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Agdzhoyan A, Iskandarov N, Ponomarev G, Pylev V, Koshel S, Salaev V, Pocheshkhova E, Kagazezheva Z, Balanovska E. Origins of East Caucasus Gene Pool: Contributions of Autochthonous Bronze Age Populations and Migrations from West Asia Estimated from Y-Chromosome Data. Genes (Basel) 2023; 14:1780. [PMID: 37761920 PMCID: PMC10530682 DOI: 10.3390/genes14091780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The gene pool of the East Caucasus, encompassing modern-day Azerbaijan and Dagestan populations, was studied alongside adjacent populations using 83 Y-chromosome SNP markers. The analysis of genetic distances among 18 populations (N = 2216) representing Nakh-Dagestani, Altaic, and Indo-European language families revealed the presence of three components (Steppe, Iranian, and Dagestani) that emerged in different historical periods. The Steppe component occurs only in Karanogais, indicating a recent medieval migration of Turkic-speaking nomads from the Eurasian steppe. The Iranian component is observed in Azerbaijanis, Dagestani Tabasarans, and all Iranian-speaking peoples of the Caucasus. The Dagestani component predominates in Dagestani-speaking populations, except for Tabasarans, and in Turkic-speaking Kumyks. Each component is associated with distinct Y-chromosome haplogroup complexes: the Steppe includes C-M217, N-LLY22g, R1b-M73, and R1a-M198; the Iranian includes J2-M172(×M67, M12) and R1b-M269; the Dagestani includes J1-Y3495 lineages. We propose J1-Y3495 haplogroup's most common lineage originated in an autochthonous ancestral population in central Dagestan and splits up ~6 kya into J1-ZS3114 (Dargins, Laks, Lezgi-speaking populations) and J1-CTS1460 (Avar-Andi-Tsez linguistic group). Based on the archeological finds and DNA data, the analysis of J1-Y3495 phylogeography suggests the growth of the population in the territory of modern-day Dagestan that started in the Bronze Age, its further dispersal, and the microevolution of the diverged population.
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Affiliation(s)
| | - Nasib Iskandarov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Georgy Ponomarev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Vladimir Pylev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Biobank of Northern Eurasia, 115201 Moscow, Russia
| | - Sergey Koshel
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Cartography and Geoinformatics, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vugar Salaev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Elvira Pocheshkhova
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Zhaneta Kagazezheva
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
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Ongun MC, Tonyali NV, Kaplan O, Deger I, Celebier M, Basci Akduman NE, Sahin D, Yucel A, Babaoglu MO. Effects of genetic polymorphisms of CYP2J2, CYP2C9, CYP2C19, CYP4F2, CYP4F3 and CYP4A11 enzymes in preeclampsia and gestational hypertension. Placenta 2023; 137:88-95. [PMID: 37141740 DOI: 10.1016/j.placenta.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/04/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
INTRODUCTION The aim of this study was to investigate the effects of cytochrome P450 (CYP) 2J2, CYP2C9, CYP2C19 and CYP4F2, CYP4F3 and CYP4A11 genetic polymorphisms in preeclampsia and gestational hypertension (GHT) patients in a sample of Turkish population. MATERIALS-METHODS Patients (n = 168; 110 GHT and 58 preeclampsia) and healthy pregnant women (n = 155, controls) participated in the study. For genotyping, polymerase chain reaction (PCR) and restriction analysis (RFLP) were used. Substance levels were measured using LC-MS. RESULTS Plasma DHET levels in GHT and preeclampsia patients were significantly lower than those in the control group (62.7%, 66.3% vs.100.0%, respectively, p < 0.0001). An increase in CYP2J2*7 allele frequency was observed in the preeclampsia group, as compared to GHT group (12.1% vs. 4.5%; odds ratio, O.R. = 2.88, p < 0.01). The frequencies of CYP2C19*2 and*17 alleles were higher in GHT group as compared to the control group (17.7% vs. 11.6%, O.R. = 1.99, p < 0.01; and 28.6% vs.18.4%, O.R. = 2.03, p < 0.01, respectively). An increased frequency of CYP4F3 rs3794987 G allele was found in GHT group as compared to the control group (48.0% vs. 38.0%; O.R. = 1.53, p < 0.01). DISCUSSION DHET plasma levels were significantly reduced in hypertensive pregnant groups as compared to the control group. The allele frequency distributions for CYP2J2*7, CYP2C19 *2, *17 and CYP4F3 rs3794987 were significantly different in hypertensive pregnant patients as compared to the healthy control subjects. Our results may suggest that investigated genetic polymorphisms may be useful in diagnosis and clinical management of GHT and preeclampsia patients.
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Affiliation(s)
- Mert C Ongun
- Hacettepe University, Faculty of Medicine, Department of Medical Pharmacology, Ankara, Turkey.
| | | | - Ozan Kaplan
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey
| | - Ilter Deger
- Hacettepe University, Faculty of Medicine, Department of Medical Pharmacology, Ankara, Turkey
| | - Mustafa Celebier
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey
| | | | - Dilek Sahin
- University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Aykan Yucel
- University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Melih O Babaoglu
- Hacettepe University, Faculty of Medicine, Department of Medical Pharmacology, Ankara, Turkey
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3
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Luis JR, Palencia-Madrid L, Deshpande K, Alfonso-Sanchez MA, Peña JA, de Pancorbo MM, Garcia-Bertrand R, Herrera RJ. On the Y chromosome of Chennai, Tamil Nadu and the Indian subcontinent. Gene 2023; 859:147175. [PMID: 36632908 DOI: 10.1016/j.gene.2023.147175] [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: 09/16/2022] [Revised: 12/14/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Several migratory waves from various origins along with cultural practices restricting marriages between people of different castes and tribes as well as continued endogamy have led to a complex and diverse society in the Indian subcontinent. Despite being widely represented in genetic studies, several interrogatives remain with regards to India's current genetic constituents and distributions, source populations and population relationships. To identify the forces that may have shaped Indian population's genetic relationships, we undertook a comprehensive comparative study of the Y-chromosomes across India utilizing Y-STR and Y-SNP chromosomal markers using the general population of Chennai in the state of Tamil Nadu as a point of reference. Our analyses identify differences in source populations for different regions within India, unique linguistic characteristics as well as demographic and cultural forces that may have shaped population structure.
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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
| | - Ketaki Deshpande
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Miguel A Alfonso-Sanchez
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, Spain
| | - Jose A Peña
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, 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
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA.
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4
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijašević G, Antonović D, Armit I, Atmaca A, Avetisyan P, Aytek Aİ, Bacvarov K, Badalyan R, Bakardzhiev S, Balen J, Bejko L, Bernardos R, Bertsatos A, Biber H, Bilir A, Bodružić M, Bonogofsky M, Bonsall C, Borić D, Borovinić N, Bravo Morante G, Buttinger K, Callan K, Candilio F, Carić M, Cheronet O, Chohadzhiev S, Chovalopoulou ME, Chryssoulaki S, Ciobanu I, Čondić N, Constantinescu M, Cristiani E, Culleton BJ, Curtis E, Davis J, Demcenco TI, Dergachev V, Derin Z, Deskaj S, Devejyan S, Djordjević V, Duffett Carlson KS, Eccles LR, Elenski N, Engin A, Erdoğan N, Erir-Pazarcı S, Fernandes DM, Ferry M, Freilich S, Frînculeasa A, Galaty ML, Gamarra B, Gasparyan B, Gaydarska B, Genç E, Gültekin T, Gündüz S, Hajdu T, Heyd V, Hobosyan S, Hovhannisyan N, Iliev I, Iliev L, Iliev S, İvgin İ, Janković I, Jovanova L, Karkanas P, Kavaz-Kındığılı B, Kaya EH, Keating D, Kennett DJ, Deniz Kesici S, Khudaverdyan A, Kiss K, Kılıç S, Klostermann P, Kostak Boca Negra Valdes S, Kovačević S, Krenz-Niedbała M, Krznarić Škrivanko M, Kurti R, Kuzman P, Lawson AM, Lazar C, Leshtakov K, Levy TE, Liritzis I, Lorentz KO, Łukasik S, Mah M, Mallick S, Mandl K, Martirosyan-Olshansky K, Matthews R, Matthews W, McSweeney K, Melikyan V, Micco A, Michel M, Milašinović L, Mittnik A, Monge JM, Nekhrizov G, Nicholls R, Nikitin AG, Nikolov V, Novak M, Olalde I, Oppenheimer J, Osterholtz A, Özdemir C, Özdoğan KT, Öztürk N, Papadimitriou N, Papakonstantinou N, Papathanasiou A, Paraman L, Paskary EG, Patterson N, Petrakiev I, Petrosyan L, Petrova V, Philippa-Touchais A, Piliposyan A, Pocuca Kuzman N, Potrebica H, Preda-Bălănică B, Premužić Z, Price TD, Qiu L, Radović S, Raeuf Aziz K, Rajić Šikanjić P, Rasheed Raheem K, Razumov S, Richardson A, Roodenberg J, Ruka R, Russeva V, Şahin M, Şarbak A, Savaş E, Schattke C, Schepartz L, Selçuk T, Sevim-Erol A, Shamoon-Pour M, Shephard HM, Sideris A, Simalcsik A, Simonyan H, Sinika V, Sirak K, Sirbu G, Šlaus M, Soficaru A, Söğüt B, Sołtysiak A, Sönmez-Sözer Ç, Stathi M, Steskal M, Stewardson K, Stocker S, Suata-Alpaslan F, Suvorov A, Szécsényi-Nagy A, Szeniczey T, Telnov N, Temov S, Todorova N, Tota U, Touchais G, Triantaphyllou S, Türker A, Ugarković M, Valchev T, Veljanovska F, Videvski Z, Virag C, Wagner A, Walsh S, Włodarczak P, Workman JN, Yardumian A, Yarovoy E, Yavuz AY, Yılmaz H, Zalzala F, Zettl A, Zhang Z, Çavuşoğlu R, Rohland N, Pinhasi R, Reich D. The genetic history of the Southern Arc: A bridge between West Asia and Europe. Science 2022; 377:eabm4247. [PMID: 36007055 PMCID: PMC10064553 DOI: 10.1126/science.abm4247] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Ayşe Acar
- Department of Anthropology, Faculty of Letters, Mardin Artuklu University, 47510 Artuklu, Mardin, Turkey
| | - Ayşen Açıkkol
- Department of Anthropology, Faculty of Letters, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | | | - Levon Aghikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Uğur Akyüz
- Samsun Museum of Archeology and Ethnography, Kale Mahallesi, Merkez, İlkadım, 55030 Samsun, Turkey
| | | | | | | | - Ian Armit
- Department of Archaeology, University of York, York YO1 7EP, UK
| | - Alper Atmaca
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Pavel Avetisyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Ahmet İhsan Aytek
- Department of Anthropology, Faculty of Arts and Science, Burdur Mehmet Akif University, 15100 Burdur, Turkey
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Ruben Badalyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Lorenc Bejko
- Department of Archaeology and Heritage Studies, University of Tirana, 1010 Tirana, Albania
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Bertsatos
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Hanifi Biber
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Department of Archaeology, Faculty of Science and Letters, Düzce University, 81620 Düzce, Turkey
| | | | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027, USA
| | - Nikola Borovinić
- Center for Conservation and Archaeology of Montenegro, 81250 Cetinje, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Stefan Chohadzhiev
- Department of Archaeology, University of Veliko Tarnovo "St. Cyril and St. Methodius," 5003 Veliko Tarnovo, Bulgaria
| | - Maria-Eleni Chovalopoulou
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Stella Chryssoulaki
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of Piraeus and the Islands, 10682 Piraeus, Greece
| | - Ion Ciobanu
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,National Archaeological Agency, 2012 Chișinău, Moldova
| | | | | | - Emanuela Cristiani
- Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jack Davis
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Department of Archaeology, Faculty of Letters, Ege University, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seda Devejyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Laurie R Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nedko Elenski
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Atilla Engin
- Department of Archaeology, Faculty of Science and Letters, Gaziantep University, 27310 Gaziantep, Turkey
| | - Nihat Erdoğan
- Mardin Archaeological Museum, Şar, Cumhuriyet Meydanı üstü, 47100 Artuklu, Mardin, Turkey
| | | | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L Galaty
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, 43002 Tarragona, Spain.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Elif Genç
- Department of Archaeology, Faculty of Science and Letters, Çukurova University, 01330 Balçalı-Sarıçam-Adana, Turkey
| | - Timur Gültekin
- Department of Anthropology, Faculty of Humanities, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Volker Heyd
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Suren Hobosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Nelli Hovhannisyan
- Department of Ecology and Nature Protection, Yerevan State University, 0025 Yerevan, Armenia
| | - Iliya Iliev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - İlkay İvgin
- Ministry of Culture and Tourism, İsmet İnönü Bulvarı, 06100 Emek, Ankara, Turkey
| | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Lence Jovanova
- Museum of the City of Skopje, 1000 Skopje, North Macedonia
| | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory, American School of Classical Studies at Athens, 10676 Athens, Greece
| | - Berna Kavaz-Kındığılı
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | - Esra Hilal Kaya
- Muğla Archaeological Museum and Yatağan Thermal Power Generation Company, Rescue Excavations, 48000 Muğla, Turkey
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Douglas J Kennett
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Seda Deniz Kesici
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | | | - Krisztián Kiss
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | | | | | | | - Rovena Kurti
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Pasko Kuzman
- National Museum in Ohrid, 6000 Ohrid, North Macedonia
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Catalin Lazar
- ArchaeoSciences Division, Research Institute of the University of Bucharest, University of Bucharest, 050663 Bucharest, Romania
| | - Krassimir Leshtakov
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Thomas E Levy
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ioannis Liritzis
- Key Research Institute of Yellow River Civilization and Sustainable Development and the Collaborative Innovation Center on Yellow River Civilization of Henan Province, Laboratory of Yellow River Cultural Heritage, Henan University, 475001 Kaifeng, China.,European Academy of Sciences and Arts, 5020 Salzburg, Austria
| | - Kirsi O Lorentz
- Science and Technology in Archaeology and Culture Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Sylwia Łukasik
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | | | - Roger Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Wendy Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Varduhi Melikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet M Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Georgi Nekhrizov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Rebecca Nicholls
- School of Archaeological and Forensic Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Vassil Nikolov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS 39762, USA
| | - Celal Özdemir
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Kadir Toykan Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nurettin Öztürk
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | | | - Niki Papakonstantinou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | | | | | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ilian Petrakiev
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Levon Petrosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Vanya Petrova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | | | - Ashot Piliposyan
- Department of Armenian History, Armenian State Pedagogical University After Khachatur Abovyan, 0010 Yerevan, Armenia
| | | | - Hrvoje Potrebica
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siniša Radović
- Institute for Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaymaniyah Directorate of Antiquities and Heritage, 46010 Sulaymaniyah, Iraq
| | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | | | - Sergei Razumov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Amy Richardson
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, 2311 Leiden, Netherlands
| | - Rudenc Ruka
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Victoria Russeva
- Institute of Experimental Morphology, Pathology and Archeology with Museum, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Department of Anthropology, Faculty of Science and Letters, Hitit University, 19040 Çorum, Turkey
| | - Emre Savaş
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Lynne Schepartz
- School of Anatomical Sciences, The University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Tayfun Selçuk
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Ayla Sevim-Erol
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Department of Anthropology, Binghamton University, Binghamton, NY 13902, USA
| | | | - Athanasios Sideris
- Institute of Classical Archaeology, Charles University, 11636 Prague, Czechia
| | - Angela Simalcsik
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,"Olga Necrasov" Centre of Anthropological Research, Romanian Academy Iași Branch, 2012 Iaşi Romania
| | - Hakob Simonyan
- Scientific Research Center of the Historical and Cultural Heritage, 0010 Yerevan, Armenia
| | - Vitalij Sinika
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ghenadie Sirbu
- Thracology Scientific Research Laboratory of the State University of Moldova, Department of Academic Management, Academy of Science of Moldova, 2009 Chișinău, Moldova
| | - Mario Šlaus
- Anthropological Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Department of Archaeology, Faculty of Science and Arts, Pamukkale University, 20070 Denizli, Turkey
| | | | - Çilem Sönmez-Sözer
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Maria Stathi
- Ephorate of Antiquities of East Attica, Ministry of Culture and Sports, 10682 Athens, Greece
| | - Martin Steskal
- Austrian Archaeological Institute at the Austrian Academy of Sciences, 1190 Vienna, Austria
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon Stocker
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Department of Anthropology, Faculty of Letters, Istanbul University, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Nikolai Telnov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Strahil Temov
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | - Nadezhda Todorova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Ulsi Tota
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania.,Culture and Patrimony Department, University of Avignon, F-84029 Avignon, France
| | - Gilles Touchais
- Department of the History of Art and Archaeology, Université Paris 1 Panthéon-Sorbonne, 75006 Paris, France
| | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Department of Archaeology, Faculty of Science and Letters, Ondokuz Mayıs University, 55139 Atakum-Samsun, Turkey
| | | | - Todor Valchev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | | | - Zlatko Videvski
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Sam Walsh
- School of Natural Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, 31-016 Kraków, Poland
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA.,Penn Museum, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evgenii Yarovoy
- History of the Ancient World and Middle Ages Department, Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Department of Anthropology, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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5
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Kotan LD. Comparative Analyses of Turkish Variome and Widely Used Genomic Variation Databases for the Evaluation of Rare Sequence Variants in Turkish Individuals: Idiopathic Hypogonadotropic Hypogonadism as a Disease Model. J Clin Res Pediatr Endocrinol 2022; 14:293-301. [PMID: 35438269 PMCID: PMC9422916 DOI: 10.4274/jcrpe.galenos.2022.2022-3-11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 12/01/2022] Open
Abstract
Objective With the increasing use of whole-exome sequencing, one of the challenges in identifying the causal allele for a Mendelian disease is the lack of availability of population-specific human genetic variation reference databases. The people of Turkey were not represented in GnomAD or other publicly available large databases until recently, when the first comprehensive genomic variation database, Turkish Variome (TRV), was published. The aim of this study was to evaluate whether TRV or other publicly available large genomic variation databases can reliably be used for rare disease variant evaluation in Turkish individuals. Methods Sixty non-disease-causing, non-synonymous variants (minor allele frequencies >1%) were identified in 58 genes that are known to be associated with idiopathic hypogonadotropic hypogonadism from a large Turkish patient cohort. The allelic frequencies of these variants were then compared with those in various public genomic variation databases, including TRV. Results Our cohort variants showed the highest correlations with those in the TRV, Iranome, and The Greater Middle East Variome, in decreasing order. Conclusion These results suggest that the TRV is the appropriate database to use for rare genomic variant evaluations in the Turkish population. Our data also suggest that variomes from geographic neighborhoods may serve as substitute references for populations devoid of their own genomic variation databases.
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Affiliation(s)
- Leman Damla Kotan
- Çukurova University Faculty of Medicine, Department of
Pediatric Endocrinology, Adana, Turkey
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6
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Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD. Sci Rep 2022; 12:6468. [PMID: 35618734 PMCID: PMC9135728 DOI: 10.1038/s41598-022-10899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.
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7
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Reyes-Madrid M, Flores-Alvarado S, Pezo-Valderrama P, Orellana-Soto M, Apata M, Moraga M, de Saint Pierre M. An approach on the migratory processes in the north of Chile based on Y chromosome analysis. Am J Hum Biol 2022; 34:e23736. [PMID: 35263492 DOI: 10.1002/ajhb.23736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/23/2021] [Accepted: 02/12/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Northern Chile is an area characterized by a complex cultural and demographic trajectory. During the last few centuries, this complex trajectory has become the destination of intra- and intercontinental migratory waves. In this study, we analyzed the Y chromosome to evaluate how migratory and admixture patterns have affected the genetic composition of the populations in northern Chile compared with other populations of the country. METHODS A total of 311 people from urban (Antofagasta and Calama), rural (Azapa and Camarones), and Native (Aymara and Atacameño) populations from northern Chile were characterized by 26 SNPs and the STR DYS393 of the Y chromosome, along with 69 individuals from Native populations (Mapuche, Pehuenche, and Huilliche) from southern Chile. In addition to characterizing the paternal lineages, multivariate analyses were performed to compare with published data from other Chilean populations. RESULTS Both the Antofagasta and Calama populations show differences compared with the rest of the Chilean population. On one side, Antofagasta shows a high diversity of non-Amerindian lineages, including the highest value for haplogroup I (12%) for all Chileans populations. Otherwise, Calama has the highest value of any Chilean urban population (31.9%) for Amerindian lineages, including the only Q-M3 sub-lineage detected in the entire sample. Regarding the Native population, Aymara presents the highest percentage of Q-M3 (94.4%). CONCLUSIONS The Y chromosome haplogroup distribution allowed us to identify recent migratory processes typical of the northern populations studied. These have shaped the demographic and cultural dynamics of local and migrant groups in the territory.
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Affiliation(s)
- Margarita Reyes-Madrid
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Bioestadística, Instituto de Salud Pública, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Michael Orellana-Soto
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mario Apata
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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8
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Simão F, Ribeiro J, Vullo C, Catelli L, Gomes V, Xavier C, Huber G, Bodner M, Quiroz A, Ferreira AP, Carvalho EF, Parson W, Gusmão L. The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture. Genes (Basel) 2021; 12:1788. [PMID: 34828394 PMCID: PMC8625094 DOI: 10.3390/genes12111788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.
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Affiliation(s)
- Filipa Simão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Laura Catelli
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal;
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), 4099-002 Porto, Portugal
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Alfredo Quiroz
- Instituto de Previsión Social, Asunción 100153, Paraguay;
| | - Ana Paula Ferreira
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Elizeu F. Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
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9
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Pamjav H, Krizsán K. Biologia futura: confessions in genes. Biol Futur 2021; 71:435-441. [PMID: 34554462 DOI: 10.1007/s42977-020-00049-x] [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: 06/08/2020] [Accepted: 10/07/2020] [Indexed: 10/23/2022]
Abstract
Y-DNA and mtDNA have been a widely used tool not only in forensic genetic applications but in human evolutionary and population genetic studies. Its paternal or maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of paternal and maternal clades among human populations at continental and regional levels. It is unbelievable, but true, that the disadvantages of paternal and maternal lineages in forensic genetic studies, i.e., everyone within a family have the same paternal or maternal haplotype and haplogroup, become advantages in human evolutionary studies, i.e., reveal the genetic history of successful mothers and successful fathers. Thanks to these amazing properties of haploid markers, they provide tools for mapping the migration routes of human populations during prehistoric and historical periods, separately as maternal and paternal lineages, and together as the genetic history of a population.
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Affiliation(s)
- Horolma Pamjav
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, PO: 314/4, Budapest, 1903, Hungary.
| | - Krisztina Krizsán
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, PO: 314/4, Budapest, 1903, Hungary
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10
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Kharkov VN. Y-Chromosome Markers in Population Genetics: Fundamental and Applied Results of Ethnogenomic Research. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421090040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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11
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The genetic structure of the Turkish population reveals high levels of variation and admixture. Proc Natl Acad Sci U S A 2021; 118:2026076118. [PMID: 34426522 DOI: 10.1073/pnas.2026076118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.
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12
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Insights into the Middle Eastern paternal genetic pool in Tunisia: high prevalence of T-M70 haplogroup in an Arab population. Sci Rep 2021; 11:15728. [PMID: 34344940 PMCID: PMC8333252 DOI: 10.1038/s41598-021-95144-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.
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13
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Kornienko IV, Faleeva TG, Schurr TG, Aramova OY, Ochir-Goryaeva MA, Batieva EF, Vdovchenkov EV, Moshkov NE, Kukanova VV, Ivanov IN, Sidorenko YS, Tatarinova TV. Y-Chromosome Haplogroup Diversity in Khazar Burials from Southern Russia. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Sahakyan H, Margaryan A, Saag L, Karmin M, Flores R, Haber M, Kushniarevich A, Khachatryan Z, Bahmanimehr A, Parik J, Karafet T, Yunusbayev B, Reisberg T, Solnik A, Metspalu E, Hovhannisyan A, Khusnutdinova EK, Behar DM, Metspalu M, Yepiskoposyan L, Rootsi S, Villems R. Origin and diffusion of human Y chromosome haplogroup J1-M267. Sci Rep 2021; 11:6659. [PMID: 33758277 PMCID: PMC7987999 DOI: 10.1038/s41598-021-85883-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/08/2021] [Indexed: 01/31/2023] Open
Abstract
Human Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency region-encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant-resides ~ 2000 km away from the other one found in the Caucasus. The region between them, although has a lower frequency, nevertheless demonstrates high genetic diversity. Studies associate this haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the history of the Jews, and the spread of Islam. Here, we study past human male demography in West Asia with 172 high-coverage whole Y chromosome sequences and 889 genotyped samples of haplogroup J1-M267. We show that this haplogroup evolved ~ 20,000 years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch-J1a1a1-P58-evolved during the early Holocene ~ 9500 years ago somewhere in the Arabian Peninsula, the Levant, and southern Mesopotamia. Haplogroup J1-M267 expanded during the Chalcolithic, the Bronze Age, and the Iron Age. Most probably, the spread of Afro-Asiatic languages, the spread of mobile pastoralism in the arid zones, or both of these events together explain the distribution of haplogroup J1-M267 we see today in the southern regions of West Asia.
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Affiliation(s)
- Hovhannes Sahakyan
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia.
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, 0014, Yerevan, Armenia.
| | - Ashot Margaryan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, 0014, Yerevan, Armenia
- Lundbeck Foundation, Department of Biology, GeoGenetics Centre, University of Copenhagen, 1350, Copenhagen, Denmark
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, Manawatu, 4442, New Zealand
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Zaruhi Khachatryan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, 0014, Yerevan, Armenia
| | - Ardeshir Bahmanimehr
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, 0014, Yerevan, Armenia
- Thalassemia and Haemophilia Genetic PND Research Center, Dastgheib Hospital, Shiraz University of Medical Sciences, 71456-83769, Shiraz, Iran
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, 51010, Tartu, Estonia
| | - Tatiana Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, 85721, USA
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia, 450076
| | - Tuuli Reisberg
- Core Facility, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Anu Solnik
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Core Facility, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Anahit Hovhannisyan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, 0014, Yerevan, Armenia
| | - Elza K Khusnutdinova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia, 450076
- Institute of Biochemistry and Genetics of Ufa Federal Research Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, 0014, Yerevan, Armenia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, 51010, Tartu, Estonia
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15
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Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas. Sci Rep 2020; 10:21428. [PMID: 33293675 PMCID: PMC7722846 DOI: 10.1038/s41598-020-78487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/19/2020] [Indexed: 11/08/2022] Open
Abstract
Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.
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16
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Autosomal genetics and Y-chromosome haplogroup L1b-M317 reveal Mount Lebanon Maronites as a persistently non-emigrating population. Eur J Hum Genet 2020; 29:581-592. [PMID: 33273712 DOI: 10.1038/s41431-020-00765-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 10/16/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Currently, there are 18 different religious communities living in Lebanon. While evolving primarily within Lebanon, these communities show a level of local isolation as demonstrated previously from their Y-haplogroup distributions. In order to trace the origins and migratory patterns that may have led to the genetic isolation and autosomal clustering in some of these communities we analyzed Y-chromosome STR and SNP sample data from 6327 individuals, in addition to whole genome autosomal sample data from 609 individuals, from Mount Lebanon and other surrounding communities. We observed Y chromosome L1b Levantine STR branching that occurred around 5000 years ago. Autosomal DNA analyses suggest that the North Lebanese Mountain Maronite community possesses an ancestral Fertile Crescent genetic component distinct from other populations in the region. We suggest that the Levantine L1b group split from the Caucasus ancestral group around 7300 years ago and migrated to the Levant. This event was distinct from the earlier expansions from the Caucasus region that contributed to the wider Levantine populations. Differential cultural adaption by populations from the North Lebanese Mountains are clearly aligned with the L1b haplotype STR haplogroup clusters, indicating pre-existing and persistent cultural barriers marked by the transmission of L1b lineages. Our findings highlight the value of uniparental haplogroups and STR haplotype data for elucidating biosocial events among these populations.
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17
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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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18
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Feldman MW. L. Luca Cavalli-Sforza: A Renaissance Scientist. Theor Popul Biol 2020; 133:75-79. [DOI: 10.1016/j.tpb.2019.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 01/01/2023]
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19
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Balanovska EV, Skhalyakho RA, Kagazezheva ZA, Zaporozhchenko VV, Urasin VM, Agdzhoyan AT, Koshel SM, Pocheshkhova EA, Balanovsky OP. Inferring the Genetic Ancestry of Ubykh People from North Caucasus. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419090035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Egorova MA, Egorov AA. The Ancestral Homeland of the Carriers of the Proto-Indo-European Language: Mathematical Models for the Study of Linguistic Information. AUTOMATIC DOCUMENTATION AND MATHEMATICAL LINGUISTICS 2019. [DOI: 10.3103/s0005105519030026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Yardumian A, Schurr TG. The Geography of Jewish Ethnogenesis. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2019. [DOI: 10.1086/702709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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22
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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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23
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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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24
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Juhász Z, Dudás E, Pamjav H. A new self-learning computational method for footprints of early human migration processes. Mol Genet Genomics 2018; 293:1579-1594. [PMID: 29974304 DOI: 10.1007/s00438-018-1469-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/28/2018] [Indexed: 11/25/2022]
Abstract
We present a new self-learning computational method searching for footprints of early migration processes determining the genetic compositions of recent human populations. The data being analysed are 26- and 18-dimensional mitochondrial and Y-chromosomal haplogroup distributions representing 50 recent and 34 ancient populations in Eurasia and America. The algorithms search for associations of haplogroups jointly propagating in a significant subset of these populations. Joint propagations of Hgs are detected directly by similar ranking lists of populations derived from Hg frequencies of the 50 Hg distributions. The method provides us the most characteristic associations of mitochondrial and Y-chromosomal haplogroups, and the set of populations where these associations propagate jointly. In addition, the typical ranking lists characterizing these Hg associations show the geographical distribution, the probable place of origin and the paths of their protection. Comparison to ancient data verifies that these recent geographical distributions refer to the most important prehistoric migrations supported by archaeological evidences.
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Affiliation(s)
- Z Juhász
- Centre for Energy Research, Institute of Technical Physics and Materials Science, PO Box. 216, Budapest, 1536, Hungary
| | - E Dudás
- National Centre of Experts and Research, Institute of Forensic Genetics, Budapest, Hungary
| | - Horolma Pamjav
- National Centre of Experts and Research, Institute of Forensic Genetics, Budapest, Hungary.
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25
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A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Sci Rep 2018; 8:7465. [PMID: 29748665 PMCID: PMC5945646 DOI: 10.1038/s41598-018-25912-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022] Open
Abstract
In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.
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26
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Bozman N, Gurkan C, Sevay H, Demirdov DK, Ozbas-Gerceker F. Genetic characterisation of 19 autosomal STR loci in a population sample from the Southeastern Anatolia Region of Turkey. Ann Hum Biol 2018. [DOI: 10.1080/03014460.2018.1444202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Nazli Bozman
- Department of Biology, Section of Molecular Biology, Faculty of Arts and Science, University of Gaziantep, Gaziantep, Turkey
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
- Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Damla Kanliada Demirdov
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Filiz Ozbas-Gerceker
- Department of Biology, Section of Molecular Biology, Faculty of Arts and Science, University of Gaziantep, Gaziantep, Turkey
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27
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D’Atanasio E, Trombetta B, Bonito M, Finocchio A, Di Vito G, Seghizzi M, Romano R, Russo G, Paganotti GM, Watson E, Coppa A, Anagnostou P, Dugoujon JM, Moral P, Sellitto D, Novelletto A, Cruciani F. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biol 2018; 19:20. [PMID: 29433568 PMCID: PMC5809971 DOI: 10.1186/s13059-018-1393-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. CONCLUSIONS Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.
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Affiliation(s)
- Eugenia D’Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Finocchio
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Genny Di Vito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Mara Seghizzi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Rita Romano
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3–Paul-Sabatier, Toulouse, France
| | - Pedro Moral
- Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | | | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
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28
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Manco L, Albuquerque J, Sousa MF, Martiniano R, de Oliveira RC, Marques S, Gomes V, Amorim A, Alvarez L, Prata MJ. The Eastern side of the Westernmost Europeans: Insights from subclades within Y-chromosome haplogroup J-M304. Am J Hum Biol 2017; 30. [PMID: 29193490 DOI: 10.1002/ajhb.23082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/22/2017] [Accepted: 11/05/2017] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. METHODS A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci. RESULTS Among J1-M267 individuals (n = 36), five different sub-haplogroups were identified, with the most common being J1a2b2-L147.1 (∼72%), which encompassed the majority of representatives of the J1a2b-P58 subclade. One sample belonged to the rare J1a1-M365.1 lineage and presented a core Y-STR haplotype consistent with the Iberian settlement during the fifth century by the Alans, a people of Iranian heritage. The analysis of J2-M172 Portuguese males (n = 74) enabled the detection of the two main subclades at very dissimilar frequencies, J2a-M410 (∼80%) and J2b-M12 (∼20%), among which the most common branches were J2a1(xJ2a1b,h)-L26 (22.9%), J2a1b(xJ2a1b1)-M67 (20.3%), J2a1h-L24 (27%), and J2b2-M241 (20.3%). CONCLUSIONS While previous inferences based on modern haplogroup J Y-chromosomes implicated a main Neolithic dissemination, here we propose a later arrival of J lineages into Iberia using a combination of novel Portuguese Y-chromosomal data and recent evidence from ancient DNA. Our analysis suggests that a substantial tranche of J1-M267 lineages was likely carried into the Iberian Peninsula as a consequence of the trans-Mediterranean contacts during the first millennium BC, while most of the J2-M172 lineages may be associated with post-Neolithic population movements within Europe.
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Affiliation(s)
- Licínio Manco
- Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Joana Albuquerque
- Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal
| | - Maria Francisca Sousa
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Rui Martiniano
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, United Kingdom
| | | | - Sofia Marques
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Verónica Gomes
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - António Amorim
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Luís Alvarez
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Maria João Prata
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
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Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81). Sci Rep 2017; 7:15941. [PMID: 29162904 PMCID: PMC5698413 DOI: 10.1038/s41598-017-16271-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/09/2017] [Indexed: 12/30/2022] Open
Abstract
E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.
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30
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A glimpse at the intricate mosaic of ethnicities from Mesopotamia: Paternal lineages of the Northern Iraqi Arabs, Kurds, Syriacs, Turkmens and Yazidis. PLoS One 2017; 12:e0187408. [PMID: 29099847 PMCID: PMC5669434 DOI: 10.1371/journal.pone.0187408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/09/2017] [Indexed: 01/22/2023] Open
Abstract
Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others. As such, the genetics of the contemporary Iraqi populations are of anthropological and forensic interest. In an effort to contribute to a better understanding of the genetic basis of this ethnic diversity, a total of 500 samples were collected from Northern Iraqi volunteers belonging to five major ethnic groups, namely: Arabs (n = 102), Kurds (n = 104), Turkmens (n = 102), Yazidis (n = 106) and Syriacs (n = 86). 17-loci Y-STR analyses were carried out using the AmpFlSTR Yfiler system, and subsequently in silico haplogroup assignments were made to gain insights from a molecular anthropology perspective. Systematic comparisons of the paternal lineages of these five Northern Iraqi ethnic groups, not only among themselves but also in the context of the larger genetic landscape of the Near East and beyond, were then made through the use of two different genetic distance metric measures and the associated data visualization methods. Taken together, results from the current study suggested the presence of intricate Y-chromosomal lineage patterns among the five ethic groups analyzed, wherein both interconnectivity and independent microvariation were observed in parallel, albeit in a differential manner. Notably, the novel Y-STR data on Turkmens, Syriacs and Yazidis from Northern Iraq constitute the first of its kind in the literature. Data presented herein is expected to contribute to further population and forensic investigations in Northern Iraq in particular and the Near East in general.
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Yardumian A, Shengelia R, Chitanava D, Laliashvili S, Bitadze L, Laliashvili I, Villanea F, Sanders A, Azzam A, Groner V, Edleson K, Vilar MG, Schurr TG. Genetic diversity in Svaneti and its implications for the human settlement of the Highland Caucasus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:837-852. [PMID: 29076141 DOI: 10.1002/ajpa.23324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/19/2017] [Accepted: 09/10/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVES In this study, we characterized genetic diversity in the Svans from northwestern Georgia to better understand the phylogeography of their genetic lineages, determine whether genetic diversity in the highland South Caucasus has been shaped by language or geography, and assess whether Svan genetic diversity was structured by regional residence patterns. MATERIALS AND METHODS We analyzed mtDNA and Y-chromosome variation in 184 individuals from 13 village districts and townlets located throughout the region. For all individuals, we analyzed mtDNA diversity through control region sequencing, and, for males, we analyzed Y-chromosome diversity through SNP and STR genotyping. The resulting data were compared with those for populations from the Caucasus and Middle East. RESULTS We observed significant mtDNA heterogeneity in Svans, with haplogroups U1-U7, H, K, and W6 being common there. By contrast, ∼78% of Svan males belonged to haplogroup G2a, with the remainder falling into four other haplogroups (J2a1, I2, N, and R1a). While showing a distinct genetic profile, Svans also clustered with Caucasus populations speaking languages from different families, suggesting a deep common ancestry for all of them. The mtDNA data were not structured by geography or linguistic affiliation, whereas the NRY data were influenced only by geography. DISCUSSION These patterns of genetic variation confirm a complex set of geographic sources and settlement phases for the Caucasus highlands. Such patterns may also reflect social and cultural practices in the region. The high frequency and antiquity of Y-chromosome haplogroup G2a in this region further points to its emergence there.
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Affiliation(s)
- Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Pennsylvania 19009.,Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ramaz Shengelia
- Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 01747, Georgia
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Fernando Villanea
- Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Akiva Sanders
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Andrew Azzam
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Victoria Groner
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kristi Edleson
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Dzhaubermezov MA, Ekomasova NV, Litvinov SS, Khusainova RI, Akhmetova VL, Balinova NV, Khusnutdinova EK. Genetic characterization of Balkars and Karachays according to the variability of the Y chromosome. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Heraclides A, Bashiardes E, Fernández-Domínguez E, Bertoncini S, Chimonas M, Christofi V, King J, Budowle B, Manoli P, Cariolou MA. Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots. PLoS One 2017; 12:e0179474. [PMID: 28622394 PMCID: PMC5473566 DOI: 10.1371/journal.pone.0179474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/31/2017] [Indexed: 12/15/2022] Open
Abstract
Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7-8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.
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Affiliation(s)
- Alexandros Heraclides
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Evy Bashiardes
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | | | - Marios Chimonas
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Vasilis Christofi
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jonathan King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Panayiotis Manoli
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios A. Cariolou
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana. Sci Rep 2017; 7:3085. [PMID: 28596519 PMCID: PMC5465200 DOI: 10.1038/s41598-017-03176-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
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Kivisild T. The study of human Y chromosome variation through ancient DNA. Hum Genet 2017; 136:529-546. [PMID: 28260210 PMCID: PMC5418327 DOI: 10.1007/s00439-017-1773-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/24/2017] [Indexed: 12/15/2022]
Abstract
High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.
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Affiliation(s)
- Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 1QH, UK.
- Estonian Biocentre, 51010, Tartu, Estonia.
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36
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Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia. Hum Genet 2017; 136:437-450. [DOI: 10.1007/s00439-017-1770-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/20/2017] [Indexed: 12/22/2022]
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37
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Agdzhoyan AT, Balanovska EV, Padyukova AD, Dolinina DO, Kuznetsova MA, Zaporozhchenko VV, Skhalyakho RA, Koshel SM, Zhabagin MK, Yusupov YM, Mustafin KK, Ulyanova MV, Tychinskih ZA, Lavryashina MB, Balanovsky OP. Gene pool of Siberian Tatars: Five ways of origin for five subethnic groups. Mol Biol 2016. [DOI: 10.1134/s0026893316060029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Messina F, Finocchio A, Akar N, Loutradis A, Michalodimitrakis EI, Brdicka R, Jodice C, Novelletto A. Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean. PLoS One 2016; 11:e0167065. [PMID: 27898725 PMCID: PMC5127579 DOI: 10.1371/journal.pone.0167065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/08/2016] [Indexed: 11/18/2022] Open
Abstract
Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.
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Affiliation(s)
| | | | - Nejat Akar
- Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey
| | | | | | - Radim Brdicka
- Institute of Haematology and Blood Transfusion, Praha, Czech Republic
| | - Carla Jodice
- Department of Biology, University "Tor Vergata", Rome, Italy
| | - Andrea Novelletto
- Department of Biology, University "Tor Vergata", Rome, Italy
- * E-mail:
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39
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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 PMCID: PMC5113750 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l’Archéologie et de l’Ethnologie, 21 allée de l’Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs – UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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Gurkan C, Sevay H, Demirdov DK, Hossoz S, Ceker D, Teralı K, Erol AS. Turkish Cypriot paternal lineages bear an autochthonous character and closest resemblance to those from neighbouring Near Eastern populations. Ann Hum Biol 2016; 44:164-174. [DOI: 10.1080/03014460.2016.1207805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Damla Kanliada Demirdov
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Sinem Hossoz
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Deren Ceker
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Kerem Teralı
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Ayla Sevim Erol
- Department of Anthropology, Ankara University, Ankara, Turkey
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Canturk KM, Gurkan C, Sevay H, Emre R. Evaluation of the genetic parameters for 10 common and five new ESS core autosomal STR loci in seven major geographic regions and the largest metropolitan province of Turkey. Ann Hum Biol 2016; 44:149-163. [DOI: 10.1080/03014460.2016.1183709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Ramazan Emre
- Council of Forensic Medicine, Ministry of Justice, Istanbul, Turkey
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New native South American Y chromosome lineages. J Hum Genet 2016; 61:593-603. [PMID: 27030145 DOI: 10.1038/jhg.2016.26] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/23/2016] [Accepted: 02/22/2016] [Indexed: 11/09/2022]
Abstract
Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.
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Voskarides K, Mazières S, Hadjipanagi D, Di Cristofaro J, Ignatiou A, Stefanou C, King RJ, Underhill PA, Chiaroni J, Deltas C. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements. INVESTIGATIVE GENETICS 2016; 7:1. [PMID: 26870315 PMCID: PMC4750176 DOI: 10.1186/s13323-016-0032-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 12/15/2022]
Abstract
Background The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. Results Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography. Conclusions Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks. Electronic supplementary material The online version of this article (doi:10.1186/s13323-016-0032-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos Voskarides
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Stéphane Mazières
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Despina Hadjipanagi
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | | | - Anastasia Ignatiou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Charalambos Stefanou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Roy J King
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA USA
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California 94305 USA
| | - Jacques Chiaroni
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
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Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 2016; 6:19157. [PMID: 26754573 PMCID: PMC4709632 DOI: 10.1038/srep19157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022] Open
Abstract
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
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Affiliation(s)
- Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Raja Rajkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | | | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Amita Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Vidya Peddada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Vinee Khanna
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
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Omrak A, Günther T, Valdiosera C, Svensson EM, Malmström H, Kiesewetter H, Aylward W, Storå J, Jakobsson M, Götherström A. Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool. Curr Biol 2015; 26:270-275. [PMID: 26748850 DOI: 10.1016/j.cub.2015.12.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.
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Affiliation(s)
- Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden.
| | - Torsten Günther
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Cristina Valdiosera
- Department of Archaeology, Environment and Community Planning, La Trobe University, VIC 3086, Melbourne, Australia; Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Emma M Svensson
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ullsväg 26, 75007, Uppsala, Sweden
| | - Helena Malmström
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Henrike Kiesewetter
- Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Schloss-Burgsteige 11, 72070, Tuebingen, Germany
| | - William Aylward
- Biotechnology Center and Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, 1220 Linden Drive, Madison, WI 53706, USA
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden.
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Tarkhnishvili D, Gavashelishvili A, Murtskhvaladze M, Gabelaia M, Tevzadze G. Human paternal lineages, languages, and environment in the Caucasus. Hum Biol 2015; 86:113-30. [PMID: 25397702 DOI: 10.3378/027.086.0205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2014] [Indexed: 11/05/2022]
Abstract
Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.
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Affiliation(s)
- David Tarkhnishvili
- Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | | | - Marine Murtskhvaladze
- Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | - Mariam Gabelaia
- Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | - Gigi Tevzadze
- 4D Research Institute, Ilia State University, Tbilisi, Georgia
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Pliss L, Timša L, Rootsi S, Tambets K, Pelnena I, Zole E, Puzuka A, Sabule A, Rozane S, Lace B, Kucinskas V, Krumina A, Ranka R, Baumanis V. Y-Chromosomal Lineages of Latvians in the Context of the Genetic Variation of the Eastern-Baltic Region. Ann Hum Genet 2015; 79:418-30. [PMID: 26411886 DOI: 10.1111/ahg.12130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 06/19/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Variations of the nonrecombining Y-chromosomal region were investigated in 159 unrelated Baltic-speaking ethnic Latvians from four different geographic regions, using 28 biallelic markers and 12 short tandem repeats. Eleven different haplogroups (hgs) were detected in a regionally homogeneous Latvian population, among which N1c, R1a, and I1 cover more than 85% of its paternal lineages. When compared its closest geographic neighbors, the composition of the Latvian Y-chromosomal gene pool was found to be very similar to those of Lithuanians and Estonians. Despite the comparable frequency distribution of hg N1c in Latvians and Lithuanians with the Finno-Ugric-speaking populations from the Eastern coast of the Baltic Sea, the observed differences in allelic variances of N1c haplotypes between these two groups are in concordance with the previously stated hypothesis of different dispersal ways of this lineage in the region. More than a third of Latvian paternal lineages belong specifically to a recently defined R1a-M558 hg, indicating an influence from a common source within Eastern Slavic populations on the formation of the present-day Latvian Y-chromosome gene pool.
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Affiliation(s)
- Liana Pliss
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Līga Timša
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | - Inese Pelnena
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Egija Zole
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Areta Sabule
- State Centre for Forensic Medical Examination of the Republic of Latvia, Riga, Latvia
| | - Sandra Rozane
- State Centre for Forensic Medical Examination of the Republic of Latvia, Riga, Latvia
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vaidutis Kucinskas
- Human Genome Research Centre, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Edem E, Kirdök AH, Kınay AO, Tekin Üİ, Taş S, Alpaslan E, Pabuccu MT, Akdeniz B. Does "smoker's paradox" exist in clopidogrel-treated Turkish patients with acute coronary syndrome. Platelets 2015; 27:240-4. [PMID: 26367336 DOI: 10.3109/09537104.2015.1083544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Previously conducted studies revealed that smoking enhanced the efficacy of clopidogrel by increasing formation of the active metabolite (AM) from the prodrug through induction of the cytochrome CYP1A2. The expression of cytochrome enzymes depends on genotype and no data exists in literature conducted in Turkish patients comparing the clopidogrel responsiveness between active smokers and non-active smokers treated with clopidogrel. In this study, our aim was to investigate the clopidogrel responsiveness in clopidogrel-treated Turkish acute coronary syndrome (ACS) patients according to their smoking status. We retrospectively enrolled 258 patients who were hospitalized due to ACS. Clinical variables of the patients, especially smoking status were recorded. Clopidogrel resistance was evaluated by using adenosine diphosphate (ADP) induced platelet aggregometry. Clopidogrel resistance was detected as a change in maximal aggregation ≤20% from baseline. A total of 139 patients were active smokers while 12 were former smokers. 107 patients did not have a history of smoking. Ten of the smokers were hyporesponsive to clopidogrel, whereas 36 of non-smokers were hyporesponsive to clopidogrel (p < 0.001). Receiver-operating characteristic curve analysis demonstrated that Au-min value >612.5 predicted the clopidogrel resistance with a sensitivity of 60% (OR: 100.65, %95 CI = 19.996-506.615 p < 0.001). Results of this study demonstrated that ADP responses were lower in smokers receiving clopidogrel and aspirin than in non-smokers receiving the same drug regimen. This finding indicates that smoking was related to an enhanced clopidogrel responsiveness in Turkish patients hospitalized due to ACS, suggesting that "smoker's paradox" probably exists in Turkish ACS patients.
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Affiliation(s)
- Efe Edem
- a Department of Cardiology , Tınaztepe Hospital , Izmir , Turkey and
| | - Ali Hikmet Kirdök
- a Department of Cardiology , Tınaztepe Hospital , Izmir , Turkey and
| | - Ahmet Ozan Kınay
- a Department of Cardiology , Tınaztepe Hospital , Izmir , Turkey and
| | - Ümit İlker Tekin
- a Department of Cardiology , Tınaztepe Hospital , Izmir , Turkey and
| | - Sedat Taş
- b Department of Cardiology, Faculty of Medicine , Dokuz Eylül University , Izmir , Turkey
| | - Erkan Alpaslan
- b Department of Cardiology, Faculty of Medicine , Dokuz Eylül University , Izmir , Turkey
| | - Mustafa Türker Pabuccu
- b Department of Cardiology, Faculty of Medicine , Dokuz Eylül University , Izmir , Turkey
| | - Bahri Akdeniz
- b Department of Cardiology, Faculty of Medicine , Dokuz Eylül University , Izmir , Turkey
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Alfadhli S, Ayadi I, Ben Marzoug R, Carracedo Á, Rebai A. Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol 2015; 28:203-12. [PMID: 26293354 DOI: 10.1002/ajhb.22773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2015] [Accepted: 07/25/2015] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape. METHOD A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe. RESULTS The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan. CONCLUSION Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.
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Affiliation(s)
- Soumaya Triki-Fendri
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Suad Alfadhli
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Kuwait
| | - Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
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50
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Valverde L, Illescas MJ, Villaescusa P, Gotor AM, García A, Cardoso S, Algorta J, Catarino S, Rouault K, Férec C, Hardiman O, Zarrabeitia M, Jiménez S, Pinheiro MF, Jarreta BM, Olofsson J, Morling N, de Pancorbo MM. New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia. Eur J Hum Genet 2015; 24:437-41. [PMID: 26081640 DOI: 10.1038/ejhg.2015.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 04/19/2015] [Accepted: 04/29/2015] [Indexed: 11/09/2022] Open
Abstract
The dissection of S116 in more than 1500 individuals from Atlantic Europe and the Iberian Peninsula has provided important clues about the controversial evolutionary history of M269. First, the results do not point to an origin of M269 in the Franco-Cantabrian refuge, owing to the lack of sublineage diversity within M269, which supports the new theories proposing its origin in Eastern Europe. Second, S116 shows frequency peaks and spatial distribution that differ from those previously proposed, indicating an origin farther west, and it also shows a high frequency in the Atlantic coastline. Third, an outstanding frequency of the DF27 sublineage has been found in Iberia, with a restricted distribution pattern inside this peninsula and a frequency maximum in the area of the Franco-Cantabrian refuge. This entire panorama indicates an old arrival of M269 into Western Europe, because it has generated at least two episodes of expansion in the Franco-Cantabrian area. This study demonstrates the importance of continuing the dissection of the M269 lineage in different European populations because the discovery and study of new sublineages can adjust or even completely revise the theories about European peopling, as has been the case for the place of origin of M269.
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Affiliation(s)
- Laura Valverde
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Maria José Illescas
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Amparo M Gotor
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Ainara García
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Sergio Cardoso
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Jaime Algorta
- Progenika Biopharma SA (a Grifols company), Bizkaia Technology Park, Derio, Spain.,Department of Molecular Biology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Susana Catarino
- Progenika Biopharma SA (a Grifols company), Bizkaia Technology Park, Derio, Spain
| | - Karen Rouault
- Inserm UMR1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, France
| | - Claude Férec
- Inserm UMR1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, France
| | - Orla Hardiman
- National Neuroscience Centre, Beaumont Hospital, Dublin, Ireland
| | - Maite Zarrabeitia
- Forensic and Legal Medicine Area, Department of Physiology and Pharmacology, University of Cantabria, Cantabria, Spain
| | - Susana Jiménez
- Forensic Medicine Division, Department of Pathology and Surgery, University Miguel Hernandez Elche, Alicante, Spain
| | - Maria Fátima Pinheiro
- Forensic Genetics Department, National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
| | - Begoña M Jarreta
- Laboratory of Genetics and Genetic Identification, Department of Pharmacology, University of Zaragoza, Zaragoza, Spain
| | - Jill Olofsson
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
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