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Derenko M, Denisova G, Litvinov A, Dambueva I, Malyarchuk B. Mitogenomics of the Koryaks and Evens of the northern coast of the Sea of Okhotsk. J Hum Genet 2023; 68:705-712. [PMID: 37316650 DOI: 10.1038/s10038-023-01173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Due to the geographical proximity of the northern coast of the Sea of Okhotsk and Kamchatka Peninsula to the Beringia, the indigenous populations of these territories are of great interest for elucidating the human settlement history of northern Asia and America. Meanwhile, there is a clear shortage of genetic studies of the indigenous populations of the northern coast of the Sea of Okhotsk. Here, in order to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 203 complete mitogenomes (174 of which are new) from population samples of the Koryaks and Evens of the northern coast of the Sea of Okhotsk and the Chukchi of the extreme northeast Asia. The patterns observed underscore the reduced level of genetic diversity found in the Koryak, Even, and Chukchi populations, which, along with the high degree of interpopulation differentiation, may be the result of genetic drift. Our phylogeographic analysis reveals common Paleo-Asiatic ancestry for 51.1% of the Koryaks and 17.8% of the Evens. About third of the mitogenomes found in the Koryaks and Evens might be considered as ethno-specific, as these are virtually absent elsewhere in North, Central and East Asia. Coalescence ages of most of these lineages coincide well with the emergence and development of the Tokarev and Old Koryak archaeological cultures associated with the formation of the Koryaks, as well as with the period of separation and split of the North Tungusic groups migrated northwards from the Lake Baikal or the Amur River area.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Irina Dambueva
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
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2
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Li YC, Gao ZL, Liu KJ, Tian JY, Yang BY, Rahman ZU, Yang LQ, Zhang SH, Li CT, Achilli A, Semino O, Torroni A, Kong QP. Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan. Cell Rep 2023:112413. [PMID: 37164007 DOI: 10.1016/j.celrep.2023.112413] [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: 07/28/2022] [Revised: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023] Open
Abstract
Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zong-Liang Gao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Kai-Jun Liu
- Chengdu 23Mofang Biotechnology Co., Ltd., Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China.
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3
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Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade. Int J Mol Sci 2022; 23:ijms23169219. [PMID: 36012483 PMCID: PMC9408831 DOI: 10.3390/ijms23169219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 12/03/2022] Open
Abstract
Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries—the time of the Atlantic slave trade—thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the “greening” of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies.
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5
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Mitogenomics of modern Mongolic-speaking populations. Mol Genet Genomics 2021; 297:47-62. [PMID: 34757478 DOI: 10.1007/s00438-021-01830-w] [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: 03/11/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
Here, we present a comprehensive data set of 489 complete mitogenomes (211 of which are new) from four Mongolic-speaking populations (Mongols, Barghuts, Khamnigans, and Buryats) to investigate their matrilineal genetic structure, ancestry and relationship with other ethnic groups. We show that along with very high levels of genetic diversity and lack of genetic differentiation, Mongolic-speaking populations exhibit strong genetic resemblance to East Asian populations of Chinese, Japanese, and Uyghurs. Phylogeographic analysis of complete mitogenomes reveals the presence of different components in the gene pools of modern Mongolic-speaking populations-the main East Eurasian component is represented by mtDNA lineages of East Asian, Siberian and autochthonous (the Baikal region/Mongolian) ancestry, whereas the less pronounced West Eurasian component can be ascribed to Europe and West Asia/Caucasus. We also observed that up to one third of the mtDNA subhaplogroups identified in Mongolic-speaking populations can be considered as Mongolic-specific with the coalescence age of most of them not exceeding 1.7 kya. This coincides well with the population size growth which started around 1.1 kya and is detectable only in the Bayesian Skyline Plot constructed based on Mongolic-specific mitogenomes. Our data suggest that the genetic structure established during the Mongol empire is still retained in present-day Mongolic-speaking populations.
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6
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Sacks BN, Mitchell KJ, Quinn CB, Hennelly LM, Sinding MHS, Statham MJ, Preckler-Quisquater S, Fain SR, Kistler L, Vanderzwan SL, Meachen JA, Ostrander EA, Frantz LAF. Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote. Mol Ecol 2021; 30:4292-4304. [PMID: 34181791 DOI: 10.1111/mec.16048] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022]
Abstract
The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant "coyote-like" ancestry obtained from post-colonial coyote hybridization (2-species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3-species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2-species model and to investigate a broader phylogeographic 3-species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid-continent 60-80 ka; red wolves subsequently disappeared from the mid-continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50-30 ka); by the early Holocene (12-10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre-dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD) and ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Lauren M Hennelly
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Steven R Fain
- National Fish & Wildlife Forensic Laboratory, Ashland, OR, USA
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Stevi L Vanderzwan
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, IA, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laurent A F Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Munich, Germany.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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7
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Almeida J, Fehn AM, Ferreira M, Machado T, Hagemeijer T, Rocha J, Gayà-Vidal M. The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea. Genes (Basel) 2021; 12:833. [PMID: 34071462 PMCID: PMC8229774 DOI: 10.3390/genes12060833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022] Open
Abstract
The forced migration of millions of Africans during the Atlantic Slave Trade led to the emergence of new genetic and linguistic identities, thereby providing a unique opportunity to study the mechanisms giving rise to human biological and cultural variation. Here we focus on the archipelago of São Tomé and Príncipe in the Gulf of Guinea, which hosted one of the earliest plantation societies relying exclusively on slave labor. We analyze the genetic variation in 25 individuals from three communities who speak distinct creole languages (Forros, Principenses and Angolares), using genomic data from expanded exomes in combination with a contextual dataset from Europe and Africa, including newly generated data from 28 Bantu speakers from Angola. Our findings show that while all islanders display mixed contributions from the Gulf of Guinea and Angola, the Angolares are characterized by extreme genetic differentiation and inbreeding, consistent with an admixed maroon isolate. In line with a more prominent Bantu contribution to their creole language, we additionally found that a previously reported high-frequency Y-chromosome haplotype in the Angolares has a likely Angolan origin, suggesting that their genetic, linguistic and social characteristics were influenced by a small group of dominant men who achieved disproportionate reproductive success.
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Affiliation(s)
- João Almeida
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Anne-Maria Fehn
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- Department of Linguistic and Cultural Evolution, Max-Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Margarida Ferreira
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Teresa Machado
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
| | - Tjerk Hagemeijer
- Centro de Linguística da Universidade de Lisboa, 1600-214 Lisboa, Portugal;
- Faculdade de Letras, Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Jorge Rocha
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Magdalena Gayà-Vidal
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
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8
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Complete mitogenomes document substantial genetic contribution from the Eurasian Steppe into northern Pakistani Indo-Iranian speakers. Eur J Hum Genet 2021; 29:1008-1018. [PMID: 33637889 DOI: 10.1038/s41431-021-00829-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/26/2022] Open
Abstract
To elucidate whether Bronze Age population dispersals from the Eurasian Steppe to South Asia contributed to the gene pool of Indo-Iranian-speaking groups, we analyzed 19,568 mitochondrial DNA (mtDNA) sequences from northern Pakistani and surrounding populations, including 213 newly generated mitochondrial genomes (mitogenomes) from Iranian and Dardic groups, both speakers from the ancient Indo-Iranian branch in northern Pakistan. Our results showed that 23% of mtDNA lineages with west Eurasian origin arose in situ in northern Pakistan since ~5000 years ago (kya), a time depth very close to the documented Indo-European dispersals into South Asia during the Bronze Age. Together with ancient mitogenomes from western Eurasia since the Neolithic, we identified five haplogroups (~8.4% of maternal gene pool) with roots in the Steppe region and subbranches arising (age ~5-2 kya old) in northern Pakistan as genetic legacies of Indo-Iranian speakers. Some of these haplogroups, such as W3a1b that have been found in the ancient samples from the late Bronze Age to the Iron Age period individuals of Swat Valley northern Pakistan, even have sub-lineages (age ~4 kya old) in the southern subcontinent, consistent with the southward spread of Indo-Iranian languages. By showing that substantial genetic components of Indo-Iranian speakers in northern Pakistan can be traced to Bronze Age in the Steppe region, our study suggests a demographic link with the spread of Indo-Iranian languages, and further highlights the corridor role of northern Pakistan in the southward dispersal of Indo-Iranian-speaking groups.
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Zhabagin M, Sabitov Z, Tazhigulova I, Alborova I, Agdzhoyan A, Wei LH, Urasin V, Koshel S, Mustafin K, Akilzhanova A, Li H, Balanovsky O, Balanovska E. Medieval Super-Grandfather founder of Western Kazakh Clans from Haplogroup C2a1a2-M48. J Hum Genet 2021; 66:707-716. [PMID: 33510364 DOI: 10.1038/s10038-021-00901-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/09/2022]
Abstract
Western Kazakhstan is populated by three clans totaling 2 million people. Since the clans are patrilineal, the Y-chromosome is the most informative genetic system for tracing their origin. We genotyped 40 Y-SNP and 17 Y-STR markers in 330 Western Kazakhs. High phylogenetic resolution within haplogroup C2a1a2-M48 was achieved by using additional SNPs. Three lines of evidence indicate that the Alimuly and Baiuly clans (but not the Zhetiru clan) have a common founder placed 700 ± 200 years back by the STR data and 500 ± 200 years back by the sequencing data. This supports traditional genealogy claims about the descent of these clans from Emir Alau, who lived 650 years ago and whose lineage might be carried by two-thirds of Western Kazakhs. There is accumulation of specific haplogroups in the subclans representing other lineages, confirming that the clan structure corresponds with the paternal genetic structure of the steppe population.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic science center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Irina Alborova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasiya Agdzhoyan
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Lan-Hai Wei
- MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Kharis Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Biobank of North Eurasia, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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10
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Rito T, Richards MB, Pala M, Correia-Neves M, Soares PA. Phylogeography of 27,000 SARS-CoV-2 Genomes: Europe as the Major Source of the COVID-19 Pandemic. Microorganisms 2020; 8:E1678. [PMID: 33137892 PMCID: PMC7693378 DOI: 10.3390/microorganisms8111678] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a phylogeny with 20,247 mutation events and adopted a phylogeographic approach. We confirmed that the phylogeny pinpoints China as the origin of the pandemic with major founders worldwide, mainly during January 2020. However, a single specific East Asian founder underwent massive radiation in Europe and became the main actor of the subsequent spread worldwide during March 2020. This lineage accounts for the great majority of cases detected globally and even spread back to the source in East Asia. Despite an East Asian source, therefore, the global pandemic was mainly fueled by its expansion across and out of Europe. It seems likely that travel bans established throughout the world in the second half of March helped to decrease the number of intercontinental exchanges, particularly from mainland China, but were less effective between Europe and North America where exchanges in both directions are visible up to April, long after bans were imposed.
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Affiliation(s)
- Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (T.R.); (M.C.-N.)
- ICVS/3B’s, PT Government Associate Laboratory, University of Minho, 4710-057 Braga, Portugal
| | - Martin B. Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK; (M.B.R.); (M.P.)
| | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK; (M.B.R.); (M.P.)
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (T.R.); (M.C.-N.)
- ICVS/3B’s, PT Government Associate Laboratory, University of Minho, 4710-057 Braga, Portugal
| | - Pedro A. Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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11
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Zhabagin M, Sabitov Z, Tarlykov P, Tazhigulova I, Junissova Z, Yerezhepov D, Akilzhanov R, Zholdybayeva E, Wei LH, Akilzhanova A, Balanovsky O, Balanovska E. The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan. BMC Genet 2020; 21:87. [PMID: 33092538 PMCID: PMC7583311 DOI: 10.1186/s12863-020-00897-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 12/02/2022] Open
Abstract
Background The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. There are three main hypotheses of the clans’ origin, namely, origin from early Wusuns, from Niru’un Mongols, or from Darligin Mongols. We genotyped 490 samples of South Kazakhs by 35 Y-chromosomal SNPs (single nucleotide polymorphism) and 17 STRs (short tandem repeat). Additionally, 133 samples from citizen science projects were included into the study. Results We found that three Uissun clans have unique Y-chromosomal profiles, but the remaining six Uissun clans and one non-Uissun clan share a common paternal gene pool. They share a high frequency (> 40%) of the C2*-ST haplogroup (marked by the SNP F3796), which is associated with the early Niru’un Mongols. Phylogenetic analysis of this haplogroup carried out on 743 individuals from 25 populations of Eurasia has revealed a set of haplotype clusters, three of which contain the Uissun haplotypes. The demographic expansion of these clusters dates back to the 13-fourteenth century, coinciding with the time of the Uissun’s ancestor Maiky-biy known from historical sources. In addition, it coincides with the expansion period of the Mongol Empire in the Late Middle Ages. A comparison of the results with published aDNA (ancient deoxyribonucleic acid) data and modern Y haplogroups frequencies suggest an origin of Uissuns from Niru’un Mongols rather than from Wusuns or Darligin Mongols. Conclusions The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th–14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor. The majority of the Y-chromosomal lineages of South Kazakhstan was brought by the migration of the population related to the medieval Niru’un Mongols.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan.,Young Researchers Alliance, Nur-Sultan, Republic of Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic Science Center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Zukhra Junissova
- Research Institute of Archeology named after K.A. Akishev, Nur-Sultan, Republic of Kazakhstan
| | - Dauren Yerezhepov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Lan-Hai Wei
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
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12
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Cabrera VM. Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock. BMC Evol Biol 2020; 20:78. [PMID: 32600249 PMCID: PMC7325269 DOI: 10.1186/s12862-020-01640-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The molecular clock is an important genetic tool for estimating evolutionary timescales. However, the detection of a time-dependent effect on substitution rate estimates complicates its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study, I propose a new algorithm for estimating the coalescent age of phylogenetically related sequences, taking into account the observed time-dependent effect on the molecular rate detected by others. RESULTS By applying this method to real human mitochondrial DNA trees with shallow and deep topologies, I obtained significantly older molecular ages for the main events of human evolution than were previously estimated. These ages are in close agreement with the most recent archaeological and paleontological records favoring the emergence of early anatomically modern humans in Africa 315 ± 34 thousand years ago (kya) and the presence of recent modern humans outside of Africa as early as 174 ± 48 thousand years ago. Furthermore, during the implementation process, I demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size, which is in better accordance with the fact that under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift. CONCLUSIONS I suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and I propose a new method that corrects for this effect.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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13
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Inlamea OF, Soares P, Ikuta CY, Heinemann MB, Achá SJ, Machado A, Ferreira Neto JS, Correia-Neves M, Rito T. Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans. PLoS Negl Trop Dis 2020; 14:e0008081. [PMID: 32119671 PMCID: PMC7077849 DOI: 10.1371/journal.pntd.0008081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/17/2020] [Accepted: 01/22/2020] [Indexed: 01/05/2023] Open
Abstract
Mycobacterium bovis is the pathogenic agent responsible for bovine tuberculosis (bTB), a zoonotic disease affecting mostly cattle, but also transmittable to humans and wildlife. Genetic studies on M. bovis allow to detect possible routes of bTB transmission and the identification of genetic reservoirs that may provide an essential framework for public health action. We used a database with 1235 M. bovis genotypes collected from different regions in Africa with 45 new Mozambican samples. Our analyses, based on phylogeographic and population genetics’ approaches, allowed to identify two clear trends. First, the genetic diversity of M. bovis is geographically clustered across the continent, with the only incidences of long-distance sharing of genotypes, between South Africa and Algeria, likely due to recent European introductions. Second, there is a broad gradient of diversity from Northern to Southern Africa with a diversity focus on the proximity to the Near East, where M. bovis likely emerged with animal domestication in the last 10,000 years. Diversity indices are higher in Eastern Africa, followed successively by Northern, Central, Southern and Western Africa, roughly correlating with the regional archaeological records of introduction of animal domesticates. Given this scenario M. bovis in Africa was probably established millennia ago following a concomitant spread with cattle, sheep and goat. Such scenario could translate into long-term locally adapted lineages across Africa. This work describes a novel scenario for the spread of M. bovis in Africa using the available genetic data, opening the field to further studies using higher resolution genomic data. We describe the genetic diversity distribution in Africa of the pathogen Mycobacterium bovis, the responsible for bovine tuberculosis, mostly present in cattle but also transmittable to other animals including humans. This diversity is geographically clustered within the African continent meaning that the genetic diversity was established through independent evolution within different areas. Higher diversity values of M. bovis are found in Eastern and Northern Africa, followed by Central Africa, with Western and Southern Africa displaying the lowest diversity. These levels of diversity correlate well with the introduction of domesticated livestock in the different regions of Africa, following their domestication in the Near East 10,000 ago. We hypothesize that M. bovis emerged in the Near East and it was carried across Africa together with domesticated animals and people that developed herding practices and biological tolerance for digesting milk in adulthood. Such scenario implies a strong evolution and co-evolution of M. bovis across Africa leading to locally adapted strains that could prove a challenge for public health actions.
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Affiliation(s)
- Osvaldo Frederico Inlamea
- Programa de pós-graduação Ciência Para o desenvolvimento (PGCD)–Instituto Gulbenkian de Ciência–Portugal
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
- Instituto Nacional de Saúde, Ministério de Saúde, Moçambique
- Faculdade de Veterinária (FAVET), Universidade Eduardo Mondlane, Maputo, Moçambique
- * E-mail: (OFI); (TR)
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), School of Sciences, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Cassia Yumi Ikuta
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
| | - Marcos Bryan Heinemann
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
| | - Sara Juma Achá
- Direcção de Ciências Animais, Instituto de Investigação Agrária de Moçambique, Ministério de Agricultura e Segurança Alimentar, Maputo, Moçambique
| | - Adelina Machado
- Faculdade de Veterinária (FAVET), Universidade Eduardo Mondlane, Maputo, Moçambique
| | | | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail: (OFI); (TR)
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