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García-Fernández C, Lizano E, Telford M, Olalde Í, de Cid R, Larmuseau MHD, M. de Pancorbo M, Calafell F. Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition. Sci Rep 2022; 12:20708. [PMID: 36456614 PMCID: PMC9715704 DOI: 10.1038/s41598-022-25200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019-2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.
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Affiliation(s)
- Carla García-Fernández
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Esther Lizano
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marco Telford
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Íñigo Olalde
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Rafael de Cid
- grid.429186.00000 0004 1756 6852Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maarten H. D. Larmuseau
- grid.5596.f0000 0001 0668 7884Laboratory of Human Genetic Genealogy, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.5284.b0000 0001 0790 3681ARCHES–Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, Antwerp, Belgium ,Histories Vzw, Gent, Belgium
| | - Marian M. de Pancorbo
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
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Palencia-Madrid L, Baeta M, Kleinbielen T, Toro-Delgado N, Villaescusa P, Sanchez-Bustamante E, de Pancorbo MM, Luis JR, Ware KE, Somarelli JA, Garcia-Bertrand R, Herrera RJ. Post-Austronesian migrational wave of West Polynesians to Micronesia. Gene 2022; 823:146357. [PMID: 35189246 DOI: 10.1016/j.gene.2022.146357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
Abstract
This study examines Y-chromosome and mtDNA markers in the population of the island of Kiritimati in the context of geographically targeted reference populations from the Pacific. Kiritimati derives its population from the atoll islands of the Gilbert Archipelago and representsa geographicaltransitional region between Micronesia, Polynesia and Melanesia that likely played a critical role during theAustronesian expansion. The large presence(84.1%)of individuals withO-M175, O2a-M324 and O2a2b-P164 sub-haplogroups, 69.9% being O2a2b-P164, the Y-STR homogeneity within O2a2b-P164 and the very recent age of the sub-haplogroup(363-548 years ago)inKiritimati suggestthe arrival ofa genetically homogenous population to the Gilberteses followed by a population expassion.The close Y-STR haplotype affinities with profiles from the Samoa and Tonga Archipelagos point to an unprecedented massive post-Austronesian expansionexodus from West Polynesia.Contrasting the abundance of AustronesianO2a2b-P164 sub-haplogroup, the most abundantMelanesian/Papuansub-haplogroup,C-M130is present at a frequency of 13.5%. Thenetwork topology suggests that C-M130 arrived to theKiribati Archipelago from West Polynesia, specifically from West Samoa, Tonga and/or Tutuila subsequent to the Austronesian expansion about 832-1408 years ago. The haplotype affinities withinO2a2b-P164 argue for anoriginal source in Taiwan and its dispersal to West Polynesia and then to Southeast Micronesia. The present investigation provides an understanding of the genetic composition and complex migration history of an understudied region of the Pacific and provides evidence for recent dispersals towards Micronesia from West Polynesia subsequent to the initial Austronesian expansion.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Tamara Kleinbielen
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Nerea Toro-Delgado
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Elena Sanchez-Bustamante
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782 Santiago de Compostela, Spain
| | - Kathryn E Ware
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC 27710, USA
| | - Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC 27710, USA
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA.
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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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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Luis JR, Palencia-Madrid L, Mendoza VC, Garcia-Bertrand R, de Pancorbo MM, Herrera RJ. The Y chromosome of autochthonous Basque populations and the Bronze Age replacement. Sci Rep 2021; 11:5607. [PMID: 33692401 PMCID: PMC7970938 DOI: 10.1038/s41598-021-84915-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/19/2021] [Indexed: 11/09/2022] Open
Abstract
Here we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.
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Affiliation(s)
- Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Vivian C Mendoza
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA
| | | | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA.
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Villaescusa P, Seidel M, Nothnagel M, Pinotti T, González-Andrade F, Alvarez-Gila O, M de Pancorbo M, Roewer L. A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373. Forensic Sci Int Genet 2020; 51:102427. [PMID: 33254102 DOI: 10.1016/j.fsigen.2020.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (RST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.
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Affiliation(s)
- Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Oscar Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Zieger M, Utz S. The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration. Forensic Sci Int Genet 2020; 48:102345. [PMID: 32622325 DOI: 10.1016/j.fsigen.2020.102345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/09/2022]
Abstract
A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.
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Affiliation(s)
- Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular BiologyDpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular BiologyDpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
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8
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Villaescusa P, Blázquez P, Martínez-Jarreta B, Jiménez S, Álvarez-Gila O, de Pancorbo MM. The impact of haplogroup R1b-DF27 in Hispanic admixed populations from Latin America. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Ibarrondo O, Lopez-Oceja A, Baeta M, M de Pancorbo M. A Statistical Method to Enhance the Analysis of the Differences Among High-Resolution Melting (HRM) Curves of PCR-Amplified DNA Fragments. J Food Sci 2019; 84:2719-2728. [PMID: 31578715 DOI: 10.1111/1750-3841.14814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 11/30/2022]
Abstract
Consistent differences among melting curves of PCR-amplified DNA fragments are treated by normalizing the relative fluorescence units (RFU) and performing a clustering analysis, but statistically significant differences among curves are not usually determined. In the present study, an analysis based on functional data analysis (FDA) was implemented to evaluate the existence of statistically significant differences between normalized RFU curves obtained from PCR-HRM (high-resolution melting) analysis by using ANOVA for functional data. The effectiveness of the FDA method was analyzed with data from a set of samples of eight animal species of interest in food analysis, as well as mixtures of DNA from these species, analyzed by PCR-HRM to differentiate them. The statistical method described in this study has been demonstrated to be a robust and precise tool to discriminate among melting curves derived from HRM analysis. This method has advantages over the current comparison methods. PRACTICAL APPLICATION: As long as food fraud and mislabeling exist, new techniques for species identification are needed. High-resolution melting (HRM) has been shown to be a rapid, reliable and inexpensive species identification method. In the present study, functional data analysis (FDA) was applied to HRM curves of DNA from eight animal species used for food, as well as to mixtures of these species in different proportions. FDA has advantages over the usual methods, providing a deeper statistical analysis and facilitating the data interpretation as shown by the HRM analysis for a clearer comparison among individual species and mixtures of species.
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Affiliation(s)
- Oliver Ibarrondo
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| | - Andrés Lopez-Oceja
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| | - Miriam Baeta
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
| | - Marian M de Pancorbo
- BIOMICS Research Group, Univ. of the Basque Country, UPV/EHU, Vitoria-Gasteiz, 01006, Spain
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10
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Olalde I, Mallick S, Patterson N, Rohland N, Villalba-Mouco V, Silva M, Dulias K, Edwards CJ, Gandini F, Pala M, Soares P, Ferrando-Bernal M, Adamski N, Broomandkhoshbacht N, Cheronet O, Culleton BJ, Fernandes D, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zhang Z, Jiménez Arenas JM, Toro Moyano IJ, Salazar-García DC, Castanyer P, Santos M, Tremoleda J, Lozano M, García Borja P, Fernández-Eraso J, Mujika-Alustiza JA, Barroso C, Bermúdez FJ, Viguera Mínguez E, Burch J, Coromina N, Vivó D, Cebrià A, Fullola JM, García-Puchol O, Morales JI, Oms FX, Majó T, Vergès JM, Díaz-Carvajal A, Ollich-Castanyer I, López-Cachero FJ, Silva AM, Alonso-Fernández C, Delibes de Castro G, Jiménez Echevarría J, Moreno-Márquez A, Pascual Berlanga G, Ramos-García P, Ramos-Muñoz J, Vijande Vila E, Aguilella Arzo G, Esparza Arroyo Á, Lillios KT, Mack J, Velasco-Vázquez J, Waterman A, Benítez de Lugo Enrich L, Benito Sánchez M, Agustí B, Codina F, de Prado G, Estalrrich A, Fernández Flores Á, Finlayson C, Finlayson G, Finlayson S, Giles-Guzmán F, Rosas A, Barciela González V, García Atiénzar G, Hernández Pérez MS, Llanos A, Carrión Marco Y, Collado Beneyto I, López-Serrano D, Sanz Tormo M, Valera AC, Blasco C, Liesau C, Ríos P, Daura J, de Pedro Michó MJ, Diez-Castillo AA, Flores Fernández R, Francès Farré J, Garrido-Pena R, Gonçalves VS, Guerra-Doce E, Herrero-Corral AM, Juan-Cabanilles J, López-Reyes D, McClure SB, Merino Pérez M, Oliver Foix A, Sanz Borràs M, Sousa AC, Vidal Encinas JM, Kennett DJ, Richards MB, Werner Alt K, Haak W, Pinhasi R, Lalueza-Fox C, Reich D. The genomic history of the Iberian Peninsula over the past 8000 years. Science 2019; 363:1230-1234. [PMID: 30872528 DOI: 10.1126/science.aav4040] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Vanessa Villalba-Mouco
- Max Planck Institute for the Science of Human History, Jena, Germany.,Departamento de Ciencias de la Antigüedad, Grupo Primeros Pobladores del Valle del Ebro (PPVE), Instituto de Investigación en Ciencias Ambientales (IUCA), Universidad de Zaragoza, Zaragoza, Spain
| | - Marina Silva
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Ceiridwen J Edwards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Francesca Gandini
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Pedro Soares
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | | | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Brendan J Culleton
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra, Portugal
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Juan Manuel Jiménez Arenas
- Departamento de Prehistoria y Arqueología, Universidad de Granada, Granada, Spain.,Instituto Universitario de la Paz y los Conflictos, Universidad de Granada, Granada, Spain.,Department of Anthropology - Anthropologisches Institut and Museum, Universität Zürich, Zürich, Switzerland
| | | | - Domingo C Salazar-García
- Departamento de Geografía, Prehistoria y Arqueología, Grupo de Investigación en Prehistoria, (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Pere Castanyer
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | - Marta Santos
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | | | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Pablo García Borja
- Departamento de Prehistoria e Historia Antigua, Universidad Nacional de Educación a Distancia, Valencia, Spain
| | - Javier Fernández-Eraso
- Departamento de Geografía, Prehistoria y Arqueología, Universidad del País Vasco, Vitoria, Spain
| | | | - Cecilio Barroso
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | - Francisco J Bermúdez
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | | | - Josep Burch
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Neus Coromina
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - David Vivó
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Artur Cebrià
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Josep Maria Fullola
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Oreto García-Puchol
- PREMEDOC Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | - Juan Ignacio Morales
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - F Xavier Oms
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Tona Majó
- Archaeom. Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | | | | | - F Javier López-Cachero
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,UNIARQ, Faculdade de Letras, Universidade de Lisboa, Lisboa, Portugal.,CEF, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Germán Delibes de Castro
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | - Adolfo Moreno-Márquez
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain.,Departamento de Geografía, Historia y Humanidades, Universidad de Almería, Almería, Spain
| | | | | | - José Ramos-Muñoz
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Eduardo Vijande Vila
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Gustau Aguilella Arzo
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Ángel Esparza Arroyo
- GIR PrehUSAL, Departamento de Prehistoria, Historia Antigua y Arqueología, Universidad de Salamanca, Salamanca, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Jennifer Mack
- Office of the State Archaeologist, University of Iowa, Iowa City, IA, USA
| | - Javier Velasco-Vázquez
- Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | - Luis Benítez de Lugo Enrich
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain.,Departamento de Prehistoria y Arqueología, Universidad Nacional de Educación a Distancia, Madrid, Spain
| | - María Benito Sánchez
- Departamento de Medicina Legal, Psiquiatría y Anatomía Patológica, Universidad Complutense de Madrid, Madrid, Spain
| | - Bibiana Agustí
- INSITU S.C.P., Centelles, Spain.,Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | - Ferran Codina
- Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | | | - Almudena Estalrrich
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria IIIPC (Universidad de Cantabria-Gobierno de Cantabria-Santander), Santander, Spain
| | | | - Clive Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Anthropology, University of Toronto, Toronto, ON, Canada.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Geraldine Finlayson
- The Gibraltar National Museum, Gibraltar.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Stewart Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Life Sciences, Anglia Ruskin University, Cambridge, UK
| | | | - Antonio Rosas
- Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales (MNCN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Virginia Barciela González
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Gabriel García Atiénzar
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Mauro S Hernández Pérez
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | | | - Yolanda Carrión Marco
- Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | | | | | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Joan Daura
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | - Agustín A Diez-Castillo
- GRAM Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | - Rafael Garrido-Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | | | | | - Sarah B McClure
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Marta Merino Pérez
- Unitat d'Antropologia Física, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Arturo Oliver Foix
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Montserrat Sanz Borràs
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Douglas J Kennett
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Martin B Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Kurt Werner Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems, Austria.,Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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11
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Hernández CL, Dugoujon JM, Sánchez-Martínez LJ, Cuesta P, Novelletto A, Calderón R. Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world. Ann Hum Biol 2019; 46:63-76. [PMID: 30822152 DOI: 10.1080/03014460.2019.1587507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. AIM To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. SUBJECT AND METHODS Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. RESULTS Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. CONCLUSION The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
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Affiliation(s)
- Candela L Hernández
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Jean-Michel Dugoujon
- b CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS) , Université Paul Sabatier Toulouse III , Toulouse , France
| | - Luis J Sánchez-Martínez
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Pedro Cuesta
- c Centro de Proceso de Datos , Universidad Complutense , Madrid , Spain
| | | | - Rosario Calderón
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
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12
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Palencia-Madrid L, Baeta M, Villaescusa P, Nuñez C, de Pancorbo MM, Luis JR, Fadhlaoui-Zid K, Somarelli J, Garcia-Bertrand R, Herrera RJ. The Marquesans at the fringes of the Austronesian expansion. Eur J Hum Genet 2019; 27:801-810. [PMID: 30683925 DOI: 10.1038/s41431-019-0336-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 12/19/2018] [Accepted: 12/25/2018] [Indexed: 11/09/2022] Open
Abstract
In the present study, 87 unrelated individuals from the Marquesas Archipelago in French Polynesia were typed using mtDNA, Y-chromosome and autosomal (STRs) markers and compared to key target populations from Island South East Asia (ISEA), Taiwan, and West and East Polynesia to investigate their genetic relationships. The Marquesas, located at the eastern-most fringes of the Austronesian expansion, offer a unique opportunity to examine the effects of a protracted population expansion wave on population structure. We explore the contribution of Melanesian, Asian and European heritage to the Marquesan islands of Nuku-Hiva, Hiva-Oa and Tahuata. Overall, the Marquesas Islands are genetically homogeneous. In the Marquesan Archipelago all of the mtDNA haplogroups are of Austronesian origin belonging to the B4a1 subhaplogroup as the region marks the end of a west to east decreasing cline of Melanesian mtDNA starting with the West Polynesian population of Tonga. Genetic discrepancies are less pronounced between the Marquesan and Society islands, and among the Marquesan islands. Interestingly, a number of Melanesian, Polynesian and European Y-chromosome haplogroups exhibit very different distribution between the Marquesan islands of Nuku Hiva and Hiva Oa, likely resulting from drift, differential migration involving various source populations and/or unique trading routes.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Carolina Nuñez
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Karima Fadhlaoui-Zid
- Faculty of Science of Tunis, Laboratory of Genetics, Immunology, and Human Pathologies, University Tunis, El Manar, Tunis, Tunisia
| | - Jason Somarelli
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC, 27710, USA
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA.
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13
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Alonso Morales LA, Casas-Vargas A, Rojas Castro M, Resque R, Ribeiro-dos-Santos ÂK, Santos S, Gusmão L, Usaquén W. Paternal portrait of populations of the middle Magdalena River region (Tolima and Huila, Colombia): New insights on the peopling of Central America and northernmost South America. PLoS One 2018; 13:e0207130. [PMID: 30439976 PMCID: PMC6237345 DOI: 10.1371/journal.pone.0207130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 11/18/2022] Open
Abstract
The valley of the Magdalena River is one of the main population pathways in Colombia. The gene pool and spatial configuration of human groups in this territory have been outlined throughout three historical stages: the Native pre-Hispanic world, Spanish colonization, and XIX century migrations. This research was designed with the goal of characterizing the diversity and distribution pattern of Y-chromosome lineages that are currently present in the Tolima and Huila departments (middle Magdalena River region). Historic cartography was used to identify the main geographic sites where the paternal lineages belonging to this area have gathered. Twelve municipalities were chosen, and a survey that included genealogical information was administered. Samples collected from 83 male volunteers were analyzed for 48 Y-SNPs and 17 Y-STRs. The results showed a highly diverse region characterized by the presence of 16 sublineages within the major clades R, Q, J, G, T and E and revealed that 93% (n = 77) of haplotypes were different. Among these haplogroups, European-specific R1b-M269 lineages were the most representative (57.83%), with six different subhaplogroups and 43 unique haplotypes. Native American paternal ancestry was also detected based on the presence of the Q1a2-M3*(xM19, M194, M199) and Q1a2-M346*(xM3) lineages. Interestingly, all Q1a2-M346*(xM3) samples (n = 7, with five different haplotypes) carried allele six at the DYS391 locus. This allele has a worldwide frequency of 0.169% and was recently associated with a new Native subhaplogroup. An in-depth phylogenetic analysis of these samples suggests the Tolima and Huila region to be the principal area in all Central and South America where this particular Native lineage is found. This lineage has been present in the region for at least 1,809 (+/- 0,5345) years.
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Affiliation(s)
- Luz Angela Alonso Morales
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail: (LAAM); (WU)
| | - Andrea Casas-Vargas
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Madelyn Rojas Castro
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Rafael Resque
- Laboratório de Toxicologia e Química Farmacêutica, Departamento de Ciências da Saúde e Biológicas, Universidade Federal do Amapá, Macapá, Brazil
| | - Ândrea Kelly Ribeiro-dos-Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará - UFPA), Belém, state of Pará (PA), Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará - UFPA), Belém, state of Pará (PA), Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail: (LAAM); (WU)
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Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes. Int J Legal Med 2018; 133:17-23. [PMID: 30229332 DOI: 10.1007/s00414-018-1936-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) found within the non-recombining region of the Y chromosome (NRY) represent a powerful tool in forensic genetics for inferring the paternal ancestry of a vestige and complement the determination of biogeographical origin in combination with other markers like AIMs. In the present study, we introduce a panel of 15 Y-SNPs for a fine-resolution subtyping of the haplogroup R1b-DF27, in a single minisequencing reaction. This is the first minisequencing panel that allows a fine subtyping of R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. This panel includes subhaplogroups of DF27 that display moderate geographical differentiation, of interest to link a sample with a specific location of the Iberian Peninsula or with Iberian ancestry. Conversely, part of the intricacy of a new minisequencing panel is to have all the included variants available to test the effectiveness of the analysis method. We have overcome the absence of the least common variants through site-directed mutagenesis. Overall, the results show that our panel is a robust and effective method for subtyping R1b-DF27 lineages from a minimal amount of DNA, and its high resolution enables to improve male lineage discrimination in Iberian and Southwest European descent individuals. The small length of the amplicons and its reproducibility makes this assay suitable for forensic and population genetics purposes.
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15
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Grugni V, Raveane A, Mattioli F, Battaglia V, Sala C, Toniolo D, Ferretti L, Gardella R, Achilli A, Olivieri A, Torroni A, Passarino G, Semino O. Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective. Ann Hum Biol 2018; 45:44-56. [PMID: 29382284 DOI: 10.1080/03014460.2017.1409801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then. AIM This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation. SUBJECTS AND METHODS High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals. RESULTS Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones. CONCLUSIONS A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.
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Affiliation(s)
- Viola Grugni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Alessandro Raveane
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Francesca Mattioli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Vincenza Battaglia
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Cinzia Sala
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Daniela Toniolo
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Luca Ferretti
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Rita Gardella
- c Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Brescia , Italy
| | - Alessandro Achilli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Anna Olivieri
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Antonio Torroni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Giuseppe Passarino
- d Dipartimento di Biologia, Ecologia e Scienze della Terra , Università della Calabria , Arcavacata di Rende , Cosenza , Italy
| | - Ornella Semino
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
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16
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Assessment of a subset of Slowly Mutating Y-STRs for forensic and evolutionary studies. Forensic Sci Int Genet 2018; 34:e7-e12. [DOI: 10.1016/j.fsigen.2018.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 11/22/2017] [Accepted: 03/19/2018] [Indexed: 11/21/2022]
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17
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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 2018; 555:190-196. [PMID: 29466337 PMCID: PMC5973796 DOI: 10.1038/nature25738] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/04/2018] [Indexed: 12/19/2022]
Abstract
From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | | | - Thomas Booth
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alissa Mittnik
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
- Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Kurt Werner Alt
- Center of Natural and Cultural History of Man, Danube Private University, Krems 3500, Austria
- Department of Biomedical Engineering, Basel University, Basel 4123, Switzerland
- Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | | | | | - Eszter Bánffy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
- Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main 60325, Germany
| | | | - David Billoin
- INRAP, Institut National de Recherches Archéologiques Préventives, Buffard 25440, France
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Tim Allen
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Lindsey Büster
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Sophie Carver
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Laura Castells Navarro
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
| | - Gordon T Cook
- Scottish Universities Environmental Research Centre, East Kilbride G75 0QF, UK
| | - Barry Cunliffe
- Institute of Archaeology, University of Oxford, Oxford OX1 2PG, UK
| | | | | | | | - Michal Ernée
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Christopher Evans
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | | | - Joan Francès Farré
- Museu i Poblat Ibèric de Ca n'Oliver, Cerdanyola del Vallès 08290, Spain
| | - Chris Fowler
- School of History, Classics & Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michiel Gazenbeek
- INRAP, Institut National de Recherches Archéologiques Préventives, Nice 06300, France
| | - Rafael Garrido Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Elżbieta Haduch
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków 31-007, Poland
| | - Gill Hey
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Nick Jowett
- Great Orme Mines, Great Orme, Llandudno LL30 2XG, UK
| | - Timothy Knowles
- Bristol Radiocarbon Accelerator Mass Spectrometry Facility, University of Bristol, Bristol BS8 1UU, UK
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Philippe Lefranc
- INRAP, Institut National de Recherches Archéologiques Préventives, Strasbourg 67100, France
| | - Olivier Lemercier
- Université Paul-Valéry - Montpellier 3, UMR 5140 ASM, Montpellier 34199, France
| | - Arnaud Lefebvre
- INRAP, Institut National de Recherches Archéologiques Préventives, Metz 57063, France
- UMR 5199, Pacea, équipe A3P, Université de Bordeaux, Talence 33400, France
| | - César Heras Martínez
- TRÉBEDE, Patrimonio y Cultura SL, Torres de la Alameda 28813, Spain
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | - Virginia Galera Olmo
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | | | | | - Tona Majó
- Archaeom, Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | | | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Gabriella Kulcsár
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - Róbert Patay
- Ferenczy Museum Center, Szentendre 2100, Hungary
| | | | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
| | | | - Zsolt Bernert
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Maya Hoole
- Historic Environment Scotland, Edinburgh EH9 1SH, UK
| | - Olivia Cheronet
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Denise Keating
- Humanities Institute, University College Dublin, Dublin 4, Ireland
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - Miroslav Dobeš
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Francesca Candilio
- Soprintendenza Archeologia belle arti e paesaggio per la città metropolitana di Cagliari e per le province di Oristano e Sud Sardegna, Cagliari 9124, Italy
- Physical Anthropology Section, University of Philadelphia Museum of Archaeology and Anthropology, Philadelphia, Pennsylvania 19104, USA
- Department of Environmental Biology, Sapienza University of Rome, Rome 00185, Italy
| | | | | | | | | | - Emiliano Carnieri
- Facoltà di Lettere e Filosofia, Università di Palermo, Palermo 90133, Italy
| | - Luigi Lentini
- Soprintendenza per i beni culturali e ambientali di Trapani, Trapani 91100, Italy
| | | | | | | | - Germán Delibes
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Benjamin Neil
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Marcus Brittain
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Mike Luke
- Albion Archaeology, Bedford MK42 0AS, UK
| | | | - Jocelyne Desideri
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Marie Besse
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Günter Brücken
- General Department of Cultural Heritage Rhineland Palatinate, Department of Archaeology, Mainz 55116, Germany
| | - Mirosław Furmanek
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Agata Hałuszko
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Maksym Mackiewicz
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Artur Rapiński
- Institute of Archaeology, Silesian University in Opava, Opava 746 01, Czech Republic
| | - Stephany Leach
- Department of Archaeology, University of Exeter, Exeter EX4 4QE, UK
| | - Ignacio Soriano
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, Iowa 52240, USA
| | - João Luís Cardoso
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Universidade Aberta, Lisboa 1269-001, Portugal
| | | | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 31-016, Poland
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Pilar Prieto
- University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pierre-Jérôme Rey
- UMR 5204 Laboratoire Edytem, Université Savoie Mont Blanc, Chambéry 73376, France
| | - Roberto Risch
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manuel A Rojo Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Valladolid University, Valladolid 47011, Spain
| | - Aurore Schmitt
- UMR 7268 ADES, CNRS, Aix-Marseille Univ, EFS, Faculté de médecine Nord, Marseille 13015, France
| | - Joël Serralongue
- Service archéologique, Conseil Général de la Haute-Savoie, Annecy 74000, France
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, Prague 121 08, Czech Republic
| | - Luc Vergnaud
- ANTEA Bureau d'étude en Archéologie, Habsheim 68440, France
| | - João Zilhão
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
- Departament d'Història i Arqueologia, Universitat de Barcelona, Barcelona 08001, Spain
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford OX1 3QY, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Douglas J Kennett
- Department of Anthropology & Institute for Energy and the Environment, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Harry Fokkens
- Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Volker Heyd
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
- Department of Philosophy, History, Culture and Art Studies, Section of Archaeology, University of Helsinki, Helsinki 00014, Finland
| | | | | | - Philipp W Stockhammer
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, South Australia, Australia
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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18
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Solé-Morata N, Villaescusa P, García-Fernández C, Font-Porterias N, Illescas MJ, Valverde L, Tassi F, Ghirotto S, Férec C, Rouault K, Jiménez-Moreno S, Martínez-Jarreta B, Pinheiro MF, Zarrabeitia MT, Carracedo Á, de Pancorbo MM, Calafell F. Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ. Sci Rep 2017; 7:7341. [PMID: 28779148 PMCID: PMC5544771 DOI: 10.1038/s41598-017-07710-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/28/2017] [Indexed: 11/28/2022] Open
Abstract
Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.
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Affiliation(s)
- Neus Solé-Morata
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Carla García-Fernández
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Neus Font-Porterias
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - María José Illescas
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Laura Valverde
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Claude Férec
- Inserm, UMR 1078, Brest, France.,Laboratoire de Génétique Moléculaire, CHRU Brest, Hôpital Morvan, Brest, France.,Université de Bretagne Occidentale, Brest, France.,Etablissement Français du Sang-Bretagne, Brest, France
| | - Karen Rouault
- Inserm, UMR 1078, Brest, France.,Laboratoire de Génétique Moléculaire, CHRU Brest, Hôpital Morvan, Brest, France
| | - Susana Jiménez-Moreno
- Forensic and Legal Medicine Area, Department of Pathology and Surgery, University Miguel Hernández, Elche, Spain
| | | | - Maria Fátima Pinheiro
- Forensic Genetics Department, National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
| | | | - Ángel Carracedo
- Genomic Medicine Group, CIBERER- University of Santiago de Compostela, Galician Foundation of Genomic Medicine (SERGAS), Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
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19
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Population genetic data of 38 insertion-deletion markers in six populations of the northern fringe of the Iberian Peninsula. Forensic Sci Int Genet 2017; 27:175-179. [DOI: 10.1016/j.fsigen.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 12/17/2022]
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20
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Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. Forensic Sci Int Genet 2017; 27:142-148. [DOI: 10.1016/j.fsigen.2016.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 12/22/2016] [Accepted: 12/29/2016] [Indexed: 11/20/2022]
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21
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Resque R, Gusmão L, Geppert M, Roewer L, Palha T, Alvarez L, Ribeiro-dos-Santos Â, Santos S. Male Lineages in Brazil: Intercontinental Admixture and Stratification of the European Background. PLoS One 2016; 11:e0152573. [PMID: 27046235 PMCID: PMC4821637 DOI: 10.1371/journal.pone.0152573] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 03/16/2016] [Indexed: 12/27/2022] Open
Abstract
The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time.
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Affiliation(s)
- Rafael Resque
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Toxicologia e Química Farmacêutica, Departamento de Ciências da Saúde e Biológicas, Universidade Federal do Amapá, Macapá, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.,IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria Geppert
- 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
| | - Teresinha Palha
- Laboratório de Genética Forense, Instituto de Criminalística, Centro de Perícias Científicas Renato Chaves, Belém, Pará, Brasil
| | - Luis Alvarez
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
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22
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The Paternal Landscape along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers. PLoS One 2015; 10:e0141510. [PMID: 26544036 PMCID: PMC4636292 DOI: 10.1371/journal.pone.0141510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/08/2015] [Indexed: 11/19/2022] Open
Abstract
Patterns of genetic variation in human populations across the African continent are still not well studied in comparison with Eurasia and America, despite the high genetic and cultural diversity among African populations. In population and forensic genetic studies a single sample is often used to represent a complete African region. In such a scenario, inappropriate sampling strategies and/or the use of local, isolated populations may bias interpretations and pose questions of representativeness at a macrogeographic-scale. The non-recombining region of the Y-chromosome (NRY) has great potential to reveal the regional representation of a sample due to its powerful phylogeographic information content. An area poorly characterized for Y-chromosomal data is the West-African region along the Bight of Benin, despite its important history in the trans-Atlantic slave trade and its large number of ethnic groups, languages and lifestyles. In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed. A thorough methodology was developed allowing comparison of population samples using Y-chromosomal lineage data based on different Y-SNP panels and phylogenies. Geographic proximity turned out to be the best predictor of genetic affinity between populations along the Bight of Benin. Nevertheless, based on Y-chromosomal data from the literature two population samples differed strongly from others from the same or neighbouring areas and are not regionally representative within large-scale studies. Furthermore, the analysis of the HapMap sample YRI of a Yoruban population from South-western Nigeria based on Y-SNPs and Y-STR data showed for the first time its regional representativeness, a result which is important for standard population and forensic genetic applications using the YRI sample. Therefore, the uniquely and powerful geographical information carried by the Y-chromosome makes it an important locus to test the representativeness of a certain sample even in the genomic era, especially in poorly investigated areas like Africa.
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