanea
- Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Akiva Sanders
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Andrew Azzam
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Victoria Groner
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kristi Edleson
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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10
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Ibrahim M, Osman M, Peprah E. Understanding the Evolutionary Biology of CVD From Analysis of Ancestral Population Genomes. Glob Heart 2017; 12:73-75. [PMID: 28302549 DOI: 10.1016/j.gheart.2017.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 01/29/2023] Open
Affiliation(s)
- Muntaser Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.
| | - Maha Osman
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Emmanuel Peprah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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11
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Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Hum Mutat 2015; 36:1100-11. [DOI: 10.1002/humu.22849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Department of Biology; CBMA (Centre of Molecular and Environmental Biology); University of Minho; Braga 4704-553 Portugal
| | - Rui Camacho
- INESC TEC; Porto 4200-465 Portugal
- Departamento de Engenharia Informática; Faculdade de Engenharia da Universidade do Porto; Porto 4200-465 Portugal
| | - Andreia Brandão
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS); Porto 4050-313 Portugal
| | - Marta D. Costa
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - David C. Samuels
- Vanderbilt Genetics Institute; Department of Molecular Physiology and Biophysics; Vanderbilt University Medical Center; Nashville Tennessee 37232-0700
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Faculdade de Medicina da Universidade do Porto; Porto 4200-319 Portugal
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12
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Rivollat M, Mendisco F, Pemonge MH, Safi A, Saint-Marc D, Brémond A, Couture-Veschambre C, Rottier S, Deguilloux MF. When the waves of European Neolithization met: first paleogenetic evidence from early farmers in the southern Paris Basin. PLoS One 2015; 10:e0125521. [PMID: 25928633 PMCID: PMC4415815 DOI: 10.1371/journal.pone.0125521] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/14/2015] [Indexed: 11/19/2022] Open
Abstract
An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.
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Affiliation(s)
- Maïté Rivollat
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Fanny Mendisco
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Audrey Safi
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Didier Saint-Marc
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Antoine Brémond
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Christine Couture-Veschambre
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Stéphane Rottier
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-France Deguilloux
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
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13
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Lorkiewicz W, Płoszaj T, Jędrychowska-Dańska K, Żądzińska E, Strapagiel D, Haduch E, Szczepanek A, Grygiel R, Witas HW. Between the Baltic and Danubian Worlds: the genetic affinities of a Middle Neolithic population from central Poland. PLoS One 2015; 10:e0118316. [PMID: 25714361 PMCID: PMC4340919 DOI: 10.1371/journal.pone.0118316] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 01/14/2015] [Indexed: 11/29/2022] Open
Abstract
For a long time, anthropological and genetic research on the Neolithic revolution in Europe was mainly concentrated on the mechanism of agricultural dispersal over different parts of the continent. Recently, attention has shifted towards population processes that occurred after the arrival of the first farmers, transforming the genetically very distinctive early Neolithic Linear Pottery Culture (LBK) and Mesolithic forager populations into present-day Central Europeans. The latest studies indicate that significant changes in this respect took place within the post-Linear Pottery cultures of the Early and Middle Neolithic which were a bridge between the allochthonous LBK and the first indigenous Neolithic culture of north-central Europe--the Funnel Beaker culture (TRB). The paper presents data on mtDNA haplotypes of a Middle Neolithic population dated to 4700/4600-4100/4000 BC belonging to the Brześć Kujawski Group of the Lengyel culture (BKG) from the Kuyavia region in north-central Poland. BKG communities constituted the border of the "Danubian World" in this part of Europe for approx. seven centuries, neighboring foragers of the North European Plain and the southern Baltic basin. MtDNA haplogroups were determined in 11 individuals, and four mtDNA macrohaplogroups were found (H, U5, T, and HV0). The overall haplogroup pattern did not deviate from other post-Linear Pottery populations from central Europe, although a complete lack of N1a and the presence of U5a are noteworthy. Of greatest importance is the observed link between the BKG and the TRB horizon, confirmed by an independent analysis of the craniometric variation of Mesolithic and Neolithic populations inhabiting central Europe. Estimated phylogenetic pattern suggests significant contribution of the post-Linear BKG communities to the origin of the subsequent Middle Neolithic cultures, such as the TRB.
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Affiliation(s)
- Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Tomasz Płoszaj
- Department of Molecular Biology, Medical University of Łódź, Łódź, Poland
| | | | - Elżbieta Żądzińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Elżbieta Haduch
- Department of Anthropology, Faculty of Biology and Earth Sciences, Jagiellonian University in Kraków, Kraków, Poland
| | - Anita Szczepanek
- Department of Anthropology, Faculty of Biology and Earth Sciences, Jagiellonian University in Kraków, Kraków, Poland
| | | | - Henryk W. Witas
- Department of Molecular Biology, Medical University of Łódź, Łódź, Poland
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14
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Brandt G, Szécsényi-Nagy A, Roth C, Alt KW, Haak W. Human paleogenetics of Europe--the known knowns and the known unknowns. J Hum Evol 2014; 79:73-92. [PMID: 25467114 DOI: 10.1016/j.jhevol.2014.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/25/2014] [Accepted: 06/19/2014] [Indexed: 12/01/2022]
Abstract
The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Anna Szécsényi-Nagy
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany; Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1014 Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Kurt Werner Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Richard-Wagner-Straße 9, D-06114 Halle, Germany; Institute for Prehistory and Archaeological Science, Basel University, Petersplatz 1, 4003 Basel, Switzerland; Danube Private University, Faculty of Medicine and Dentistry, Doktor-Karl-Dorrek-Straße 23, 3500 Krems an der Donau, Austria
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia.
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15
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Benguigui M, Arenas M. Spatial and temporal simulation of human evolution. Methods, frameworks and applications. Curr Genomics 2014; 15:245-55. [PMID: 25132795 PMCID: PMC4133948 DOI: 10.2174/1389202915666140506223639] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/05/2014] [Accepted: 05/04/2014] [Indexed: 01/29/2023] Open
Abstract
Analyses of human evolution are fundamental to understand the current gradients of human diversity. In this concern, genetic samples collected from current populations together with archaeological data are the most important resources to study human evolution. However, they are often insufficient to properly evaluate a variety of evolutionary scenarios, leading to continuous debates and discussions. A commonly applied strategy consists of the use of computer simulations based on, as realistic as possible, evolutionary models, to evaluate alternative evolutionary scenarios through statistical correlations with the real data. Computer simulations can also be applied to estimate evolutionary parameters or to study the role of each parameter on the evolutionary process. Here we review the mainly used methods and evolutionary frameworks to perform realistic spatially explicit computer simulations of human evolution. Although we focus on human evolution, most of the methods and software we describe can also be used to study other species. We also describe the importance of considering spatially explicit models to better mimic human evolutionary scenarios based on a variety of phenomena such as range expansions, range shifts, range contractions, sex-biased dispersal, long-distance dispersal or admixtures of populations. We finally discuss future implementations to improve current spatially explicit simulations and their derived applications in human evolution.
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Affiliation(s)
- Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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16
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Gómez-Sánchez D, Olalde I, Pierini F, Matas-Lalueza L, Gigli E, Lari M, Civit S, Lozano M, Vergès JM, Caramelli D, Ramírez O, Lalueza-Fox C. Mitochondrial DNA from El Mirador cave (Atapuerca, Spain) reveals the heterogeneity of Chalcolithic populations. PLoS One 2014; 9:e105105. [PMID: 25116044 PMCID: PMC4130614 DOI: 10.1371/journal.pone.0105105] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/18/2014] [Indexed: 12/31/2022] Open
Abstract
Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.
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Affiliation(s)
- Daniel Gómez-Sánchez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Federica Pierini
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Laura Matas-Lalueza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Elena Gigli
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
- Àrea de Prehistòria, Departament d’Història i Història de l’Art, Universitat Rovira i Virgili, Tarragona, Spain
| | - David Caramelli
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Oscar Ramírez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- * E-mail:
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17
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Tassi F, Ghirotto S, Caramelli D, Barbujani G. Genetic evidence does not support an Etruscan origin in Anatolia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152:11-8. [PMID: 23900768 DOI: 10.1002/ajpa.22319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/20/2013] [Indexed: 01/22/2023]
Abstract
The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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18
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Rasteiro R, Chikhi L. Female and male perspectives on the neolithic transition in Europe: clues from ancient and modern genetic data. PLoS One 2013; 8:e60944. [PMID: 23613761 PMCID: PMC3629215 DOI: 10.1371/journal.pone.0060944] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 03/05/2013] [Indexed: 11/19/2022] Open
Abstract
The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.
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19
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Riccio ME, Buhler S, Nunes JM, Vangenot C, Cuénod M, Currat M, Di D, Andreani M, Boldyreva M, Chambers G, Chernova M, Chiaroni J, Darke C, Di Cristofaro J, Dubois V, Dunn P, Edinur HA, Elamin N, Eliaou JF, Grubic Z, Jaatinen T, Kanga U, Kervaire B, Kolesar L, Kunachiwa W, Lokki ML, Mehra N, Nicoloso G, Paakkanen R, Voniatis DP, Papasteriades C, Poli F, Richard L, Romón Alonso I, Slavčev A, Sulcebe G, Suslova T, Testi M, Tiercy JM, Varnavidou A, Vidan-Jeras B, Wennerström A, Sanchez-Mazas A. 16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report). Int J Immunogenet 2012; 40:21-30. [PMID: 23280239 DOI: 10.1111/iji.12033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 01/05/2023]
Abstract
We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May-June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well-defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA-NET recommendations. The new data included, among others, large sets of well-defined populations from north-east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation-maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy-Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th-15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA-A, -B and -DRB1 loci but not for HLA-DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south-east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian-speaking South-East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.
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Affiliation(s)
- M E Riccio
- Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, Geneva, Switzerland
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20
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Diniz-Filho JAF, Bini LM. Thirty-five years of spatial autocorrelation analysis in population genetics: an essay in honour of Robert Sokal (1926-2012). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01987.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Luis Mauricio Bini
- Departamento de Ecologia, Instituto de Ciências Biológicas; Universidade Federal de Goiás; CP 131 Campus II 74001-970; Goiânia; GO; Brazil
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21
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Arenas M, François O, Currat M, Ray N, Excoffier L. Influence of admixture and paleolithic range contractions on current European diversity gradients. Mol Biol Evol 2012; 30:57-61. [PMID: 22923464 DOI: 10.1093/molbev/mss203] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cavalli-Sforza and Edwards (Analysis of human evolution. 1963. In: Geerts SJ, editor. Genetics today: Proceedings of the 11th International Congress of Genetics, The Hague, The Netherlands. New York: Pergamon. p. 923-993.) initiated the representation of genetic relationships among human populations with principal component (PC) analysis (PCA). Their study revealed the presence of a southeast-northwest (SE-NW) gradient of genetic variation in current European populations, which was interpreted as the result of the demic diffusion of early neolithic farmers during their expansion from the near east. However, this interpretation has been questioned, as PCA gradients can occur even when there is no expansion and because the first PC axis is often orthogonal to the expansion axis. Here, we revisit PCA patterns obtained under realistic scenarios of the settlement of Europe, focusing on the effects of various levels of admixture between paleolithic and neolithic populations, and of range contractions during the last glacial maximum (LGM). Using extensive simulations, we find that the first PC (PC1) gradients are orthogonal to the expansion axis, but only when the expansion is recent (neolithic). More ancient (paleolithic) expansions alter the orientation of the PC1 gradient due to a spatial homogenization of genetic diversity over time, and to the exact location of LGM refugia from which re-expansions proceeded. Overall we find that PC1 gradients consistently follow an SE-NW orientation if there is a large paleolithic contribution to the current European gene pool, and if the main refuge area during the last ice age was in the Iberian Peninsula. Our study suggests that an SE-NW PC1 gradient is compatible with little genetic impact of neolithic populations on the current European gene pool, and that range contractions have affected observed genetic patterns.
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Affiliation(s)
- Miguel Arenas
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
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22
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Pinhasi R, von Cramon-Taubadel N. A craniometric perspective on the transition to agriculture in Europe. Hum Biol 2012; 84:45-66. [PMID: 22452428 DOI: 10.3378/027.084.0102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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23
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Sánchez-Quinto F, Schroeder H, Ramirez O, Avila-Arcos MC, Pybus M, Olalde I, Velazquez AMV, Marcos MEP, Encinas JMV, Bertranpetit J, Orlando L, Gilbert MTP, Lalueza-Fox C. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr Biol 2012; 22:1494-9. [PMID: 22748318 DOI: 10.1016/j.cub.2012.06.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/08/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.
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24
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Sanchez-Mazas A, Vidan-Jeras B, Nunes JM, Fischer G, Little AM, Bekmane U, Buhler S, Buus S, Claas FHJ, Dormoy A, Dubois V, Eglite E, Eliaou JF, Gonzalez-Galarza F, Grubic Z, Ivanova M, Lie B, Ligeiro D, Lokki ML, da Silva BM, Martorell J, Mendonça D, Middleton D, Voniatis DP, Papasteriades C, Poli F, Riccio ME, Vlachou MS, Sulcebe G, Tonks S, Nevessignsky MT, Vangenot C, van Walraven AM, Tiercy JM. Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations. Int J Immunogenet 2012; 39:459-72; quiz 473-6. [PMID: 22533604 PMCID: PMC3533781 DOI: 10.1111/j.1744-313x.2012.01113.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics’ analyses) recommends avoiding outdated racial classifications and population names (e.g. ‘Caucasian’) and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. ‘pan-European’). A standard ‘HLA-NET POPULATION DATA QUESTIONNAIRE’ has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in ‘HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS’. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable of dealing with ambiguous data, such as the ‘gene[rate]’ computer tools to estimate frequencies, test for Hardy–Weinberg equilibrium and selective neutrality on data containing any number and kind of ambiguities. WG4 (Ethical issues) proposes to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. All HLA-NET guidelines and tools are available through its website http://hla-net.eu.
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Hervella M, Izagirre N, Alonso S, Fregel R, Alonso A, Cabrera VM, de la Rúa C. Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe. PLoS One 2012; 7:e34417. [PMID: 22563371 PMCID: PMC3340892 DOI: 10.1371/journal.pone.0034417] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 02/28/2012] [Indexed: 11/25/2022] Open
Abstract
Background/Principal Findings The phenomenon of Neolithisation refers to the transition of prehistoric
populations from a hunter-gatherer to an agro-pastoralist lifestyle.
Traditionally, the spread of an agro-pastoralist economy into Europe has
been framed within a dichotomy based either on an acculturation phenomenon
or on a demic diffusion. However, the nature and speed of this transition is
a matter of continuing scientific debate in archaeology, anthropology, and
human population genetics. In the present study, we have analyzed the
mitochondrial DNA diversity in hunter-gatherers and first farmers from
Northern Spain, in relation to the debate surrounding the phenomenon of
Neolithisation in Europe. Methodology/Significance Analysis of mitochondrial DNA was carried out on 54 individuals from Upper
Paleolithic and Early Neolithic, which were recovered from nine
archaeological sites from Northern Spain (Basque Country, Navarre and
Cantabria). In addition, to take all necessary precautions to avoid
contamination, different authentication criteria were applied in this study,
including: DNA quantification, cloning, duplication (51% of the
samples) and replication of the results (43% of the samples) by two
independent laboratories. Statistical and multivariate analyses of the
mitochondrial variability suggest that the genetic influence of
Neolithisation did not spread uniformly throughout Europe, producing
heterogeneous genetic consequences in different geographical regions,
rejecting the traditional models that explain the Neolithisation in
Europe. Conclusion The differences detected in the mitochondrial DNA lineages of Neolithic
groups studied so far (including these ones of this study) suggest different
genetic impact of Neolithic in Central Europe, Mediterranean Europe and the
Cantabrian fringe. The genetic data obtained in this study provide support
for a random dispersion model for Neolithic farmers. This random dispersion
had a different impact on the various geographic regions, and thus
contradicts the more simplistic total acculturation and replacement models
proposed so far to explain Neolithisation.
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Affiliation(s)
- Montserrat Hervella
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Rosa Fregel
- Department of Genetics, University of La
Laguna, La Laguna, Santa Cruz de Tenerife, Spain
| | - Antonio Alonso
- Department of Biology, National Institute of
Toxicology and Forensic Sciences, Madrid, Spain
| | - Vicente M. Cabrera
- Department of Genetics, University of La
Laguna, La Laguna, Santa Cruz de Tenerife, Spain
| | - Concepción de la Rúa
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
- * E-mail:
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Deguilloux MF, Leahy R, Pemonge MH, Rottier S. European neolithization and ancient DNA: an assessment. Evol Anthropol 2012; 21:24-37. [PMID: 22307722 DOI: 10.1002/evan.20341] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neolithic processes underlying the distribution of genetic diversity among European populations have been the subject of intense debate since the first genetic data became available. However, patterns observed in the current European gene pool are the outcome of Paleolithic and Neolithic processes, overlaid with four millennia of further developments. This observation encouraged paleogeneticists to contribute to the debate by directly comparing genetic variation from the ancient inhabitants of Europe to their contemporary counterparts. Pre-Neolithic and Neolithic paleogenetic data are becoming increasingly available for north and northwest European populations. Despite the numerous problems inherent in the paleogenetic approach, the accumulation of ancient DNA datasets offers new perspectives from which to interpret the interactions between hunter-gatherer and farming communities. In light of information emerging from diverse disciplines, including recent paleogenetic studies, the most plausible model explaining the movement of Neolithic pioneer groups in central Europe is that of leapfrog migration.
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Young KL, Sun G, Deka R, Crawford MH. Paternal genetic history of the Basque population of Spain. Hum Biol 2012; 83:455-75. [PMID: 21846204 DOI: 10.3378/027.083.0402] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This study examines the genetic variation in Basque Y chromosome lineages using data on 12 Y-short tandem repeat (STR) loci in a sample of 158 males from four Basque provinces of Spain (Alava, Vizcaya, Guipuzcoa, and Navarre). As reported in previous studies, the Basques are characterized by high frequencies of haplogroup R1b (83%). AMOVA analysis demonstrates genetic homogeneity, with a small but significant amount of genetic structure between provinces (Y-short tandem repeat loci STRs: 1.71%, p = 0.0369). Gene and haplotype diversity levels in the Basque population are on the low end of the European distribution (gene diversity: 0.4268; haplotype diversity: 0.9421). Post-Neolithic contribution to the paternal Basque gene pool was estimated by measuring the proportion of those haplogroups with a Time to Most Recent Common Ancestor (TMRCA) previously dated either prior (R1b, I2a2) or subsequent to (E1b1b, G2a, J2a) the Neolithic. Based on these estimates, the Basque provinces show varying degrees of post-Neolithic contribution in the paternal lineages (10.9% in the combined sample).
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Affiliation(s)
- Kristin L Young
- Department of Family Medicine, Research Division, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Matern A, Drees C, Härdtle W, von Oheimb G, Assmann T. Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae) populations inhabiting ancient and recent woodlands in north-western Germany. Zookeys 2011:545-63. [PMID: 21738433 PMCID: PMC3131037 DOI: 10.3897/zookeys.100.1546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 04/13/2010] [Indexed: 11/12/2022] Open
Abstract
Only very few cases have documented that an increase in connectivity after a period of fragmentation in ecological time has had an effect on the distribution, genetic structure and morphology of stenotopic species. In this study we present an example of clinal variability in a woodland ground beetle as a result of changes in the connectivity of a landscape during the last two centuries. The study area hosts both the nominate form Carabus violaceus s. str. and the subspecies Carabus violaceus purpurascens, which is ranked as a distinct species by some authors. We studied 12 Carabus violaceus populations from a 30 km transect of ancient and recent forests in north-western Germany. We analyzed three polymorphic enzyme loci, classified the elytron sculpture and measured the shape of the aedeagus tip of the specimens. Carabus violaceus showed secondary gradients both in allozyme markers and morphometric characters in our study area. A genetic differentiation of 16% between the populations is high but lies within the range of intraspecific variability in habitat specialists of the genus Carabus. Populations had no significant deficit of heterozygotes. We found many hybrid populations in terms of morphological properties. This study highlights the conservation value of ancient woodland and the consequences of landscape connectivity and defragmentation on the genetic setting of a ground beetle. Moreover, it shows that differences in the external shape of male genitalia do not prevent gene flow within the genus Carabus. Thus, the establishment of species status should not exclusively be based on this property.
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Affiliation(s)
- Andrea Matern
- Institute of Ecology and Environmental Chemistry, Leuphana University Lüneburg, Scharnhorststraße 1, D - 21335 Lüneburg, Germany
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Sjödin P, François O. Wave-of-advance models of the diffusion of the Y chromosome haplogroup R1b1b2 in Europe. PLoS One 2011; 6:e21592. [PMID: 21720564 PMCID: PMC3123369 DOI: 10.1371/journal.pone.0021592] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
Whether or not the spread of agriculture in Europe was accompanied by movements of people is a long-standing question in archeology and anthropology, which has been frequently addressed with the help of population genetic data. Estimates on dates of expansion and geographic origins obtained from genetic data are however sensitive to the calibration of mutation rates and to the mathematical models used to perform inference. For instance, recent data on the Y chromosome haplogroup R1b1b2 (M269) have either suggested a Neolithic origin for European paternal lineages or a more ancient Paleolithic origin depending on the calibration of Y-STR mutation rates. Here we examine the date of expansion and the geographic origin of hgR1b1b2 considering two current estimates of mutation rates in a total of fourteen realistic wave-of-advance models. We report that a range expansion dating to the Paleolithic is unlikely to explain the observed geographical distribution of microsatellite diversity, and that whether the data is informative with respect to the spread of agriculture in Europe depends on the mutation rate assumption in a critical way.
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Affiliation(s)
- Per Sjödin
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden.
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30
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Ancient DNA reveals male diffusion through the Neolithic Mediterranean route. Proc Natl Acad Sci U S A 2011; 108:9788-91. [PMID: 21628562 DOI: 10.1073/pnas.1100723108] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.
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Sanchez-Mazas A, Fernandez-Viña M, Middleton D, Hollenbach JA, Buhler S, Di D, Rajalingam R, Dugoujon JM, Mack SJ, Thorsby E. Immunogenetics as a tool in anthropological studies. Immunology 2011; 133:143-64. [PMID: 21480890 DOI: 10.1111/j.1365-2567.2011.03438.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The genes coding for the main molecules involved in the human immune system--immunoglobulins, human leucocyte antigen (HLA) molecules and killer-cell immunoglobulin-like receptors (KIR)--exhibit a very high level of polymorphism that reveals remarkable frequency variation in human populations. 'Genetic marker' (GM) allotypes located in the constant domains of IgG antibodies have been studied for over 40 years through serological typing, leading to the identification of a variety of GM haplotypes whose frequencies vary sharply from one geographic region to another. An impressive diversity of HLA alleles, which results in amino acid substitutions located in the antigen-binding region of HLA molecules, also varies greatly among populations. The KIR differ between individuals according to both gene content and allelic variation, and also display considerable population diversity. Whereas the molecular evolution of these polymorphisms has most likely been subject to natural selection, principally driven by host-pathogen interactions, their patterns of genetic variation worldwide show significant signals of human geographic expansion, demographic history and cultural diversification. As current developments in population genetic analysis and computer simulation improve our ability to discriminate among different--either stochastic or deterministic--forces acting on the genetic evolution of human populations, the study of these systems shows great promise for investigating both the peopling history of modern humans in the time since their common origin and human adaptation to past environmental (e.g. pathogenic) changes. Therefore, in addition to mitochondrial DNA, Y-chromosome, microsatellites, single nucleotide polymorphisms and other markers, immunogenetic polymorphisms represent essential and complementary tools for anthropological studies.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Department of Genetics and Evolution, Anthropology unit, Laboratory of Anthropology, Genetics and peopling history, University of Geneva, 12 rue Gustave-Revilliod, Geneva, Switzerland.
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Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CSI, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A. Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol 2010; 8:e1000536. [PMID: 21085689 PMCID: PMC2976717 DOI: 10.1371/journal.pbio.1000536] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 09/27/2010] [Indexed: 01/29/2023] Open
Abstract
The first farmers from Central Europe reveal a genetic affinity to modern-day populations from the Near East and Anatolia, which suggests a significant demographic input from this area during the early Neolithic. In Europe, the Neolithic transition (8,000–4,000 b.c.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 b.c.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated b.c.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated b.c.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic. The transition from a hunter–gatherer existence to a sedentary farming-based lifestyle has had key consequences for human groups around the world and has profoundly shaped human societies. Originating in the Near East around 11,000 y ago, an agricultural lifestyle subsequently spread across Europe during the New Stone Age (Neolithic). Whether it was mediated by incoming farmers or driven by the transmission of innovative ideas and techniques remains a subject of continuing debate in archaeology, anthropology, and human population genetics. Ancient DNA from the earliest farmers can provide a direct view of the genetic diversity of these populations in the earliest Neolithic. Here, we compare Neolithic haplogroups and their diversity to a large database of extant European and Eurasian populations. We identified Neolithic haplotypes that left clear traces in modern populations, and the data suggest a route for the migrating farmers that extends from the Near East and Anatolia into Central Europe. When compared to indigenous hunter–gatherer populations, the unique and characteristic genetic signature of the early farmers suggests a significant demographic input from the Near East during the onset of farming in Europe.
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Affiliation(s)
- Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, Australia.
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Abstract
A new timescale has recently been established for human mitochondrial DNA (mtDNA) lineages, making mtDNA at present the most informative genetic marker system for studying European prehistory. Here, we review the new chronology and compare mtDNA with Y-chromosome patterns, in order to summarize what we have learnt from archaeogenetics concerning five episodes over the past 50,000 years which significantly contributed to the settlement history of Europe: the pioneer colonisation of the Upper Palaeolithic, the Late Glacial re-colonisation of the continent from southern refugia after the Last Glacial Maximum, the postglacial re-colonization of deserted areas after the Younger Dryas cold snap, the arrival of Near Easterners with an incipient Neolithic package, and the small-scale migrations along continent-wide economic exchange networks beginning with the Copper Age. The available data from uniparental genetic systems have already transformed our view of the prehistory of Europe, but our knowledge of these processes remains limited. Nevertheless, their legacy remains as sedimentary layers in the gene pool of modern Europeans, and our understanding of them will improve substantially when more mtDNAs are completely sequenced, the Y chromosome more thoroughly analysed, and haplotype blocks of the autosomal genome become amenable to phylogeographic studies.
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François O, Currat M, Ray N, Han E, Excoffier L, Novembre J. Principal component analysis under population genetic models of range expansion and admixture. Mol Biol Evol 2010; 27:1257-68. [PMID: 20097660 DOI: 10.1093/molbev/msq010] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East approximately 10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the "allele surfing" phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.
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Affiliation(s)
- Olivier François
- Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité, Faculty of Medicine, University Joseph Fourier, Grenoble Institute of Technology, Centre National de la Recherche Scientifique UMR5525, La Tronche, France.
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A predominantly neolithic origin for European paternal lineages. PLoS Biol 2010; 8:e1000285. [PMID: 20087410 PMCID: PMC2799514 DOI: 10.1371/journal.pbio.1000285] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 12/10/2009] [Indexed: 11/19/2022] Open
Abstract
The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.
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Paschetta C, de Azevedo S, Castillo L, Martínez-Abadías N, Hernández M, Lieberman DE, González-José R. The influence of masticatory loading on craniofacial morphology: A test case across technological transitions in the Ohio valley. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 141:297-314. [DOI: 10.1002/ajpa.21151] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Pinhasi R, von Cramon-Taubadel N. Craniometric data supports demic diffusion model for the spread of agriculture into Europe. PLoS One 2009; 4:e6747. [PMID: 19707595 PMCID: PMC2727056 DOI: 10.1371/journal.pone.0006747] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 07/20/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The spread of agriculture into Europe and the ancestry of the first European farmers have been subjects of debate and controversy among geneticists, archaeologists, linguists and anthropologists. Debates have centred on the extent to which the transition was associated with the active migration of people as opposed to the diffusion of cultural practices. Recent studies have shown that patterns of human cranial shape variation can be employed as a reliable proxy for the neutral genetic relationships of human populations. METHODOLOGY/PRINCIPAL FINDINGS Here, we employ measurements of Mesolithic (hunter-gatherers) and Neolithic (farmers) crania from Southwest Asia and Europe to test several alternative population dispersal and hunter-farmer gene-flow models. We base our alternative hypothetical models on a null evolutionary model of isolation-by-geographic and temporal distance. Partial Mantel tests were used to assess the congruence between craniometric distance and each of the geographic model matrices, while controlling for temporal distance. Our results demonstrate that the craniometric data fit a model of continuous dispersal of people (and their genes) from Southwest Asia to Europe significantly better than a null model of cultural diffusion. CONCLUSIONS/SIGNIFICANCE Therefore, this study does not support the assertion that farming in Europe solely involved the adoption of technologies and ideas from Southwest Asia by indigenous Mesolithic hunter-gatherers. Moreover, the results highlight the utility of craniometric data for assessing patterns of past population dispersal and gene flow.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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Gallagher A, Gunther MM, Bruchhaus H. Population continuity, demic diffusion and Neolithic origins in central-southern Germany: the evidence from body proportions. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2009; 60:95-126. [PMID: 19264304 DOI: 10.1016/j.jchb.2008.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 05/13/2008] [Indexed: 10/21/2022]
Abstract
The transition to agro-pastoralism in central Europe has been framed within a dichotomy of "regional continuity" versus exogenous "demic diffusion". While substantial genetic support exists for a model of demographic diffusion from an ancestral source in the Near East, archaeological data furnish weak support for the "wave of advance" model. Nevertheless, archaeological evidence attests the widespread introduction of an exogenous "package" comprising ceramics, cereals, pulses and domesticated animals to central Europe at 5600calBCE. Body proportions are under strong climatic selection and evince remarkable stability within regional lineages. As such, they offer a viable and robust alternative to cranio-facial data in assessing hypothesised continuity and replacement with the transition to agro-pastoralism in central Europe. Humero-clavicular, brachial and crural indices in a large sample (n=75) of Linienbandkeramik (LBK), Late Neolithic and Early Bronze Age specimens from the middle Elbe-Saale-Werra valley (MESV) were compared with Eurasian and African terminal Pleistocene, European Mesolithic and geographically disparate recent human specimens. Mesolithic Europeans display considerable variation in humero-clavicular and brachial indices yet none approach the extreme "hyper-polar" morphology of LBK humans from the MESV. In contrast, Late Neolithic and Early Bronze Age peoples display elongated brachial and crural indices reminiscent of terminal Pleistocene and "tropically adapted" recent humans. These marked morphological changes likely reflect exogenous immigration during the terminal Fourth millennium cal BC. Population expansion and diffusion is a function of increased mobility and settlement dispersal concomitant with significant technological and subsistence changes in later Neolithic societies during the late fourth millennium cal BCE.
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Affiliation(s)
- A Gallagher
- School of Anatomical Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, Republic of South Africa.
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Holt BM, Formicola V. Hunters of the Ice Age: The biology of Upper Paleolithic people. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; Suppl 47:70-99. [PMID: 19003886 DOI: 10.1002/ajpa.20950] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Upper Paleolithic represents both the phase during which anatomically modern humans appeared and the climax of hunter-gatherer cultures. Demographic expansion into new areas that took place during this period and the diffusion of burial practices resulted in an unprecedented number of well-preserved human remains. This skeletal record, dovetailed with archeological, environmental, and chronological contexts, allows testing of hypotheses regarding biological processes at the population level. In this article, we review key studies about the biology of Upper Paleolithic populations based primarily on European samples, but integrating information from other areas of the Old World whenever possible. Data about cranial morphology, skeletal robusticity, stature, body proportions, health status, diet, physical activity, and genetics are evaluated in Late Pleistocene climatic and cultural contexts. Various lines of evidence delineate the Last Glacial Maximum (LGM) as a critical phase in the biological and cultural evolution of Upper Paleolithic populations. The LGM, a long phase of climatic deterioration culminating around 20,000 BP, had a profound impact on the environment, lifestyle, and behavior of human groups. Some of these effects are recorded in aspects of skeletal biology of these populations. Groups living before and after the LGM, Early Upper Paleolithic (EUP) and Late Upper Paleolithic (LUP), respectively, differ significantly in craniofacial dimensions, stature, robusticity, and body proportions. While paleopathological and stable isotope data suggest good health status throughout the Upper Paleolithic, some stress indicators point to a slight decline in quality of life in LUP populations. The intriguing and unexpected incidence of individuals affected by congenital disorders probably indicates selective burial practices for these abnormal individuals. While some of the changes observed can be explained through models of biocultural or environmental adaptation (e.g., decreased lower limb robusticity following decreased mobility; changes in body proportions along with climatic change), others are more difficult to explain. For instance, craniodental and upper limb robusticity show complex evolutionary patterns that do not always correspond to expectations. In addition, the marked decline in stature and the mosaic nature of change in body proportions still await clarifications. These issues, as well as systematic analysis of specific pathologies and possible relationships between genetic lineages, population movements and cultural complexes, should be among the goals of future research.
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Affiliation(s)
- Brigitte M Holt
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003, USA.
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Adams SM, Bosch E, Balaresque PL, Ballereau SJ, Lee AC, Arroyo E, López-Parra AM, Aler M, Grifo MSG, Brion M, Carracedo A, Lavinha J, Martínez-Jarreta B, Quintana-Murci L, Picornell A, Ramon M, Skorecki K, Behar DM, Calafell F, Jobling MA. The genetic legacy of religious diversity and intolerance: paternal lineages of Christians, Jews, and Muslims in the Iberian Peninsula. Am J Hum Genet 2008; 83:725-36. [PMID: 19061982 PMCID: PMC2668061 DOI: 10.1016/j.ajhg.2008.11.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/13/2008] [Accepted: 11/17/2008] [Indexed: 11/05/2022] Open
Abstract
Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times could also have had profound effects on the genetic landscape. The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins and their own particular cultural and religious characteristics—North African Muslims and Sephardic Jews. To address this issue, we analyzed Y chromosome haplotypes, which provide the necessary phylogeographic resolution, in 1140 males from the Iberian Peninsula and Balearic Islands. Admixture analysis based on binary and Y-STR haplotypes indicates a high mean proportion of ancestry from North African (10.6%) and Sephardic Jewish (19.8%) sources. Despite alternative possible sources for lineages ascribed a Sephardic Jewish origin, these proportions attest to a high level of religious conversion (whether voluntary or enforced), driven by historical episodes of social and religious intolerance, that ultimately led to the integration of descendants. In agreement with the historical record, analysis of haplotype sharing and diversity within specific haplogroups suggests that the Sephardic Jewish component is the more ancient. The geographical distribution of North African ancestry in the peninsula does not reflect the initial colonization and subsequent withdrawal and is likely to result from later enforced population movement—more marked in some regions than in others—plus the effects of genetic drift.
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Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa. Proc Natl Acad Sci U S A 2008; 105:10693-8. [PMID: 18678889 DOI: 10.1073/pnas.0801184105] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa approximately 2,000 years ago.
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Nowak J, Mika-Witkowska R, Polak M, Zajko M, Rogatko-Koroś M, Graczyk-Pol E, Lange A. Allele and extended haplotype polymorphism of HLA-A, -C, -B, -DRB1 and -DQB1 loci in Polish population and genetic affinities to other populations. ACTA ACUST UNITED AC 2008; 71:193-205. [DOI: 10.1111/j.1399-0039.2007.00991.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sampietro M, Lao O, Caramelli D, Lari M, Pou R, Martí M, Bertranpetit J, Lalueza-Fox C. Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe. Proc Biol Sci 2007; 274:2161-7. [PMID: 17609193 PMCID: PMC2706191 DOI: 10.1098/rspb.2007.0465] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The peopling of Europe is a complex process. One of the most dramatic demographic events, the Neolithic agricultural revolution, took place in the Near East roughly 10000 years ago and then spread through the European continent. Nevertheless, the nature of this process (either cultural or demographic) is still a matter of debate among scientists. We have retrieved HVRI mitochondrial DNA sequences from 11 Neolithic remains from Granollers (Catalonia, northeast Spain) dated to 5500 years BP. We followed the proposed authenticity criteria, and we were also able, for the first time, to track down the pre-laboratory-derived contaminant sequences and consequently eliminate them from the generated cloning dataset. Phylogeographic analysis shows that the haplogroup composition of the Neolithic population is very similar to that found in modern populations from the Iberian Peninsula, suggesting a long-time genetic continuity, at least since Neolithic times. This result contrasts with that recently found in a Neolithic population from Central Europe and, therefore, raises new questions on the heterogeneity of the Neolithic dispersals into Europe. We propose here a dual model of Neolithic spread: acculturation in Central Europe and demic diffusion in southern Europe.
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Affiliation(s)
- M.L Sampietro
- Departament de Ciències de la Salut i de la Vida, Universitat Pompeu FabraDr Aiguader 80, 08003 Barcelona, Spain
| | - O Lao
- Department of Forensic Molecular Biology, Erasmus Medical Center RotterdamRotterdam 3000, The Netherlands
| | - D Caramelli
- Laboratory of Anthropology, Department of Animal Biology and Genetics, University of Florencevia del Proconsolo 12, 50122 Florence, Italy
| | - M Lari
- Laboratory of Anthropology, Department of Animal Biology and Genetics, University of Florencevia del Proconsolo 12, 50122 Florence, Italy
| | - R Pou
- Museu d'Arqueologia de Granollers,Anselm Clave 40, 084400 Granollers, Spain
| | - M Martí
- Museu d'Arqueologia de Granollers,Anselm Clave 40, 084400 Granollers, Spain
| | - J Bertranpetit
- Departament de Ciències de la Salut i de la Vida, Universitat Pompeu FabraDr Aiguader 80, 08003 Barcelona, Spain
| | - C Lalueza-Fox
- Unitat d'Antropologia, Departament de Biologia Animal, Facultat de Biologia, Universitat de BarcelonaAvinguda Diagonal 645, 08028 Barcelona, Spain
- Author for correspondence ()
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Kullo IJ, Ding K. Patterns of population differentiation of candidate genes for cardiovascular disease. BMC Genet 2007; 8:48. [PMID: 17626638 PMCID: PMC1937006 DOI: 10.1186/1471-2156-8-48] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 07/12/2007] [Indexed: 12/19/2022] Open
Abstract
Background The basis for ethnic differences in cardiovascular disease (CVD) susceptibility is not fully understood. We investigated patterns of population differentiation (FST) of a set of genes in etiologic pathways of CVD among 3 ethnic groups: Yoruba in Nigeria (YRI), Utah residents with European ancestry (CEU), and Han Chinese (CHB) + Japanese (JPT). We identified 37 pathways implicated in CVD based on the PANTHER classification and 416 genes in these pathways were further studied; these genes belonged to 6 biological processes (apoptosis, blood circulation and gas exchange, blood clotting, homeostasis, immune response, and lipoprotein metabolism). Genotype data were obtained from the HapMap database. Results We calculated FST for 15,559 common SNPs (minor allele frequency ≥ 0.10 in at least one population) in genes that co-segregated among the populations, as well as an average-weighted FST for each gene. SNPs were classified as putatively functional (non-synonymous and untranslated regions) or non-functional (intronic and synonymous sites). Mean FST values for common putatively functional variants were significantly higher than FST values for nonfunctional variants. A significant variation in FST was also seen based on biological processes; the processes of 'apoptosis' and 'lipoprotein metabolism' showed an excess of genes with high FST. Thus, putative functional SNPs in genes in etiologic pathways for CVD show greater population differentiation than non-functional SNPs and a significant variance of FST values was noted among pairwise population comparisons for different biological processes. Conclusion These results suggest a possible basis for varying susceptibility to CVD among ethnic groups.
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Affiliation(s)
- Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester MN, USA
| | - Keyue Ding
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester MN, USA
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Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: an allele frequency database for microevolutionary studies. Evol Bioinform Online 2007; 1:1-10. [PMID: 19325849 PMCID: PMC2658869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Kei-Hoi Cheung
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA, Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Rohit Gadagkar
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Shannon Stein
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Perry L Miller
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA,Correspondence: Kenneth K. Kidd, Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8005, USA, Telephone: 203-785-2654, Fax: 203-785-6568,
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Belle EM, Landry PA, Barbujani G. Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci. Proc Biol Sci 2006; 273:1595-602. [PMID: 16769629 PMCID: PMC1634924 DOI: 10.1098/rspb.2006.3494] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is general agreement that the current European gene pool is mainly derived from Palaeolithic hunting-gathering and Neolithic farming ancestors, but different studies disagree on the relative weight of these contributions. We estimated admixture rates in European populations from data on 377 autosomal microsatellite loci in 235 individuals, using five different numerical methods. On average, the Near Eastern (and presumably Neolithic) contribution was between 46 and 66%, and admixture estimates showed, with all methods, a strong and significant negative correlation with distance from the Near East. If the assumptions of the model are approximately correct, i.e. if the Basques' and Near Easterners' genomes represent a good approximation to the Palaeolithic and Neolithic settlers of Europe, respectively, these results imply that half or more of the Europeans' genes are descended from Near Eastern ancestors who immigrated in Europe 10000 years ago. If these assumptions are incorrect, our results show anyway that clinal variation is the rule in the Europeans' genomes and that lower estimates of Near Eastern admixture obtained from the analysis of single markers do not reflect the patterns observed at the genomic level.
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Affiliation(s)
- Elise M.S Belle
- Dipartimento di Biologia, Università di FerraraVia Borsari 46, 44100 Ferrara, Italy
| | | | - Guido Barbujani
- Dipartimento di Biologia, Università di FerraraVia Borsari 46, 44100 Ferrara, Italy
- Author for correspondence ()
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Bosch E, Calafell F, González-Neira A, Flaiz C, Mateu E, Scheil HG, Huckenbeck W, Efremovska L, Mikerezi I, Xirotiris N, Grasa C, Schmidt H, Comas D. Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns. Ann Hum Genet 2006; 70:459-87. [PMID: 16759179 DOI: 10.1111/j.1469-1809.2005.00251.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Balkan Peninsula is a complex cultural mosaic comprising populations speaking languages from several branches of the Indo-European family and Altaic, as well as culturally-defined minorities such as the Aromuns who speak a Romance language. The current cultural and linguistic landscape is a palimpsest in which different peoples have contributed their cultures in a historical succession. We have sought to find any evidence of genetic stratification related to those cultural layers by typing both mtDNA and Y chromosomes, in Albanians, Romanians, Macedonians, Greeks, and five Aromun populations. We have paid special attention to the Aromuns, and sought to test genetically various hypotheses on their origins. MtDNA and Y-chromosome haplogroup frequencies in the Balkans were found to be similar to those elsewhere in Europe. MtDNA sequences and Y-chromosome STR haplotypes revealed decreased variation in some Aromun populations. Variation within Aromun populations was the primary source of genetic differentiation. Y-chromosome haplotypes tended to be shared across Aromuns, but not across non-Aromun populations. These results point to a possible common origin of the Aromuns, with drift acting to differentiate the separate Aromun communities. The homogeneity of Balkan populations prevented testing for the origin of the Aromuns, although a significant Roman contribution can be ruled out.
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Affiliation(s)
- E Bosch
- Unitat de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
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Capelli C, Redhead N, Romano V, Calì F, Lefranc G, Delague V, Megarbane A, Felice AE, Pascali VL, Neophytou PI, Poulli Z, Novelletto A, Malaspina P, Terrenato L, Berebbi A, Fellous M, Thomas MG, Goldstein DB. Population structure in the Mediterranean basin: a Y chromosome perspective. Ann Hum Genet 2006; 70:207-25. [PMID: 16626331 DOI: 10.1111/j.1529-8817.2005.00224.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.
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Affiliation(s)
- C Capelli
- Department of Biology, University College of London, London, UK.
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