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Navarro-López B, .Baeta M, Moreno-López O, Kleinbielen T, Raffone C, Granizo-Rodríguez E, Ferragut J, Alvarez-Gila O, Barbaro A, Picornell A, de Pancorbo E M. Y-chromosome analysis recapitulates key events of Mediterranean populations. Heliyon 2024; 10:e35329. [PMID: 39220888 PMCID: PMC11365299 DOI: 10.1016/j.heliyon.2024.e35329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
The remarkable geographical situation of the Mediterranean region, located between Europe, Africa, and Asia, with numerous migratory routes, has made this area a crucible of cultures. Studying the Y-chromosome variability is a very performant tool to explore the genetic ancestry and evaluate scenarios that may explain the current Mediterranean gene pool. Here, six Mediterranean populations, including three Balearic Islands (Ibiza, Majorca, and Minorca) and three Southern Italian regions (Catanzaro, Cosenza, and Reggio di Calabria) were typed using 23 Y-STR loci and up to 39 Y-SNPs and compared to geographically targeted key reference populations to explore their genetic relationship and provide an overview of Y-chromosome variation across the Mediterranean basin. Pairwise RST genetic distances calculated with STRs markers and Y-haplogroups mirror the West to East geographic distribution of European and Asian Mediterranean populations, highlighting the North-South division of Italy, with a higher Eastern Mediterranean component in Southern Italian populations. In contrast, the African populations from the Southern coast of the Mediterranean clustered separately. Overall, these results support the notion that migrations from Magna Graecia or the Byzantine Empire, which followed similar Neolithic and post-Neolithic routes into Southern Italy, may have contributed to maintaining and/or reinforcing the Eastern Mediterranean genetic component in Southern Italian populations.
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Affiliation(s)
- B. Navarro-López
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - M. .Baeta
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - O. Moreno-López
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - T. Kleinbielen
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - C. Raffone
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - E. Granizo-Rodríguez
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - J.F. Ferragut
- Departament de Biologia, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Universitat de les Illes Balears, Palma de Mallorca, Illes Balears, Spain
| | - O. Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - A. Barbaro
- Forensic Genetics Section, Studio Indagini Mediche e Forensi (SIMEF), Reggio Calabria, Italy
| | - A. Picornell
- Departament de Biologia, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Universitat de les Illes Balears, Palma de Mallorca, Illes Balears, Spain
| | - M.M. de Pancorbo E
- BIOMICs Research Group, Department of Z. and Cell Biology A., Faculty of Pharmacy, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
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2
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Umar S, Khanna R, Lohlun B, Maldonado JC, Zollinger M, Osei-Tutu A, Gonzales A, Chouhan K, Nusbaum A. Follicular Unit Excision in Patients of African Descent: A Skin-Responsive Technique. Dermatol Surg 2023; 49:949-955. [PMID: 37530735 PMCID: PMC10521773 DOI: 10.1097/dss.0000000000003881] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
BACKGROUND Follicular unit excision is a favored minimally invasive hair transplantation method. However, it is suboptimal for many patients of African descent because of wide variations in hair and skin characteristics. OBJECTIVE To evaluate the performance of a skin-responsive follicular unit excision device, which accommodates hair curliness, skin thickness, and firmness in patients of African descent. MATERIALS AND METHODS The authors retrospectively evaluated patients who underwent scalp follicular unit (FU) excision using a skin-responsive technique at 7 multinational clinics. The preoperative donor grading for the anticipated difficulty used a scale with Class V indicating the highest degree of hair curliness, skin thickness, and firmness. RESULTS Of 64 eligible patients (45 males and 19 females), 28 had Class V FU excision donor grades. The mean transection rate for all patients was 3%-6%, which was highest in class V patients. Skin thickness and firmness had a greater effect on the maximum transection rate than hair curliness. Only 19 or 18 G punches were used. CONCLUSION The authors report consistence success of a new skin-responsive FU excision device for all patients of African descent with a mean graft transection rate of less than 10%. The findings support skin thickness and firmness as major influencers of graft attrition rate.
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Affiliation(s)
- Sanusi Umar
- Dermatology Division, Department of Medicine, University of California, Los Angeles, California
- Division of Dermatology, Harbor-UCLA Medical Center, Torrance, California
- Dr. U Hair and Skin Clinic, Manhattan Beach, California
| | - Raveena Khanna
- Dr. U Hair and Skin Clinic, Manhattan Beach, California
- Department of Dermatology, Howard University College of Medicine, Washington, District of Columbia
| | | | | | | | | | | | - Kavish Chouhan
- Department of Dermatology, DermaClinix, Clinic, New Delhi, India
| | - Aron Nusbaum
- Hair Transplant Institute Miami, Coral Gables, Florida
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3
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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4
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French JC, Riris P, Fernandéz-López de Pablo J, Lozano S, Silva F. A manifesto for palaeodemography in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190707. [PMID: 33250019 DOI: 10.1098/rstb.2019.0707] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jennifer C French
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Philip Riris
- Institute for the Modelling of Socio-Environmental Transitions, Bournemouth University, Poole, UK
| | | | | | - Fabio Silva
- Institute for the Modelling of Socio-Environmental Transitions, Bournemouth University, Poole, UK
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5
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Lall GM, Larmuseau MHD, Wetton JH, Batini C, Hallast P, Huszar TI, Zadik D, Aase S, Baker T, Balaresque P, Bodmer W, Børglum AD, de Knijff P, Dunn H, Harding SE, Løvvik H, Dupuy BM, Pamjav H, Tillmar AO, Tomaszewski M, Tyler-Smith C, Verdugo MP, Winney B, Vohra P, Story J, King TE, Jobling MA. Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain. Eur J Hum Genet 2020; 29:512-523. [PMID: 33139852 PMCID: PMC7940619 DOI: 10.1038/s41431-020-00747-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/08/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.
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Affiliation(s)
| | - Maarten H D Larmuseau
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.,Laboratory of Socioecology and Social Evolution, KU Leuven-University of Leuven, Leuven, Belgium.,Histories vzw, Zoutwerf 5, 2800, Mechelen, Belgium
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Pille Hallast
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Tunde I Huszar
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Daniel Zadik
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | | | - Tina Baker
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Patricia Balaresque
- UMR5288, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | - Walter Bodmer
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anders D Børglum
- Department of Biomedicine & Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hayley Dunn
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK.,Museum of Cultural History, University of Oslo, Oslo, Norway
| | | | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
| | - Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | | | - Marta Pereira Verdugo
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, UK
| | - Pragya Vohra
- School of History, Politics and International Relations, University of Leicester, Leicester, UK.,Department of History, University of York, Heslington, York, UK
| | - Joanna Story
- School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Turi E King
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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6
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Hakim HM, Khan HO, Lalung J, Nelson BR, Chambers GK, Edinur HA. Autosomal STR Profiling and Databanking in Malaysia: Current Status and Future Prospects. Genes (Basel) 2020; 11:genes11101112. [PMID: 32977385 PMCID: PMC7597947 DOI: 10.3390/genes11101112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
Science and technology are extensively used in criminal investigation. From the mid- to late-1980s, one of the scientific discoveries that has had a particularly remarkable impact on this field has been the use of highly variable DNA sequence regions (minisatellites) in the human genome for individual identification. The technique was initially referred to as DNA fingerprinting, but is now more widely referred to as DNA profiling. Since then, many new developments have occurred within this area of science. These include the introduction of new genetic markers (microsatellites also known as short tandem repeats/STRs), the use of the polymerase chain reaction for target amplification, the development of DNA databases (databanking), and the advancement and/or improvement of genotyping protocols and technologies. In 2019, we described the progress of DNA profiling and DNA databanking in Malaysia for the first time. This report included information on DNA analysis regulations and legislation, STR genotyping protocols, database management, and accreditation status. Here, we provide an update on the performance of our DNA databank (numbers of DNA profiles and hits) plus the technical issues associated with correctly assigning the weight of evidence for DNA profiles in an ethnically diverse population, and the potential application of rapid DNA testing in the country. A total of 116,534 DNA profiles were obtained and stored in the Forensic DNA Databank of Malaysia (FDDM) by 2019, having increased from 70,570 in 2017. The number of hits increased by more than three-fold in just two years, where 17 and 69 hits between the DNA profiles stored in the FDDM and those from crime scenes, suspects, detainees, drug users, convicts, missing persons, or volunteers were recorded in 2017 and 2019, respectively. Forensic DNA analysis and databanking are thus progressing well in Malaysia and have already contributed to many criminal investigations. However, several other issues are discussed here, including the need for STR population data for uncharacterized population groups, and pilot trials for adopting rapid DNA profiling technology. These aspects should be considered by policy makers and law enforcement agencies in order to increase the reliability and efficiency of DNA profiling in criminal cases and in kinship analysis in Malaysia.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, Cheras 43200, Selangor, Malaysia;
- School of Industrial Technology, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia;
- Correspondence: (H.M.H.); (H.A.E.)
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, Cheras 43200, Selangor, Malaysia;
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia;
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia;
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand;
| | - Hisham Atan Edinur
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia;
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
- Correspondence: (H.M.H.); (H.A.E.)
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7
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Abstract
We combine methodology from history and genetics to reconstruct the biosocial history of antimicrobial resistance (AMR) in the bacterium Salmonella enterica serovar Typhi (S. Typhi). We show how evolutionary divergence in S. Typhi was driven by rising global antibiotic use and by the neglect of typhoid outside of high-income countries. Although high-income countries pioneered 1960s precautionary antibiotic regulations to prevent selection for multidrug resistance, new antibiotic classes, typhoid's cultural status as a supposedly ancient disease of "undeveloped" countries, limited international funding, and narrow biosecurity agendas helped fragment effective global collective action for typhoid control. Antibiotic-intensive compensation for weak water and healthcare systems subsequently fueled AMR selection in low- and middle-income countries but often remained invisible due to lacking surveillance capabilities. The recent rise of extensively drug-resistant typhoid bears the biosocial footprint of more than half a century of antibiotic-intensive international neglect.
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Affiliation(s)
- Claas Kirchhelle
- Wellcome Unit for the History of Medicine/Oxford Martin School, University of Oxford, Addenbrooke’s Hospital, United Kingdom
| | - Zoe Anne Dyson
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
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8
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Mendisco F, Pemonge MH, Romon T, Lafleur G, Richard G, Courtaud P, Deguilloux MF. Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y-chromosome lineages in the Guadeloupe archipelago. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 170:507-518. [PMID: 31599974 DOI: 10.1002/ajpa.23931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 08/22/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The history of the Caribbean region is marked by numerous and various successive migration waves that resulted in a global blending of African, European, and Amerindian lineages. As the origin and genetic composition of the current population of French Caribbean islands has not been studied to date, we used both mitochondrial DNA and Y-chromosome markers to complete the characterization of the dynamics of admixture in the Guadeloupe archipelago. MATERIALS AND METHODS We sequenced the mitochondrial hypervariable regions and genotyped mitochondrial and Y-chromosomal single nucleotide polymorphisms (SNPs) of 198 individuals from five localities of the Guadeloupe archipelago. RESULTS The maternal haplogroups revealed a blend of 85% African lineages (mainly traced to Western, West-Central, and South-Eastern Africa), 12.5% Eurasian lineages, and 0.5% Amerindian lineages. We highlighted disequilibria between European paternal contribution (44%) and European maternal contribution (7%), pointing out an important sexual asymmetry. Finally, the estimated Native American component was strikingly low and supported the near-extinction of native lineages in the region. DISCUSSION We confirmed that all historically known migratory events indeed left a visible genetic imprint in the contemporary Caribbean populations. The data gathered clearly demonstrated the significant impact of the transatlantic slave trade on the Guadeloupean population's constitution. Altogether, the data in our study confirm that in the Caribbean region, human population variation is correlated with colonial and postcolonial policies and unique island histories.
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Affiliation(s)
- Fanny Mendisco
- University of Bordeaux, UMR 5199 PACEA, Allée Geoffroy de St Hilaire, Pessac, France
| | - Marie-Hélène Pemonge
- University of Bordeaux, UMR 5199 PACEA, Allée Geoffroy de St Hilaire, Pessac, France
| | - Thomas Romon
- University of Bordeaux, UMR 5199 PACEA, Allée Geoffroy de St Hilaire, Pessac, France.,Centre de Gourbeyre, Institut National de Recherches Archéologiques Préventives Guadeloupe, Gourbeyre, France
| | - Gérard Lafleur
- Archives Départementales de la Guadeloupe, Société D'histoire de la Guadeloupe, Basse-Terre, France
| | - Gérard Richard
- Centre de Gourbeyre, Institut National de Recherches Archéologiques Préventives Guadeloupe, Gourbeyre, France
| | - Patrice Courtaud
- University of Bordeaux, UMR 5199 PACEA, Allée Geoffroy de St Hilaire, Pessac, France
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9
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The Dutch Y-chromosomal landscape. Eur J Hum Genet 2019; 28:287-299. [PMID: 31488894 PMCID: PMC7029002 DOI: 10.1038/s41431-019-0496-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 12/05/2022] Open
Abstract
Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic–geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.
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10
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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11
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Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species. Heredity (Edinb) 2018; 122:53-68. [PMID: 29720718 DOI: 10.1038/s41437-018-0077-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/08/2018] [Accepted: 03/17/2018] [Indexed: 01/26/2023] Open
Abstract
Understanding how dispersal and gene flow link geographically separated the populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n = 1327) and nuclear markers (17 microsatellite loci, n = 222) from major wintering grounds to investigate circumpolar population structure, historical demography and effective population size. Analyses of nuclear genetic variation identify two population clusters that correspond to the South Atlantic and Indo-Pacific ocean basins that have similar effective breeder estimates. In contrast, all wintering grounds show significant differentiation for mtDNA, but no sex-biased dispersal was detected using the microsatellite genotypes. An approximate Bayesian computation (ABC) approach with microsatellite markers compared the scenarios with gene flow through time, or isolation and secondary contact between ocean basins, while modelling declines in abundance linked to whaling. Secondary-contact scenarios yield the highest posterior probabilities, implying that populations in different ocean basins were largely isolated and came into secondary contact within the last 25,000 years, but the role of whaling in changes in genetic diversity and gene flow over recent generations could not be resolved. We hypothesise that these findings are driven by factors that promote isolation, such as female philopatry, and factors that could promote dispersal, such as oceanographic changes. These findings highlight the application of ABC approaches to infer the connectivity in mobile species with complex population histories and, currently, low levels of differentiation.
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12
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Tian L, Khan A, Ning Z, Yuan K, Zhang C, Lou H, Yuan Y, Xu S. Genome-wide comparison of allele-specific gene expression between African and European populations. Hum Mol Genet 2018; 27:1067-1077. [DOI: 10.1093/hmg/ddy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lei Tian
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Asifullah Khan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200 KP, Pakistan
| | - Zhilin Ning
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyi Lou
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Yuan Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
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13
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Larmuseau MHD, Calafell F, Princen SA, Decorte R, Soen V. The black legend on the Spanish presence in the low countries: Verifying shared beliefs on genetic ancestry. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:219-227. [PMID: 29327450 DOI: 10.1002/ajpa.23409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/28/2017] [Accepted: 01/01/2018] [Indexed: 11/08/2022]
Abstract
OBJECTIVES War atrocities committed by the Spanish army in the Low Countries during the 16th century are so ingrained in the collective memory of Belgian and Dutch societies that they generally assume a signature of this history to be present in their genetic ancestry. Historians claim this assumption is a consequence of the so-called "Black Legend" and negative propaganda portraying and remembering Spanish soldiers as extreme sexual aggressors. The impact of the presence of Spaniards during the Dutch Revolt on the genetic variation in the Low Countries has been verified in this study. MATERIALS AND METHODS A recent population genetic analysis of Iberian-associated Y-chromosomal variation among Europe is enlarged with representative samples of Dutch (N = 250) and Flemish (N = 1,087) males. Frequencies of these variants are also compared between donors whose oldest reported paternal ancestors lived in-nowadays Flemish-cities affected by so-called Spanish Furies (N = 116) versus other patrilineages in current Flemish territory (N = 971). RESULTS The frequencies of Y-chromosomal markers Z195 and SRY2627 decline steeply going north from Spain and the data for the Flemish and Dutch populations fits within this pattern. No trend of higher frequencies of these variants has been found within the well-ascertained samples associated with Spanish Fury cities. DISCUSSION Although sexual aggression did occur in the 16th century, these activities did not leave a traceable "Spanish" genetic signature in the autochthonous genome of the Low Countries. Our results support the view that the 'Black Legend' and historical propaganda on sexual aggression have nurtured today's incorrect assumptions regarding genetic ancestry.
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Affiliation(s)
- Maarten H D Larmuseau
- Department of Forensic Biomedical Sciences, Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Sarah A Princen
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Department of Forensic Biomedical Sciences, Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium
| | - Violet Soen
- Early Modern History (15th-18th Centuries), Faculty of Arts, KU Leuven, Leuven, Belgium
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14
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Skowronek MF, Velazquez T, Mut P, Figueiro G, Sans M, Bertoni B, Sapiro R. Associations between male infertility and ancestry in South Americans: a case control study. BMC MEDICAL GENETICS 2017; 18:78. [PMID: 28747152 PMCID: PMC5530489 DOI: 10.1186/s12881-017-0438-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/13/2017] [Indexed: 01/20/2023]
Affiliation(s)
| | - Tatiana Velazquez
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Patricia Mut
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Gonzalo Figueiro
- Departamento de Antropología, Facultad de Humanidades y Ciencias de la Educación, UDELAR, Montevideo, Uruguay
| | - Monica Sans
- Departamento de Antropología, Facultad de Humanidades y Ciencias de la Educación, UDELAR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina UDELAR, Montevideo, Uruguay.
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15
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Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity. Sci Rep 2017; 7:6193. [PMID: 28733587 PMCID: PMC5522469 DOI: 10.1038/s41598-017-05673-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000–5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the ‘local’ Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the ‘immigrant’ haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.
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16
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Nothnagel M, Fan G, Guo F, He Y, Hou Y, Hu S, Huang J, Jiang X, Kim W, Kim K, Li C, Li H, Li L, Li S, Li Z, Liang W, Liu C, Lu D, Luo H, Nie S, Shi M, Sun H, Tang J, Wang L, Wang CC, Wang D, Wen SQ, Wu H, Wu W, Xing J, Yan J, Yan S, Yao H, Ye Y, Yun L, Zeng Z, Zha L, Zhang S, Zheng X, Willuweit S, Roewer L. Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes. Hum Genet 2017; 136:485-497. [PMID: 28138773 DOI: 10.1007/s00439-017-1759-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023]
Abstract
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.
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Affiliation(s)
- Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany.
| | - Guangyao Fan
- Department of Public Security Technology, The Center for Forensic Science Research, Railway Police College, Zhengzhou, 450053, People's Republic of China
| | - Fei Guo
- Department of Forensic Medicine, National Police University of China, Shenyang, 110854, People's Republic of China
| | - Yongfeng He
- Department of Criminal Investigation, Shaanxi Provincial Public Security Bureau, Xi'an, 710016, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, People's Republic of China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Beijing Road, 9th, Guiyang, 550004, People's Republic of China
| | - Xianhua Jiang
- Liaoning Criminal and Science Technology Research Institute, Shenyang, 110032, People's Republic of China
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Kicheol Kim
- Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Liming Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Zhao Li
- Department of Criminal Investigation, Hebei Provincial Public Security Bureau, Shijiazhuang City, 050000, People's Republic of China
| | - Weibo Liang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, 510030, People's Republic of China
| | - Di Lu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Haibo Luo
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Meisen Shi
- Center of Cooperative Innovation for Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Ministry of Education, Beijing, 100088, People's Republic of China
| | - Hongyu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510089, People's Republic of China
| | - Jianpin Tang
- Department of Forensic Medicine, Guangdong Medical University, Dongguan, 523808, People's Republic of China
| | - Lei Wang
- Department of Forensic Sciences, Police Station of Zhengzhou, Zhengzhou, Henan, 450008, People's Republic of China
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongyan Wu
- Xinxiang Medical University School of Basic Medical, Xinxiang, Henan, 453003, People's Republic of China
| | - Weiwei Wu
- Institute of Forensic Science, Zhejiang Provincial Public Security Bureau, Hangzhou, 310009, People's Republic of China
| | - Jiaxin Xing
- School of Forensic Medicine, China Medical University, Shenyang, People's Republic of China
| | - Jiangwei Yan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shi Yan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongbing Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, 730070, People's Republic of China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Zhaoshu Zeng
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, People's Republic of China
| | - Lagabaiyila Zha
- Forensic Science Department, School of Basic Medical Sciences, Central South University, Changsha, 410013, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Xiufen Zheng
- Department of Pathology, Department of Surgery, Department of Oncology, University of Western Ontario, Lawson Health Research Institute, London, Canada
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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17
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Amorim CEG, Hofer T, Ray N, Foll M, Ruiz-Linares A, Excoffier L. Long-distance dispersal suppresses introgression of local alleles during range expansions. Heredity (Edinb) 2017; 118:135-142. [PMID: 27577693 PMCID: PMC5234476 DOI: 10.1038/hdy.2016.68] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 12/24/2022] Open
Abstract
During range expansions, even low levels of interbreeding can lead to massive introgression of local alleles into an invader's genome. Nonetheless, this pattern is not always observed in human populations. For instance, European Americans in North America are barely introgressed by Amerindian genes in spite of known contact and admixture. With coalescent spatially explicit simulations, we examined the impact of long-distance dispersal (LDD) events on introgression of local alleles into the invading population using a set of different demographic scenarios applicable to a diverse range of natural populations and species. More specifically, we consider two distinct LDD models: one where LDD events originate in the range core and targets only the expansion front and a second one where LDD events can occur from any area to any other. We find that LDD generally prevents introgression, but that LDD events specifically targeting the expansion front are most efficient in suppressing introgression. This is likely due to the fact that LDD allows for the presence of a larger number of invader alleles at the wave front, where effective population size is thus increased and local introgressed alleles are rapidly outnumbered. We postulate that the documented settlement of pioneers directly on the wave front in North America has contributed to low levels of Amerindian admixture observed in European Americans and that this phenomenon may well explain the lack of introgression after a range expansion in natural populations without the need to evoke other mechanisms such as natural selection.
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Affiliation(s)
- C E G Amorim
- Department of Biological Sciences,
Columbia University, New York, NY,
USA
- CAPES Foundation, Ministry of
Education of Brazil, Brasília, Distrito
Federal, Brazil
| | - T Hofer
- Computational and Molecular
Population Genetics Lab, Institute of Ecology and Evolution, University of
Bern, Bern, Switzerland
- Swiss Institute of
Bioinformatics, Lausanne, Switzerland
| | - N Ray
- EnviroSPACE Laboratory, Institute for
Environmental Sciences, University of Geneva, Geneva,
Switzerland
| | - M Foll
- Genetic Cancer Susceptibility Group,
International Agency for Research on Cancer, Lyon,
France
| | - A Ruiz-Linares
- Department of Genetics, Evolution and
Environment, University College London, London,
UK
| | - L Excoffier
- Computational and Molecular
Population Genetics Lab, Institute of Ecology and Evolution, University of
Bern, Bern, Switzerland
- Swiss Institute of
Bioinformatics, Lausanne, Switzerland
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18
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The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 2016; 136:559-573. [DOI: 10.1007/s00439-016-1740-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
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19
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Cultural differentiation does not entail group-level structure: The case for geographically explicit analysis. Behav Brain Sci 2016; 39:e49. [PMID: 27562351 DOI: 10.1017/s0140525x15000217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Richerson et al. argue that relatively large cultural F ST values provide evidence for group structure and therefore scope for group selection. However, recent research on spatial patterns of cultural variation demonstrates that, as in the genetic case, apparent group structure can be a consequence of geographic clines, not group barriers. Such a pattern limits the scope for cultural group selection.
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20
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Schregel J, Eiken HG, Grøndahl FA, Hailer F, Aspi J, Kojola I, Tirronen K, Danilov P, Rykov A, Poroshin E, Janke A, Swenson JE, Hagen SB. Y chromosome haplotype distribution of brown bears (Ursus arctos
) in Northern Europe provides insight into population history and recovery. Mol Ecol 2015; 24:6041-60. [DOI: 10.1111/mec.13448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/17/2015] [Accepted: 10/26/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
| | | | - Frank Hailer
- School of Biosciences; Cardiff University; Cardiff CF10 3AX Wales UK
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Jouni Aspi
- Department of Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Ilpo Kojola
- Natural Resources Institute; P.O. Box 16 96301 Rovaniemi Finland
| | - Konstantin Tirronen
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Piotr Danilov
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Alexander Rykov
- Pinezhsky Strict Nature Reserve; Pervomayskaja 123a 164610 Pinega Russian Federation
| | - Eugene Poroshin
- Institute of Biology; Komi Research Centre of the Russian Academy of Science; 016761 Syktvkar Russian Federation
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
- Goethe University Frankfurt; Institute for Ecology; Evolution & Diversity; 60438 Frankfurt am Main Germany
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
- Norwegian Institute for Nature Research; 7485 Trondheim Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
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21
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Edwards SV, Shultz AJ, Campbell-Staton SC. Next-generation sequencing and the expanding domain of phylogeography. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a2.2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Shane C. Campbell-Staton
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
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22
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Larmuseau MHD, Boon N, Vanderheyden N, Van Geystelen A, Larmuseau HFM, Matthys K, De Clercq W, Decorte R. High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment. Heredity (Edinb) 2015; 115:3-12. [PMID: 25873146 DOI: 10.1038/hdy.2015.5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/20/2014] [Accepted: 12/23/2014] [Indexed: 01/02/2023] Open
Abstract
There is limited knowledge on the biological relatedness between citizens and on the demographical dynamics within villages, towns and cities in pre-17th century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it is possible to provide insights into the genetic diversity and the relatedness between indigenous paternal lineages within a particular community at the time of the surname adoption. To obtain these insights, six Flemish communities were selected in this study based on the differences in geography and historical development. After rigorous selection of appropriate DNA donors, low relatedness between Y chromosomes of different surnames was found within each community, although there is co-occurrence of these surnames in each community since the start of the surname adoption between the 14th and 15th century. Next, the high communal diversity in Y-chromosomal lineages was comparable with the regional diversity across Flanders at that time. Moreover, clinal distributions of particular Y-chromosomal lineages between the communities were observed according to the clinal distributions earlier observed across the Flemish regions and Western Europe. No significant indication for genetic differences between communities with distinct historical development was found in the analysis. These genetic results provide relevant information for studies in historical sciences, archaeology, forensic genetics and genealogy.
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Affiliation(s)
- M H D Larmuseau
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium [3] Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - N Boon
- 1] Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium [2] Institute of Tropical Medicine, Antwerp, Belgium
| | - N Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - A Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - H F M Larmuseau
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - K Matthys
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - W De Clercq
- Faculty of Arts and Philosophy, Department of Archaeology, Ghent University, Ghent, Belgium
| | - R Decorte
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
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23
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Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. INVESTIGATIVE GENETICS 2014; 5:13. [PMID: 25254093 PMCID: PMC4174254 DOI: 10.1186/2041-2223-5-13] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 02/07/2023]
Abstract
Background Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. Results We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. Conclusions The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
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Affiliation(s)
- Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Hongyang Xu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Department of Computational Genetics, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Albert Ko
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Fondation Mérieux, 17 rue Bourgelat, Lyon 69002, France
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig D04103, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
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Traces of medieval migrations in a socially stratified population from Northern Italy. Evidence from uniparental markers and deep-rooted pedigrees. Heredity (Edinb) 2014; 114:155-62. [PMID: 25204305 DOI: 10.1038/hdy.2014.77] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 02/03/2023] Open
Abstract
Social and cultural factors had a critical role in determining the genetic structure of Europe. Therefore, socially stratified populations may help to focus on specific episodes of European demographic history. In this study, we use uniparental markers to analyse the genetic structure of Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar institution whose origins date back to the Middle Ages and whose members form the patrilineal descent of a group of founder families. From a maternal point of view (mtDNA), Partecipanza is genetically homogeneous with the rest of the population. However, we observed a significant differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR profiles with deep-rooted paternal pedigrees, we estimated a Y-STR mutation rate equal to 3.90 * 10(-3) mutations per STR per generation and an average generation duration time of 33.38 years. When we used these values for tentative dating, we estimated 1300-600 years ago for the origins of the Partecipanza. These results, together with a peculiar Y-chromosomal composition and historical evidence, suggest that Germanic populations (Lombards in particular) settled in the area during the Migration Period (400-800 AD, approximately) and may have had an important role in the foundation of this community.
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Alvarez L, Ciria E, Marques SL, Santos C, Aluja MP. Y-chromosome analysis in a Northwest Iberian population: unraveling the impact of Northern African lineages. Am J Hum Biol 2014; 26:740-6. [PMID: 25123837 DOI: 10.1002/ajhb.22602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 06/03/2014] [Accepted: 06/15/2014] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES To provide new clues about the genetic origin, composition and structure of the population of the Spanish province of Zamora, with an emphasis on the genetic impact of the period of Islamic rule in the Iberian Peninsula. METHODS Polymorphisms in the paternally inherited Y-chromosome, Single Nucleotide Polymorphisms and Short Tandem Repeats, were analyzed in 235 unrelated males born in six different regions in the Zamora province. RESULTS A relatively homogenous Y-chromosome haplogroup composition was observed in the Zamora province. Haplogroups R1b1-P25 and I-M170, widespread in European populations, accounted for 64.9% of the total sample. Moreover, all of the observed African lineages, accounting for 10.2% of the total variability, belonged to haplogroups having Northwest African origin (E1b1b1b-M81, E1b1b1a-β-M78, and J1-M267). CONCLUSIONS No differences between regions or sub-structure due to geographical boundaries were detected. The specific Northwest African male lineages observed contrast with the mitochondrial DNA data, where the majority of African lineages were found to be sub-Saharan. This work made it possible to study the impact of recent historical events in the male gene pool in the province of Zamora in Spain.
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Affiliation(s)
- Luis Alvarez
- Unitat Antropologia Biològica, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, 4200-465, Porto, Portugal
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Pardiñas AF, Martínez JL, Roca A, García-Vazquez E, López B. Over the sands and far away: interpreting an Iberian mitochondrial lineage with ancient Western African origins. Am J Hum Biol 2014; 26:777-83. [PMID: 25130626 DOI: 10.1002/ajhb.22601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 07/11/2014] [Accepted: 07/17/2014] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES There is an ongoing effort to characterize the genetic links between Africa and Europe, mostly using lineages and haplotypes that are specific to one continent but had an ancient origin in the other. Mitochondrial DNA has been proven to be a very useful tool for this purpose since a high number of putatively European-specific variants of the African L* lineages have been defined over the years. Due to their geographic locations, Spain and Portugal seem to be ideal places for searching for these lineages. METHODS Five members of a minor branch of haplogroup L3f were found in recent DNA samplings in the region of Asturias (Northern Spain), which is known for its historical isolation. The frequency of L3f in this population (≈1%) is unexpectedly high in comparison with other related lineages in Europe. Complete mitochondrial DNA sequencing of these L3f lineages, as well phylogenetic and phylogeographic comparative analyses have been performed. RESULTS The L3f variant found in Asturias seems to constitute an Iberian-specific haplogroup, distantly related to lineages in Northern Africa and with a deep ancestry in Western Africa. Coalescent algorithms estimate the minimum arrival time as 8,000 years ago, and a possible route through the Gibraltar Strait. CONCLUSIONS Results are concordant with a previously proposed Neolithic connection between Southern Europe and Western Africa, which might be key to the proper understanding of the ancient links between these two continents.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, 33071, Spain
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Veeramah KR, Novembre J. Demographic events and evolutionary forces shaping European genetic diversity. Cold Spring Harb Perspect Biol 2014; 6:a008516. [PMID: 25059709 PMCID: PMC4142961 DOI: 10.1101/cshperspect.a008516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
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Natural Selection on Human Y Chromosomes. J Genet Genomics 2014; 41:47-52. [DOI: 10.1016/j.jgg.2014.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 01/23/2014] [Accepted: 01/23/2014] [Indexed: 12/24/2022]
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The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. Eur J Hum Genet 2014; 22:1111-6. [PMID: 24448544 DOI: 10.1038/ejhg.2013.303] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/21/2013] [Accepted: 11/27/2013] [Indexed: 12/29/2022] Open
Abstract
Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338,000 years ago (95% CI=237,000-581,000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100,000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208,300 (95% CI=163,900-260,200) years ago.
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Wilson Sayres MA, Lohmueller KE, Nielsen R. Natural selection reduced diversity on human y chromosomes. PLoS Genet 2014; 10:e1004064. [PMID: 24415951 PMCID: PMC3886894 DOI: 10.1371/journal.pgen.1004064] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 11/12/2013] [Indexed: 01/11/2023] Open
Abstract
The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area. The human Y chromosome is found only in males, and exhibits surprisingly low levels of genetic diversity. This low diversity could result from neutral processes, for example, if there are fewer males successfully mating (and thus fewer Y chromosomes being inherited) relative to the number of females who successfully mate. Alternatively, natural selection may act on mutations on the Y chromosome to reduce genetic diversity. Because there is no recombination across most of the Y chromosome all sites on the Y are effectively linked together. Thus, selection acting on any one site will affect all sites on the Y indirectly. Here, studying the X, Y, autosomal and mitochondrial DNA, in combination with population genetic simulations, we show that low observed Y chromosome variability is consistent with models of purifying selection removing deleterious mutations and linked variation, although positive selection may also be acting. We further infer that the number of sites affected by selection likely includes some proportion of the highly repetitive ampliconic regions on the Y. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.
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Affiliation(s)
- Melissa A. Wilson Sayres
- Statistics Department, University of California-Berkeley, Berkeley, California, United States of America
- Integrative Biology Department, University of California-Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Kirk E. Lohmueller
- Integrative Biology Department, University of California-Berkeley, Berkeley, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rasmus Nielsen
- Statistics Department, University of California-Berkeley, Berkeley, California, United States of America
- Integrative Biology Department, University of California-Berkeley, Berkeley, California, United States of America
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Pardiñas AF, Roca A, García-Vazquez E, López B. Evaluation of large-scale genetic structure in complex demographic and historical scenarios: the mitochondrial DNA and Y-chromosome pools of the Iberian Atlantic façade. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 153:617-26. [PMID: 24375152 DOI: 10.1002/ajpa.22461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 12/12/2013] [Indexed: 11/11/2022]
Abstract
Genetic structural patterns of human populations are usually a combination of long-term evolutionary forces and short-term social, cultural, and demographic processes. Recently, using mitochondrial DNA and Y-chromosome loci, various studies in northern Spain have found evidence that the geographical distribution of Iron Age tribal peoples might have influenced current patterns of genetic structuring in several autochthonous populations. Using the wealth of data that are currently available from the whole territory of the Iberian Peninsula, we have evaluated its genetic structuring in the spatial scale of the Atlantic façade. Hierarchical tree modeling procedures, combined with a classic analysis of molecular variance (AMOVA), were used to model known sociocultural divisions from the third century BCE to the eighth century CE, contrasting them with uniparental marker data. Our results show that, while mountainous and abrupt areas of the Iberian North bear the signals of long-term isolation in their maternal and paternal gene pools, the makeup of the Atlantic façade as a whole can be related to tribal population groups that predate the Roman conquest of the Peninsula. The maintenance through time of such a structure can be related to the numerous geographic barriers of the Iberian mainland, which have historically conditioned its settlement patterns and the occurrence of genetic drift processes.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
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Santos C, Fregel R, Cabrera VM, Álvarez L, Larruga JM, Ramos A, López MA, Pilar Aluja M, González AM. Mitochondrial DNA and Y-chromosome structure at the mediterranean and atlantic façades of the iberian peninsula. Am J Hum Biol 2013; 26:130-41. [DOI: 10.1002/ajhb.22497] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/31/2013] [Accepted: 12/07/2013] [Indexed: 01/24/2023] Open
Affiliation(s)
- Cristina Santos
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Rosa Fregel
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
| | - Vicente M. Cabrera
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
| | - Luis Álvarez
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
- IPATIMUP; Institute of Molecular Pathology and Immunology of the University of Porto; 4200-465 Porto Portugal
| | - Jose M. Larruga
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
| | - Amanda Ramos
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
- Centre of Research in Natural Resources (CIRN), Department of Biology; University of the Azores; 9500-321 Ponta Delgada Portugal
- Molecular and Cellular Biology Institute (IBMC); University of Porto; 4150-180 Porto Portugal
| | - Miguel A. López
- Clinical Management and Biotechnology Unit; Torre Cárdena Hospital; 04008 Almería Spain
| | - María Pilar Aluja
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Ana M. González
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
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Berger B, Niederstätter H, Erhart D, Gassner C, Schennach H, Parson W. Reprint of: High resolution mapping of Y haplogroup G in Tyrol (Austria). Forensic Sci Int Genet 2013; 7:624-631. [DOI: 10.1016/j.fsigen.2013.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
This review aims to explore the relationship between anthropology and genetics, an intellectual zone that has been occupied in different ways over the past century. One way to think about it is to contrast a classical “anthropological genetics” ( Roberts 1965 ), that is to say, a genetics that presumably informs anthropological issues or questions, with a “genomic anthropology” ( Pálsson 2008 ), that is to say, an anthropology that complements and relativizes modern genomics (on the model of, say, medical anthropology and legal anthropology). 1 This review argues that a principal contribution of anthropology to the study of human heredity lies in the ontology of genetic facts. For anthropology, genetic facts are not natural, with meanings inscribed on them, but are instead natural/cultural: The natural facts have cultural information (values, ideologies, meanings) integrated into them, not layered on them. To understand genetic facts involves confronting their production, which has classically been restricted to questions of methodology but which may be conceptualized more broadly. This review is not intended as a critique of the field of anthropological genetics, but as a reformulation of its central objects of study. I argue for reconceptualizing the ontology of scientific facts in anthropological genetics, not as (value-neutral) biological facts situated in a cultural context, but instead as inherently biocultural facts.
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Affiliation(s)
- Jonathan Marks
- Department of Anthropology, University of North Carolina, Charlotte, North Carolina 28223
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Olivieri A, Pala M, Gandini F, Hooshiar Kashani B, Perego UA, Woodward SR, Grugni V, Battaglia V, Semino O, Achilli A, Richards MB, Torroni A. Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the near east and neolithic dispersals within Europe. PLoS One 2013; 8:e70492. [PMID: 23936216 PMCID: PMC3729697 DOI: 10.1371/journal.pone.0070492] [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: 03/19/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie L. Spallanzani, Università di Pavia, Pavia, Italy.
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Berger B, Niederstätter H, Erhart D, Gassner C, Schennach H, Parson W. High resolution mapping of Y haplogroup G in Tyrol (Austria). Forensic Sci Int Genet 2013; 7:529-36. [PMID: 23948323 DOI: 10.1016/j.fsigen.2013.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/08/2013] [Accepted: 05/30/2013] [Indexed: 01/10/2023]
Abstract
The distribution of Y-chromosomal haplogroup G2a (G-P15) in present-day paternal lineages in Tyrol (Austria) was analyzed by applying a high-density regional sampling scheme that also covered remote mountain areas. There is evidence from ancient genetic data for a high frequency of Y-chromosomal haplogroup G in prehistoric populations of Central Europe, whilst nowadays levels well below 10% are routinely observed. A population sample comprising ∼3700 specimens was analyzed for Y-chromosomal variation by genotyping Y-SNPs and Y-STRs. The set of binary markers included nine SNPs specific for sub-lineages of haplogroup G. The frequency of haplogroup G in 2379 unrelated men born in Tyrol amounted to 11.3%. Nearly all of these Y chromosomes belonged to haplogroup G2a. The main sub-haplogroup within G2a was defined by the SNP L497 (G2a3b1c) and reached a population frequency of 8.6%. Although this average level is higher than reported for other countries the geographical distribution of haplogroup G-L497 showed a differentiated pattern with a clustered distribution within some alpine valleys, where maxima above 40% were found. Both, the estimation of coalescent times and a principle coordinates analysis based on RST values derived from Y-STR haplotypes from different sub-regions of Tyrol revealed evidence for an old settlement history associated with Y chromosomes belonging to haplogroup G in the Tyrolean Alps.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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Larmuseau MHD, Van Geystelen A, van Oven M, Decorte R. Genetic genealogy comes of age: perspectives on the use of deep-rooted pedigrees in human population genetics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:505-11. [PMID: 23440589 DOI: 10.1002/ajpa.22233] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 11/06/2022]
Abstract
In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies.
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Affiliation(s)
- M H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium.
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Hu R, Wang X, Zhan X. Multi-parameter systematic strategies for predictive, preventive and personalised medicine in cancer. EPMA J 2013; 4:2. [PMID: 23339750 PMCID: PMC3564825 DOI: 10.1186/1878-5085-4-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/09/2013] [Indexed: 12/11/2022]
Abstract
Cancer is a complex disease that causes the alterations in the levels of gene, RNA, protein and metabolite. With the development of genomics, transcriptomics, proteomics and metabolomic techniques, the characterisation of key mutations and molecular pathways responsible for tumour progression has led to the identification of a large number of potential targets. The increasing understanding of molecular carcinogenesis has begun to change paradigms in oncology from traditional single-factor strategy to multi-parameter systematic strategy. The therapeutic model of cancer has changed from adopting the general radiotherapy and chemotherapy to personalised strategy. The development of predictive, preventive and personalised medicine (PPPM) will allow prediction of response with substantially increased accuracy, stratification of particular patient groups and eventual personalisation of medicine. The PPPM will change the approach to tumour diseases from a systematic and comprehensive point of view in the future. Patients will be treated according to the specific molecular profiles that are found in the individual tumour tissue and preferentially with targeted substances, if available.
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Affiliation(s)
- Rong Hu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, People's Republic of China.
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Altmann DM, Balloux F, Boyton RJ. Diverse approaches to analysing the history of human and pathogen evolution: how to tell the story of the past 70 000 years. Philos Trans R Soc Lond B Biol Sci 2012; 367:765-9. [PMID: 22312043 DOI: 10.1098/rstb.2011.0318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The meeting 'Human evolution, migration and history revealed by genetics, immunity and infection', along with the follow-on satellite meeting at the Kavli Centre over the subsequent two days, brought together diverse talents. The aim was to see if new insights could be gained by bringing together those who have interests in the past 50-100 000 years of human history, overlaying the perspectives of palaeogeneticists, anthropologists, human geneticists, pathogen geneticists, immunologists, disease modellers, linguists, immunogeneticists, historians and archaeologists. It rapidly became clear that while all may agree on the broad brush-strokes including 'out-of-Africa' and the general approximations of timelines, diverse approaches may often suggest somewhat different ways of telling the story.
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Affiliation(s)
- D M Altmann
- Section of Infectious Diseases and Immunity, Department of Medicine, Imperial College, Hammersmith Hospital, London, UK.
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