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Wang XT(X, Miller G. Biracial Faces Offer Visual Cues of Successful Intergroup Contact: Genetic Admixture and Coalition Detection. Evol Psychol 2024; 22:14747049241238623. [PMID: 38477637 PMCID: PMC10938625 DOI: 10.1177/14747049241238623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
This research explores how biracial facial cues affect racial perception and social judgment. We tested a coalition-signaling hypothesis of biracial cues in two studies conducted in the United States (n = 227) and China (n = 116). From the perspective of intergroup and interpersonal relations theories in social psychology, biracial features would likely be perceived as cues of threat or resource competition. In contrast, we propose an evolutionary hypothesis that biracial facial cues reveal the ancestral history of intergroup alliances between members of two races or ethnic groups. When racial cues are mixed, we predict that biracial individuals may be viewed more positively than other-race or even own-race members who often compete for limited ingroup resources. The participants observed facial images that ranged from 100% Asian to 100% Caucasian, including morphed biracial composites of 30%, 40%, 50%, 60%, and 70% Caucasian or Asian. The participants evaluated each image regarding perceived Caucasianness (Asianness), attractiveness, trustworthiness, health, intelligence, and career prospects. The US and Chinese samples yielded a similar pattern of own-race bias in racial perception and biracial favoritism in social judgment. The social judgment ratings were not correlated with the racial perception scores and were independent of the sex of the participants or biracial images, indicating a coalitional motive, instead of a mating motive, underlying social perception of biracial individuals. Overall, the results suggest that biracial facial features signal a successful genetic admixture and coalition in parental generations and thus increase the trustworthiness and cooperative potential of a biracial person.
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Affiliation(s)
- XT (XiaoTian) Wang
- Applied Psychology Division, School of Humanities and Social Science, The Chinese University of Hong Kong (Shenzhen), Shenzhen, China
| | - Geoffrey Miller
- Psychology Department, University of New Mexico, Albuquerque, NM, USA
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Chan TF, Rui X, Conti DV, Fornage M, Graff M, Haessler J, Haiman C, Highland HM, Jung SY, Kenny EE, Kooperberg C, Le Marchand L, North KE, Tao R, Wojcik G, Gignoux CR, Chiang CWK, Mancuso N. Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics. Am J Hum Genet 2023; 110:1853-1862. [PMID: 37875120 PMCID: PMC10645552 DOI: 10.1016/j.ajhg.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The heritability explained by local ancestry markers in an admixed population (hγ2) provides crucial insight into the genetic architecture of a complex disease or trait. Estimation of hγ2 can be susceptible to biases due to population structure in ancestral populations. Here, we present heritability estimation from admixture mapping summary statistics (HAMSTA), an approach that uses summary statistics from admixture mapping to infer heritability explained by local ancestry while adjusting for biases due to ancestral stratification. Through extensive simulations, we demonstrate that HAMSTA hγ2 estimates are approximately unbiased and are robust to ancestral stratification compared to existing approaches. In the presence of ancestral stratification, we show a HAMSTA-derived sampling scheme provides a calibrated family-wise error rate (FWER) of ∼5% for admixture mapping, unlike existing FWER estimation approaches. We apply HAMSTA to 20 quantitative phenotypes of up to 15,988 self-reported African American individuals in the Population Architecture using Genomics and Epidemiology (PAGE) study. We observe hˆγ2 in the 20 phenotypes range from 0.0025 to 0.033 (mean hˆγ2 = 0.012 ± 9.2 × 10-4), which translates to hˆ2 ranging from 0.062 to 0.85 (mean hˆ2 = 0.30 ± 0.023). Across these phenotypes we find little evidence of inflation due to ancestral population stratification in current admixture mapping studies (mean inflation factor of 0.99 ± 0.001). Overall, HAMSTA provides a fast and powerful approach to estimate genome-wide heritability and evaluate biases in test statistics of admixture mapping studies.
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Affiliation(s)
- Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christopher Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Su Yon Jung
- Translational Sciences Section, School of Nursing, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Genevieve Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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Zollner L, Boekstegers F, Barahona Ponce C, Scherer D, Marcelain K, Gárate-Calderón V, Waldenberger M, Morales E, Rojas A, Munoz C, Retamales J, De Toro G, Kortmann AV, Barajas O, Rivera MT, Cortés A, Loader D, Saavedra J, Gutiérrez L, Ortega A, Bertrán ME, Bartolotti L, Gabler F, Campos M, Alvarado J, Moisán F, Spencer L, Nervi B, Carvajal D, Losada H, Almau M, Fernández P, Olloquequi J, Carter AR, Miquel Poblete JF, Bustos BI, Fuentes Guajardo M, Gonzalez-Jose R, Bortolini MC, Acuña-Alonzo V, Gallo C, Ruiz Linares A, Rothhammer F, Lorenzo Bermejo J. Gallbladder Cancer Risk and Indigenous South American Mapuche Ancestry: Instrumental Variable Analysis Using Ancestry-Informative Markers. Cancers (Basel) 2023; 15:4033. [PMID: 37627062 PMCID: PMC10452561 DOI: 10.3390/cancers15164033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A strong association between the proportion of indigenous South American Mapuche ancestry and the risk of gallbladder cancer (GBC) has been reported in observational studies. Chileans show the highest incidence of GBC worldwide, and the Mapuche are the largest indigenous people in Chile. We set out to assess the confounding-free effect of the individual proportion of Mapuche ancestry on GBC risk and to investigate the mediating effects of gallstone disease and body mass index (BMI) on this association. Genetic markers of Mapuche ancestry were selected based on the informativeness for assignment measure, and then used as instrumental variables in two-sample Mendelian randomization analyses and complementary sensitivity analyses. Results suggested a putatively causal effect of Mapuche ancestry on GBC risk (inverse variance-weighted (IVW) risk increase of 0.8% per 1% increase in Mapuche ancestry proportion, 95% CI 0.4% to 1.2%, p = 6.7 × 10-5) and also on gallstone disease (3.6% IVW risk increase, 95% CI 3.1% to 4.0%), pointing to a mediating effect of gallstones on the association between Mapuche ancestry and GBC. In contrast, the proportion of Mapuche ancestry showed a negative effect on BMI (IVW estimate -0.006 kg/m2, 95% CI -0.009 to -0.003). The results presented here may have significant implications for GBC prevention and are important for future admixture mapping studies. Given that the association between the individual proportion of Mapuche ancestry and GBC risk previously noted in observational studies appears to be free of confounding, primary and secondary prevention strategies that consider genetic ancestry could be particularly efficient.
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Affiliation(s)
- Linda Zollner
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
| | - Carol Barahona Ponce
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
| | - Dominique Scherer
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.)
| | - Valentina Gárate-Calderón
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.)
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Erik Morales
- Hospital Regional de Talca, Talca 3460000, Chile; (E.M.); (C.M.)
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | - Armando Rojas
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | - César Munoz
- Hospital Regional de Talca, Talca 3460000, Chile; (E.M.); (C.M.)
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | | | - Gonzalo De Toro
- Hospital de Puerto Montt, Puerto Montt 5480000, Chile; (G.D.T.); (A.V.K.)
- Escuela de Tecnología Médica, Universidad Austral de Chile sede Puerto Montt, Puerto Montt 5480000, Chile
| | | | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.)
- Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
| | | | - Analía Cortés
- Hospital del Salvador, Santiago 7500922, Chile; (M.T.R.); (A.C.)
| | - Denisse Loader
- Hospital Padre Hurtado, Santiago 8880456, Chile; (D.L.); (J.S.)
| | | | | | | | | | | | - Fernando Gabler
- Hospital San Borja Arriarán, Santiago 8320000, Chile; (F.G.); (M.C.)
| | - Mónica Campos
- Hospital San Borja Arriarán, Santiago 8320000, Chile; (F.G.); (M.C.)
| | - Juan Alvarado
- Hospital Regional Guillermo Grant Benavente, Concepción 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Fabricio Moisán
- Hospital Regional Guillermo Grant Benavente, Concepción 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Loreto Spencer
- Hospital Regional Guillermo Grant Benavente, Concepción 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Bruno Nervi
- Departamento de Hematología y Oncología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330077, Chile;
| | - Daniel Carvajal
- Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7650568, Chile;
| | - Héctor Losada
- Departamento de Cirugía, Universidad de la Frontera, Temuco 4780000, Chile;
| | - Mauricio Almau
- Hospital de Rancagua, Rancagua 2820000, Chile; (M.A.); (P.F.)
| | | | - Jordi Olloquequi
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain;
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Alice R. Carter
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK;
| | - Juan Francisco Miquel Poblete
- Departamento de Gastroenterología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile;
| | - Bernabe Ignacio Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Macarena Fuentes Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica 1000815, Chile;
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9120ACD, Argentina;
| | - Maria Cátira Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre 15053, Brazil;
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru;
| | - Andres Ruiz Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200434, China;
- ADES (Anthropologie Bio-Culturelle, Droit, Éthique et Santé), UFR de Médecine, Aix-Marseille University, 13007 Marseille, France
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
- Department of Biostatistics for Precision Oncology, Institut de Cancérologie Strasbourg Europe, 67200 Strasbourg, France
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Farhat P, Siljak-Yakovlev S, Takvorian N, Bou Dagher Kharrat M, Robert T. Allopolyploidy: An Underestimated Driver in Juniperus Evolution. Life (Basel) 2023; 13:1479. [PMID: 37511854 PMCID: PMC10381917 DOI: 10.3390/life13071479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Allopolyploidy is considered as a principal driver that shaped angiosperms' evolution in terms of diversification and speciation. Despite the unexpected high frequency of polyploidy that was recently discovered in the coniferous genus Juniperus, little is known about the origin of these polyploid taxa. Here, we conducted the first study devoted to deciphering the origin of the only hexaploid taxon in Juniperus along with four of its closely related tetraploid taxa using AFLP markers with four primers combinations. Phylogenetic analysis revealed that the 10 studied species belong to 2 major clusters. J. foetidissima appeared to be more related to J. thurifera, J. sabina, and J. chinensis. The Bayesian clustering analysis showing a slight variation in genetic admixture between the studied populations of J. foetidissima, suggesting an allopolyploid origin of this species involving J. thurifera and J. sabina lineages, although a purely autopolyploidy origin of both J. thurifera and J. foetidissima cannot be ruled out. The admixed genetic pattern revealed for J. seravschanica showed that the tetraploid cytotypes of this species originated from allopolyploidy, whereas no clear evidence of hybridization in the origin of the tetraploid J. thurifera and J. chinensis was detected. This study provides first insights into the polyploidy origin of the Sabina section and highlights the potential implication of allopolyploidy in the evolution of the genus Juniperus. Further analyses are needed for a more in-depth understanding of the evolutionary scenarios that produced the observed genetic patterns.
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Affiliation(s)
- Perla Farhat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP, 1514 Riad el Solh, Beirut 1107 2050, Lebanon
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Najat Takvorian
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Faculté des Sciences et Ingénierie, Sorbonne Université, UFR 927, 4 Place Jussieu, 75252 Paris, France
| | - Magda Bou Dagher Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP, 1514 Riad el Solh, Beirut 1107 2050, Lebanon
- European Forest Institute, Mediterranean, Sant Pau Art Nouveau Site, St. Antoni M. Claret, 167, 08025 Barcelona, Spain
| | - Thierry Robert
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Faculté des Sciences et Ingénierie, Sorbonne Université, UFR 927, 4 Place Jussieu, 75252 Paris, France
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Ren X, Guan Z, Li H, Wen J, Zhao X, Wang G, Zhang X, Wang H, Zhang L, Yu F, Qu L. Extensive intra- and inter- genetic admixture of Chinese gamecock and other indigenous chicken breeds revealed by genomic data. Poult Sci 2023; 102:102766. [PMID: 37229885 DOI: 10.1016/j.psj.2023.102766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
Genomic admixture is a widespread phenomenon among domestic animal breeds, including chickens. However, reports on admixture within Chinese gamecocks or other indigenous chickens are limited. This study focuses on the population genetic structure and admixture of 5 Chinese gamecock breeds and the admixture with 9 other indigenous Chinese chicken breeds. Our results showed that Turpan and Henan gamecocks were grouped into one cluster, whereas Luxi, Zhangzhou, and Xishuangbanna gamecocks were grouped into the other cluster. Gene flow occurred between Xishuangbanna and Turpan and Turpan and Luxi gamecocks. Simultaneously, gene flow was observed between gamecocks and indigenous chickens, such as Xishuangbanna and Wenchang. Ancestral component analysis indicated that modern domestic chickens in southern China played an important role in the history of the domestication of modern Chinese gamecock. Our study will be helpful in better understanding the domestication and evolution of Chinese gamecock.
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Affiliation(s)
- Xufang Ren
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zi Guan
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China
| | - Junhui Wen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huie Wang
- Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Li Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Fuqing Yu
- National Animal Husbandry Station, Beijing 100125, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China.
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Arias L, Emlen NQ, Norder S, Julmi N, Lemus Serrano M, Chacon T, Wiegertjes J, Howard A, Azevedo MCBC, Caine A, Dunn S, Stoneking M, Van Gijn R. Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan). Interface Focus 2023; 13:20220056. [PMID: 36655193 PMCID: PMC9732642 DOI: 10.1098/rsfs.2022.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Northwestern Amazonia is home to a great degree of linguistic diversity, and the human societies in that region are part of complex networks of interaction that predate the arrival of Europeans. This study investigates the population and language contact dynamics between two languages found within this region, Yukuna and Tanimuka, which belong to the Arawakan and Tukanoan language families, respectively. We use evidence from linguistics, ethnohistory, ethnography and population genetics to provide new insights into the contact dynamics between these and other human groups in NWA. Our results show that the interaction between these groups intensified in the last 500 years, to the point that it is difficult to differentiate between them genetically. However, this close interaction has led to more substantial contact-induced language changes in Tanimuka than in Yukuna, consistent with a scenario of language shift and asymmetrical power relations.
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Affiliation(s)
- Leonardo Arias
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nicholas Q. Emlen
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- University of Groningen (Campus Fryslân), Groningen, The Netherlands
| | - Sietze Norder
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- Copernicus Institute of Sustainable Development, Environmental Science Group, Utrecht University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
| | - Nora Julmi
- Leiden University Centre for Linguistics, Leiden, The Netherlands
| | | | | | | | - Austin Howard
- Leiden University Centre for Linguistics, Leiden, The Netherlands
| | | | - Allison Caine
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- University of Wyoming, Laramie, WY, USA
| | - Saskia Dunn
- Leiden University Centre for Linguistics, Leiden, The Netherlands
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
| | - Rik Van Gijn
- Leiden University Centre for Linguistics, Leiden, The Netherlands
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Abstract
As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
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Affiliation(s)
| | | | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
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Zhang R, Ni X, Yuan K, Pan Y, Xu S. MultiWaverX: modeling latent sex-biased admixture history. Brief Bioinform 2022; 23:6590437. [PMID: 35598333 DOI: 10.1093/bib/bbac179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Sex-biased gene flow has been common in the demographic history of modern humans. However, the lack of sophisticated methods for delineating the detailed sex-biased admixture process prevents insights into complex admixture history and thus our understanding of the evolutionary mechanisms of genetic diversity. Here, we present a novel algorithm, MultiWaverX, for modeling complex admixture history with sex-biased gene flow. Systematic simulations showed that MultiWaverX is a powerful tool for modeling complex admixture history and inferring sex-biased gene flow. Application of MultiWaverX to empirical data of 17 typical admixed populations in America, Central Asia, and the Middle East revealed sex-biased admixture histories that were largely consistent with the historical records. Notably, fine-scale admixture process reconstruction enabled us to recognize latent sex-biased gene flow in certain populations that would likely be overlooked by much of the routine analysis with commonly used methods. An outstanding example in the real world is the Kazakh population that experienced complex admixture with sex-biased gene flow but in which the overall signature has been canceled due to biased gene flow from an opposite direction.
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Affiliation(s)
- Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xumin Ni
- School of Mathematics and Statistics, Beijing Jiaotong University, Beijing, 100044, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.,Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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9
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Perez-Roman E, Borredá C, Tadeo FR, Talon M. Transcriptome analysis of the pulp of citrus fruitlets suggests that domestication enhanced growth processes and reduced chemical defenses increasing palatability. Front Plant Sci 2022; 13:982683. [PMID: 36119632 PMCID: PMC9478336 DOI: 10.3389/fpls.2022.982683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
To identify key traits brought about by citrus domestication, we have analyzed the transcriptomes of the pulp of developing fruitlets of inedible wild Ichang papeda (Citrus ichangensis), acidic Sun Chu Sha Kat mandarin (C. reticulata) and three palatable segregants of a cross between commercial Clementine (C. x clementina) and W. Murcott (C. x reticulata) mandarins, two pummelo/mandarin admixtures of worldwide distribution. RNA-seq comparison between the wild citrus and the ancestral sour mandarin identified 7267 differentially expressed genes, out of which 2342 were mapped to 117 KEGG pathways. From the remaining genes, a set of 2832 genes was functionally annotated and grouped into 45 user-defined categories. The data suggest that domestication promoted fundamental growth processes to the detriment of the production of chemical defenses, namely, alkaloids, terpenoids, phenylpropanoids, flavonoids, glucosinolates and cyanogenic glucosides. In the papeda, the generation of energy to support a more active secondary metabolism appears to be dependent upon upregulation of glycolysis, fatty acid degradation, Calvin cycle, oxidative phosphorylation, and ATP-citrate lyase and GABA pathways. In the acidic mandarin, downregulation of cytosolic citrate degradation was concomitant with vacuolar citrate accumulation. These changes affected nitrogen and carbon allocation in both species leading to major differences in organoleptic properties since the reduction of unpleasant secondary metabolites increases palatability while acidity reduces acceptability. The comparison between the segregants and the acidic mandarin identified 357 transcripts characterized by the occurrence in the three segregants of additional downregulation of secondary metabolites and basic structural cell wall components. The segregants also showed upregulation of genes involved in the synthesis of methyl anthranilate and furaneol, key substances of pleasant fruity aroma and flavor, and of sugar transporters relevant for sugar accumulation. Transcriptome and qPCR analysis in developing and ripe fruit of a set of genes previously associated with citric acid accumulation, demonstrated that lower acidity is linked to downregulation of these regulatory genes in the segregants. The results suggest that the transition of inedible papeda to sour mandarin implicated drastic gene expression reprograming of pivotal pathways of the primary and secondary metabolism, while palatable mandarins evolved through progressive refining of palatability properties, especially acidity.
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10
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Kutanan W, Changmai P, Wang CC. Editorial: A Genetic Perspective on Asian Populations. Front Genet 2022; 13:883843. [PMID: 35754811 PMCID: PMC9214032 DOI: 10.3389/fgene.2022.883843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022] Open
Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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11
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Luo T, Wang R, Wang CC. Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on Genome-wide SNP genotyping. Ann Hum Biol 2021; 48:418-429. [PMID: 34763584 DOI: 10.1080/03014460.2021.2005825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hmong-Mien speaking Miao, also called Hmong, is the sixthlargest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes. AIM To further investigate the population substructure and admixture history of the Guizhou Miao minority. SUBJECTS AND METHODS We collected 29 samples from three Miao tribes of Guizhou province in southwest China and genotyped about 700,000 genome-wide SNPs of each sample. We analysed newly generated data in together with published modern/ancient East Asian populations datasets via a series of population genetic methods, including principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm. RESULTS PCA and ADMIXTURE results showed that the three studied Guizhou Miao groups consistently fell on the Hmong-Mien-related genetic cline and were relatively genetically homogeneous, displayingd a genetic affinity with neighbouring Tai-Kadai speaking populations such as Dong. These results were further confirmed by the observed genetic clade in Fst, TreeMix, outgroup-f3 -statistics, and f4 -statistics. Furthermore, f4 -based allele sharing patterns illustrated that compared with Hunan Miao in central China, Guizhou Miao shared more alleles with Hmong-Mien-speaking Vietnam Hmong and Tai-Kadai-speaking CoLao, Dong, while exhibiting less northeast Asian-related ancestry. Admixture-f3 and f4 statistics revealed the North-South admixture pattern for the studied Guizhou Miao. A qpAdm-based two-way admixture model further revealed that the studied Guizhou Miao harboured 44%∼55.4% indigenous Austronesian-speaking Atayal-related ancestry and 44.6%∼56% Late Neolithic Yellow River farmer-related ancestry. CONCLUSIONS The population structure within Hmong-Mien-related populations showed a geographic correlation. Hmong-Mien speaking Hunan Miao, Guizhou Miao, and Vietnam Hmong presented closer genetic relationships although they dwelt in different regions, suggesting the preservation of the original Hmong-related genetic diversity. The results based on genome-wide SNPs data generally matched the migration history for the Miao population. Our study contributes to a better knowledge of Miao populations and the population structure in southwest China.
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Affiliation(s)
- Ting Luo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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12
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Bin X, Wang R, Huang Y, Wei R, Zhu K, Yang X, Ma H, He G, Guo J, Zhao J, Yang M, Chen J, Zhang X, Tao L, Liu Y, Huang X, Wang CC. Genomic Insight Into the Population Structure and Admixture History of Tai-Kadai-Speaking Sui People in Southwest China. Front Genet 2021; 12:735084. [PMID: 34616433 PMCID: PMC8489805 DOI: 10.3389/fgene.2021.735084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2-54.7%) and ancient coastal Southeast Asian-related ancestry (45.3-63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.
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Affiliation(s)
- Xiaoyun Bin
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Youyi Huang
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Rongyao Wei
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | | | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yilan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiufeng Huang
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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13
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Scally A. Complexity in human ancestral demography. J Anthropol Sci 2021; 99:179-182. [PMID: 34601463 DOI: 10.4436/jass.99009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing St, Cambridge, CB2 3EH, UK,
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14
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Zhang X, He G, Li W, Wang Y, Li X, Chen Y, Qu Q, Wang Y, Xi H, Wang CC, Wen Y. Genomic Insight Into the Population Admixture History of Tungusic-Speaking Manchu People in Northeast China. Front Genet 2021; 12:754492. [PMID: 34659368 PMCID: PMC8515022 DOI: 10.3389/fgene.2021.754492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Manchu is the third-largest ethnic minority in China and has the largest population size among the Tungusic-speaking groups. However, the genetic origin and admixture history of the Manchu people are far from clear due to the sparse sampling and a limited number of markers genotyped. Here, we provided the first batch of genome-wide data of genotyping approximate 700,000 single-nucleotide polymorphisms (SNPs) in 93 Manchu individuals collected from northeast China. We merged the newly generated data with data of publicly available modern and ancient East Asians to comprehensively characterize the genetic diversity and fine-scale population structure, as well as explore the genetic origin and admixture history of northern Chinese Manchus. We applied both descriptive methods of ADMIXTURE, fineSTRUCTURE, F ST , TreeMix, identity by decedent (IBD), principal component analysis (PCA), and qualitative f-statistics (f 3, f 4, qpAdm, and qpWave). We found that Liaoning Manchus have a close genetic relationship and significant admixture signal with northern Han Chinese, which is in line with the cluster patterns in the haplotype-based results. Additionally, the qpAdm-based admixture models showed that modern Manchu people were formed as major ancestry related to Yellow River farmers and minor ancestry linked to ancient populations from Amur River Bain, or others. In summary, the northeastern Chinese Manchu people in Liaoning were an exception to the coherent genetic structure of Tungusic-speaking populations, probably due to the large-scale population migrations and genetic admixtures in the past few hundred years.
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Affiliation(s)
- Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Wenhui Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Yunfeng Wang
- Xinbin Manchu Autonomous County People’s Hospital, Fushun, China
| | - Xin Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Chen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Quanying Qu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Wang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Huanjiu Xi
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Youfeng Wen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
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15
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia. Front Genet 2021; 12:685285. [PMID: 34239544 PMCID: PMC8258170 DOI: 10.3389/fgene.2021.685285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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16
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Liu Y, Yang J, Li Y, Tang R, Yuan D, Wang Y, Wang P, Deng S, Zeng S, Li H, Chen G, Zou X, Wang M, He G. Significant East Asian Affinity of the Sichuan Hui Genomic Structure Suggests the Predominance of the Cultural Diffusion Model in the Genetic Formation Process. Front Genet 2021; 12:626710. [PMID: 34194465 PMCID: PMC8237860 DOI: 10.3389/fgene.2021.626710] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
The ancestral origin and genomic history of Chinese Hui people remain to be explored due to the paucity of genome-wide data. Some evidence argues that an eastward migration of Central Asians gave rise to modern Hui people, which is referred to as the demic diffusion hypothesis; other evidence favors the cultural diffusion hypothesis, which posits that East Asians adopted Muslim culture to form the modern culturally distinct populations. However, the extent to which the observed genetic structure of the Huis was mediated by the movement of people or the assimilation of Muslim culture also remains highly contentious. Analyses of over 700 K SNPs in 109 western Chinese individuals (49 Sichuan Huis and 60 geographically close Nanchong Hans) together with the available ancient and modern Eurasian sequences allowed us to fully explore the genomic makeup and origin of Hui and neighboring Han populations. The results from PCA, ADMIXTURE, and allele-sharing-based f-statistics revealed a strong genomic affinity between Sichuan Huis and Neolithic-to-modern Northern East Asians, which suggested a massive gene influx from East Asians into the Sichuan Hui people. Three-way admixture models in the qpWave/qpAdm analyses further revealed a small stream of gene influx from western Eurasians into the Sichuan Hui people, which was further directly confirmed via the admixture event from the temporally distinct Western sources to Sichuan Hui people in the qpGraph-based phylogenetic model, suggesting the key role of the cultural diffusion model in the genetic formation of the Sichuan Huis. ALDER-based admixture date estimation showed that this observed western Eurasian admixture signal was introduced into the Sichuan Huis during the historic periods, which was concordant with the extensive western-eastern communication along the Silk Road and historically documented Huis' migration history. In summary, although significant cultural differentiation exists between Hui people and their neighbors, our genomic analysis showed their strong genetic affinity with modern and ancient Northern East Asians. Our results support the hypothesis that the Sichuan Huis arose from a mixture of minor western Eurasian ancestry and predominant East Asian ancestry.
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Affiliation(s)
- Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Junbao Yang
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | | | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Didi Yuan
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yicheng Wang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Peixin Wang
- College of Medical Information, Chongqing Medical University, Chongqing, China
| | - Shudan Deng
- School of Medical Imaging, North Sichuan Medical College, Nanchong, China
| | - Simei Zeng
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Hongliang Li
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Xing Zou
- Department of Forensic Genetics, Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Department of Forensic Genetics, Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Department of Forensic Genetics, Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
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17
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Zecherle LJ, Nichols HJ, Bar‐David S, Brown RP, Hipperson H, Horsburgh GJ, Templeton AR. Subspecies hybridization as a potential conservation tool in species reintroductions. Evol Appl 2021; 14:1216-1224. [PMID: 34025762 PMCID: PMC8127701 DOI: 10.1111/eva.13191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/11/2020] [Accepted: 12/27/2020] [Indexed: 11/30/2022] Open
Abstract
Reintroductions are a powerful tool for the recovery of endangered species. However, their long-term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations.
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Affiliation(s)
- Lilith J. Zecherle
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | - Shirli Bar‐David
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Richard P. Brown
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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18
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Yang X, Wang XX, He G, Guo J, Zhao J, Sun J, Li Y, Cheng HZ, Hu R, Wei LH, Chen G, Wang CC. Genomic insight into the population history of Central Han Chinese. Ann Hum Biol 2021; 48:49-55. [PMID: 33191788 DOI: 10.1080/03014460.2020.1851396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND In recent decades, considerable attention has been paid to exploring the population genetic characteristics of Han Chinese, mainly documenting a north-south genetic substructure. However, the central Han Chinese have been largely underrepresented in previous studies. AIM To infer a comprehensive understanding of the homogenisation process and population history of Han Chinese. SUBJECTS AND METHODS We collected samples from 122 Han Chinese from seven counties of Hubei province in central China and genotyped 534,000 genome-wide SNPs. We compared Hubei Han with both ancient and present-day Eurasian populations using Principal Component Analysis, ADMIXTURE, f statistics, qpWave and qpAdm. RESULTS We observed Hubei Han Chinese are at a genetically intermediate position on the north-south Han Chinese cline. We have not detected any significant genetic substructure in the studied groups from seven different counties. Hubei Han show significant evidence of genetic admixture deriving about 63% of ancestry from Tai-Kadai or Austronesian-speaking southern indigenous groups and 37% from Tungusic or Mongolic related northern populations. CONCLUSIONS The formation of Han Chinese has involved extensive admixture with Tai-Kadai or Austronesian-speaking populations in the south and Tungusic or Mongolic speaking populations in the north. The convenient transportation and central location of Hubei make it the key region for the homogenisation of Han Chinese.
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Affiliation(s)
- Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiao-Xun Wang
- Department of Medical Laboratory, Taihe Hospital Affiliated to Hubei University of Medicine, Shiyan, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China.,Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
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19
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Palacio-Mejía JD, Grabowski PP, Ortiz EM, Silva-Arias GA, Haque T, Des Marais DL, Bonnette J, Lowry DB, Juenger TE. Geographic patterns of genomic diversity and structure in the C 4 grass Panicum hallii across its natural distribution. AoB Plants 2021; 13:plab002. [PMID: 33708370 PMCID: PMC7937184 DOI: 10.1093/aobpla/plab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 06/01/2023]
Abstract
Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.
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Affiliation(s)
| | - Paul P Grabowski
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Edgardo M Ortiz
- Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Freising, Germany
| | - Gustavo Adolfo Silva-Arias
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David L Des Marais
- Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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20
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Fernandes MR, Rodrigues JCG, Maroñas O, Latorre-Pellicer A, Cruz R, Guerreiro JF, Burbano RMR, de Assumpção PP, Ribeiro-Dos-Santos A, Dos Santos SEB, Carracedo A, Dos Santos NPC. Genetic Diversity of Drug-Related Genes in Native Americans of the Brazilian Amazon. Pharmgenomics Pers Med 2021; 14:117-133. [PMID: 33519226 PMCID: PMC7837547 DOI: 10.2147/pgpm.s274741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 12/25/2022]
Abstract
Introduction The genetic admixture of the Brazilian population has considerable relevance to the implementation of the principles of pharmacogenomics (PGx), as it may compromise the extrapolation of data obtained in more homogeneous world populations. Purpose This study aims to investigate a panel of 117 polymorphisms in 35 pharmacogenes, which contains label recommendations or clinical evidence by international drug regulatory agencies, in Amazonian Native American populations, and compare the results obtained with continental population data from the 1000 Genomes Project Consortium. Patients and Methods The study population is composed of 109 Native American individuals from three Brazilian Amazon groups. The genotyping of the PGx polymorphisms was performed by allelic discrimination using TaqMan® OpenArray Genotyping with a panel of 120 customized assays on the QuantStudio™ 12K Flex Real-Time PCR System. Results Statistical differences within the Native American populations were observed regarding both genotypes and phenotypes of some genes of the CYP family. The discriminant analysis of principal components (DAPCs) between the NAM group and the continental populations of the 1000 Genomes Project resulted in the clustering of the three Native American populations. Additionally, in general, the NAM group was determined to be closely situated between East Asia, America, and South Asia groups, which enabled us to infer a genetic similarity between these populations. The DAPC analysis further demonstrated that eight polymorphisms and six polymorphisms were more relevant in differentiating the NAM from the continental populations and the NAM populations among themselves, respectively. Conclusion Some investigated polymorphisms show differences among world populations, particularly with populations of European origin, for whom precision medicine protocols are primarily designed. The accumulated knowledge regarding these variations may assist in the design of specific protocols for Native American populations and populations admixed with them.
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Affiliation(s)
- Marianne Rodrigues Fernandes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Departamento de ensino e pesquisa, Hospital Ophir Loyola, Belém, Pará, Brazil
| | | | - Olalla Maroñas
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, España
| | - Ana Latorre-Pellicer
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, España.,Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología, Escuela de Medicina, Universidad de Zaragoza, IIS-Aragón, E-50009 Zaragoza, España
| | - Raquel Cruz
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Grupo de Medicina Genómica, CIMUS, Universidad de Santiago de Compostela, Santiago de Compostela, España
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Rommel Mario Rodriguez Burbano
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Departamento de ensino e pesquisa, Hospital Ophir Loyola, Belém, Pará, Brazil
| | | | - Andrea Ribeiro-Dos-Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Sidney Emanuel Batista Dos Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Angel Carracedo
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, España.,Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Grupo de Medicina Genómica, CIMUS, Universidad de Santiago de Compostela, Santiago de Compostela, España.,Fundación Pública de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, España
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21
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Zhao J, Wurigemule, Sun J, Xia Z, He G, Yang X, Guo J, Cheng HZ, Li Y, Lin S, Yang TL, Hu X, Du H, Cheng P, Hu R, Chen G, Yuan H, Zhang XF, Wei LH, Zhang HQ, Wang CC. Genetic substructure and admixture of Mongolians and Kazakhs inferred from genome-wide array genotyping. Ann Hum Biol 2020; 47:620-628. [PMID: 33059477 DOI: 10.1080/03014460.2020.1837952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Mongolian populations are widely distributed geographically, showing abundant ethnic diversity with geographic and tribal differences. AIM To infer the genetic substructure, admixture and ancient genetic sources of Mongolians together with Kazakhs. SUBJECTS AND METHODS We genotyped more than 690,000 genome-wide SNPs from 33 Mongolian and Chinese Kazakh individuals and compared these with both ancient and present-day Eurasian populations using Principal Component Analysis (PCA), ADMIXTURE, Refine-IBD, f statistics, qpWave and qpAdm. RESULTS We found genetic substructures within Mongolians corresponding to Ölöd, Chahar, and Inner Mongolian clusters, which was consistent with tribe classifications. Mongolian and Kazakh groups derived about 6-40% of West Eurasian related ancestry, most likely from Bronze Age Steppe populations. The East Asian related ancestry in Mongolian and Kazakh groups was well represented by the Neolithic DevilsCave related nomadic lineage, comprising 42-64% of studied groups. We also detected 10-51% of Han Chinese related ancestry in Mongolian and Kazakh groups, especially in Inner Mongolians. The average admixture times for Inner Mongolian, Mongolian_Chahar, Mongolian_Ölöd and Chinese Kazakh were about 1381, 626, 635 and 632 years ago, respectively, with Han and French as the sources. CONCLUSION The DevilsCave related ancestry was once widespread westwards covering a wide geographical range from Far East Russia to the Mongolia Plateau. The formation of present-day Mongolic and Turkic-speaking populations has also received genetic influence from agricultural expansion.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.,Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Wurigemule
- School of Ethnology and Sociology, Inner Mongolia University, Huhhot, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Ziyang Xia
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Song Lin
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xi Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Hua Du
- Xi'an AMS Center, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Peng Cheng
- Xi'an AMS Center, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education and Department of Archaeology, Sichuan University, Chengdu, China
| | | | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Hu-Qin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
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22
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Abstract
Hybrid zones are important windows into ecological and evolutionary processes. Our understanding of the significance and prevalence of hybridization in nature has expanded with the generation and analysis of genome‐spanning data sets. That said, most hybridization research still has restricted temporal and spatial resolution, which limits our ability to draw broad conclusions about evolutionary and conservation related outcomes. Here, we argue that rapidly advancing environmental DNA (eDNA) methodology could be adopted for studies of hybrid zones to increase temporal sampling (contemporary and historical), refine and geographically expand sampling density, and collect data for taxa that are difficult to directly sample. Genomic data in the environment offer the potential for near real‐time biological tracking of hybrid zones, and eDNA provides broad, but as yet untapped, potential to address eco‐evolutionary questions.
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Affiliation(s)
- Kathryn A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Scott A Taylor
- Department Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
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23
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Davenport KM, Hiemke C, McKay SD, Thorne JW, Lewis RM, Taylor T, Murdoch BM. Genetic structure and admixture in sheep from terminal breeds in the United States. Anim Genet 2020; 51:284-291. [PMID: 31970815 PMCID: PMC7065203 DOI: 10.1111/age.12905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 11/29/2022]
Abstract
Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross‐validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.
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Affiliation(s)
- K M Davenport
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, 83844, USA
| | - C Hiemke
- Niman Ranch and Mapleton Mynd Shropshires, Stoughton, MA, 53589, USA
| | - S D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - J W Thorne
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, 83844, USA.,Texas A&M AgriLife Extension, San Angelo, TX, 76901, USA
| | - R M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - T Taylor
- Department of Animal Science, Arlington Research Station, University of Wisconsin-Madison, Arlington, WI, 53911, USA
| | - B M Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, 83844, USA
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24
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Shang L, Li LF, Song ZP, Wang Y, Yang J, Wang CC, Qiu SY, Huang JX, Nie M, Wolfe LM, Li B. High Genetic Diversity With Weak Phylogeographic Structure of the Invasive Spartina alterniflora (Poaceae) in China. Front Plant Sci 2019; 10:1467. [PMID: 31850008 PMCID: PMC6896949 DOI: 10.3389/fpls.2019.01467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Biological invasion represents a global issue of concern due to its large negative impacts on native ecosystems and society. Elucidating the evolutionary history and genetic basis underpinning invasiveness is critical to understanding how alien species invade and adapt to novel environments. Smooth cordgrass (Spartina alterniflora, 2n = 6x = 62) is a notorious invasive species that causes heavily negative effects on native ecosystems worldwide. Here we addressed the evolutionary mechanisms underlying the invasion and dispersal history of this species along the China coast in the past decades. We employed nine microsatellites and three chloroplast fragments to investigate phylogeographic structure and genetic diversity of 11 native US and 11 invasive Chinese S. alterniflora populations. Demographic history simulation was also performed for both the native and invasive populations, respectively. Comparative genetic analyses of these natural populations revealed that although all the Chinese populations were introduced only once, high level of genetic diversity with weak geographic structure was observed. In particular, both the genetic features and mathematical simulation illustrated very recent population expansion in the Chinese populations. We found that genetic variants identified in native US populations were mixed in the Chinese populations, suggesting the recombination of these original variants during the invasion process. These genetic attributes indicate that Chinese populations might not have experienced a genetic bottleneck during the invasion process. High genetic diversity and genetic admixture might have contributed to the success of invasion of S. alterniflora in China. Our study provides a framework of how the smooth cordgrass spreads along the China coast as well as its potential genetic mechanisms underlying the invasion.
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Affiliation(s)
- Lei Shang
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Lin-Feng Li
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Zhi-Ping Song
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Key Laboratory of Biodiversity and Evolution, Fudan University, Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, China
| | - Shi-Yun Qiu
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Jing-Xin Huang
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
- School of Energy and Environment Science, Yunan Normal University, Kunming, China
| | - Ming Nie
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Lorne M. Wolfe
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Bo Li
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
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25
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Qiao H, Liu W, Zhang Y, Zhang YY, Li QQ. Genetic admixture accelerates invasion via provisioning rapid adaptive evolution. Mol Ecol 2019; 28:4012-4027. [PMID: 31339595 DOI: 10.1111/mec.15192] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/26/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022]
Abstract
Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short-lived, provisioning adaptation is anticipated to be the dominant and long-term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic-scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a "hybrid swarm" that spread throughout the coast of China. In the northern and mid-latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically-based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid-latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.
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Affiliation(s)
- Hongmei Qiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Wenwen Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yihui Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA
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26
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Guzmán-Castañeda SJ, Ortega-Vega EL, de la Cuesta-Zuluaga J, Velásquez-Mejía EP, Rojas W, Bedoya G, Escobar JS. Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry. Gut Microbes 2019; 11:191-204. [PMID: 31311405 PMCID: PMC7053924 DOI: 10.1080/19490976.2019.1634416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/10/2019] [Accepted: 06/16/2019] [Indexed: 02/03/2023] Open
Abstract
Cardiometabolic affections greatly contribute to the global burden of disease. The susceptibility to obesity, cardiovascular disease, and type-2 diabetes, conditions that add to the cardiometabolic syndrome (CMS), was associated with the ancestral genetic composition and gut microbiota. Studies explicitly testing associations between genetic ancestry and gut microbes are growing. We here examined whether the host genetic ancestry was associated with gut microbiota composition, and distinguished the effects of genetic ancestry and non-genetic factors on human cardiometabolic health. We performed a cross-sectional study with 441 community-dwelling Colombian mestizos from five cities spanning the Andes, Pacific, and Caribbean coasts. We characterized the host genetic ancestry by genotyping 40 ancestry informative markers; characterized gut microbiota through 16S rRNA gene sequencing; assessed diet intake, physical activity, cigarette, and medicament consumption; and measured cardiometabolic outcomes that allowed calculating a CMS risk scale. On average, each individual of our cohort was 67 ± 6% European, 21 ± 5% Native American and 12 ± 5% African. Multivariable-adjusted generalized linear models showed that individuals with higher Native American and African ancestries had increased fasting insulin, body mass index and CMS risk, as assessed by the CMS risk scale. Furthermore, we identified 21 OTUs associated to the host genetic ancestry and 20 to cardiometabolic health. While we highlight novel associations between genetic ancestry and gut microbiota, we found that the effect of intestinal microbes was more likely to explain the variance in CMS risk scale than the contributions of European, Native American and African genetic backgrounds.
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Affiliation(s)
- Sandra J. Guzmán-Castañeda
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Esteban L. Ortega-Vega
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Jacobo de la Cuesta-Zuluaga
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eliana P. Velásquez-Mejía
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Winston Rojas
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Gabriel Bedoya
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
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27
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Sherpa S, Blum MGB, Capblancq T, Cumer T, Rioux D, Després L. Unravelling the invasion history of the Asian tiger mosquito in Europe. Mol Ecol 2019; 28:2360-2377. [PMID: 30849200 DOI: 10.1111/mec.15071] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 01/15/2023]
Abstract
Multiple introductions are key features for the establishment and persistence of introduced species. However, little is known about the contribution of genetic admixture to the invasive potential of populations. To address this issue, we studied the recent invasion of the Asian tiger mosquito (Aedes albopictus) in Europe. Combining genome-wide single nucleotide polymorphisms and historical knowledge using an approximate Bayesian computation framework, we reconstruct the colonization routes and establish the demographic dynamics of invasion. The colonization of Europe involved at least three independent introductions in Albania, North Italy and Central Italy that subsequently acted as dispersal centres throughout Europe. We show that the topology of human transportation networks shaped demographic histories with North Italy and Central Italy being the main dispersal centres in Europe. Introduction modalities conditioned the levels of genetic diversity in invading populations, and genetically diverse and admixed populations promoted more secondary introductions and have spread farther than single-source invasions. This genomic study provides further crucial insights into a general understanding of the role of genetic diversity promoted by modern trade in driving biological invasions.
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Affiliation(s)
| | - Michael G B Blum
- Université Grenoble Alpes, CNRS UMR 5525 TIMC-IMAG, Grenoble, France
| | | | - Tristan Cumer
- Université Grenoble Alpes, CNRS UMR 5553 LECA, Grenoble, France
| | - Delphine Rioux
- Université Grenoble Alpes, CNRS UMR 5553 LECA, Grenoble, France
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28
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Qiao R, Li X, Han X, Wang K, Lv G, Ren G, Li X. Population structure and genetic diversity of four Henan pig populations. Anim Genet 2019; 50:262-265. [PMID: 30883844 DOI: 10.1111/age.12775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 12/22/2022]
Abstract
To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping-by-sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor-joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome-wide association studies.
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Affiliation(s)
- R Qiao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - K Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - G Lv
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - G Ren
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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29
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Miller MD, Devor EJ, Salinas EA, Newtson AM, Goodheart MJ, Leslie KK, Gonzalez-Bosquet J. Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA. Int J Mol Sci 2019; 20:E1192. [PMID: 30857229 PMCID: PMC6429328 DOI: 10.3390/ijms20051192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 01/18/2023] Open
Abstract
In the era of large genetic and genomic datasets, it has become crucially important to validate results of individual studies using data from publicly available sources, such as The Cancer Genome Atlas (TCGA). However, how generalizable are results from either an independent or a large public dataset to the remainder of the population? The study presented here aims to answer that question. Utilizing next generation sequencing data from endometrial and ovarian cancer patients from both the University of Iowa and TCGA, genomic admixture of each population was analyzed using STRUCTURE and ADMIXTURE software. In our independent data set, one subpopulation was identified, whereas in TCGA 4⁻6 subpopulations were identified. Data presented here demonstrate how different the genetic substructures of the TCGA and University of Iowa populations are. Validation of genomic studies between two different population samples must be aware of, account for and be corrected for background genetic substructure.
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Affiliation(s)
- Marina D Miller
- Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
| | - Eric J Devor
- Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
| | | | - Andreea M Newtson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
| | - Michael J Goodheart
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
| | - Kimberly K Leslie
- Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
| | - Jesus Gonzalez-Bosquet
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.
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30
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Grinde KE, Brown LA, Reiner AP, Thornton TA, Browning SR. Genome-wide Significance Thresholds for Admixture Mapping Studies. Am J Hum Genet 2019; 104:454-465. [PMID: 30773276 PMCID: PMC6407497 DOI: 10.1016/j.ajhg.2019.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/17/2019] [Indexed: 01/25/2023] Open
Abstract
Admixture mapping studies have become more common in recent years, due in part to technological advances and growing international efforts to increase the diversity of genetic studies. However, many open questions remain about appropriate implementation of admixture mapping studies, including how best to control for multiple testing, particularly in the presence of population structure. In this study, we develop a theoretical framework to characterize the correlation of local ancestry and admixture mapping test statistics in admixed populations with contributions from any number of ancestral populations and arbitrary population structure. Based on this framework, we develop an analytical approach for obtaining genome-wide significance thresholds for admixture mapping studies. We validate our approach via analysis of simulated traits with real genotype data for 8,064 unrelated African American and 3,425 Hispanic/Latina women from the Women's Health Initiative SNP Health Association Resource (WHI SHARe). In an application to these WHI SHARe data, our approach yields genome-wide significant p value thresholds of 2.1 × 10-5 and 4.5 × 10-6 for admixture mapping studies in the African American and Hispanic/Latina cohorts, respectively. Compared to other commonly used multiple testing correction procedures, our method is fast, easy to implement (using our publicly available R package), and controls the family-wise error rate even in structured populations. Importantly, we note that the appropriate admixture mapping significance threshold depends on the number of ancestral populations, generations since admixture, and population structure of the sample; as a result, significance thresholds are not, in general, transferable across studies.
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Affiliation(s)
- Kelsey E Grinde
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | - Lisa A Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Seattle Genetics, Bothell, WA 98021, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
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31
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Sunde J, Tibblin P, Larsson P, Forsman A. Sex-specific effects of outbreeding on offspring quality in pike ( Esox lucius). Ecol Evol 2018; 8:10448-10459. [PMID: 30464817 PMCID: PMC6238122 DOI: 10.1002/ece3.4510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
Intraspecific genetic admixture occurs when previously separated populations within a species start interbreeding, and it can have either positive, negative, or neutral effects on reproductive performance. As there currently is no reliable predictor for the outcome of admixture, an increased knowledge about admixture effects in different species and populations is important to increase the understanding about what determines the response to admixture. We tested for effects of admixture on F1 offspring quality in three subpopulations of pike (Esox lucius). Gametes were collected in the field, and eggs from each female were experimentally fertilized with milt from a male from each population (one "pure" and two "admixed" treatments). Three offspring quality measures (hatching success, fry survival, and fry length) were determined and compared between (a) pure and admixed population combinations and (b) the sex-specific treatments within each admixed population combination (based on the origin of the male and female, respectively). The results suggested that although there were no overall effects of admixture on offspring quality, the consequences for a given population combination could be sex-specific and thus differ depending on which of the parents originated from one or the other population. All offspring quality traits were influenced by both maternal ID and paternal ID. Sex- and individual-specific effects can have implications for dispersal behavior and gene flow between natural populations, and are important to consider in conservation efforts.
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Affiliation(s)
- Johanna Sunde
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
| | - Petter Tibblin
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
| | - Per Larsson
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
| | - Anders Forsman
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
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32
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Ortego J, Gugger PF, Sork VL. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). New Phytol 2018; 218:804-818. [PMID: 29274282 DOI: 10.1111/nph.14951] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 05/15/2023]
Abstract
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, Seville, E-41092, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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33
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Pugach I, Duggan AT, Merriwether DA, Friedlaender FR, Friedlaender JS, Stoneking M. The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data. Mol Biol Evol 2018; 35:871-886. [PMID: 29301001 PMCID: PMC5889034 DOI: 10.1093/molbev/msx333] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration circa 50,000 years ago (ya), and the more recent Austronesian expansion, which reached the Bismarck Archipelago by 3,450 ya. Whereas earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic, and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide data set of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal single nucleotide polymorphisms (SNPs). We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a "leapfrog" fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bidirectional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ana T Duggan
- Department of Anthropology, McMaster University, Hamilton, Canada
| | | | | | | | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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34
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Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, Lansing JS, Hammer MF, Cox MP. Complex Patterns of Admixture across the Indonesian Archipelago. Mol Biol Evol 2017; 34:2439-2452. [PMID: 28957506 PMCID: PMC5850824 DOI: 10.1093/molbev/msx196] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.
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Affiliation(s)
- Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Estonian Biocentre, 51010 Tartu, Estonia
| | | | - Daniel J Lawson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Sean Downey
- Department of Anthropology, University of Maryland, College Park, MD
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | | | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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35
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Scheriau CL, Nuerk NM, Sharbel TF, Koch MA. Cryptic gene pools in the Hypericum perforatum-H. maculatum complex: diploid persistence versus trapped polyploid melting. Ann Bot 2017; 120:955-966. [PMID: 29182722 PMCID: PMC5710527 DOI: 10.1093/aob/mcx110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/09/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS In Central Europe Hypericum perforatum and Hypericum maculatum show significant hybridization and introgression as a consequence of Pleistocene range fluctuations, and their gene pools are merging on higher ploidy levels. This paper discusses whether polyploid hybrid gene pools are trapped in the ecological climatic niche space of their diploid ancestors, and tests the idea of geographical parthenogenesis. METHODS DNA sequence information of nuclear ribosomal DNA and plastid loci, ploidy level estimates and ecological niche modelling are used to characterize the various diploid and polyploid gene pools and unravel spatio-temporal patterns of gene flow among them. KEY RESULTS On the diploid level, the three gene pools are clearly distinct between and within species of H. perforatum (two gene pools) and H. maculatum, and their divergence dates back to the first half of the Pleistocene. All polyploids in Central Europe show high levels of past and contemporary gene flow between all three gene pools. The correlation of genetic and geographical distances breaks down if the latter is larger than 250 km, indicating recent and ongoing gene flow. The two species are ecologically differentiated, but in particular hybrids among all three gene pools do not show significant niche differences compared to their parental gene pools, except for some combinations with H. maculatum. CONCLUSIONS Inter- and intraspecific gene flow between inter- and intra-species gene pools is limited on the diploid level, and the geographical distribution of the diploids largely reflects Pleistocene evolutionary history. Secondary contact promoted hybridization and introgression on the polyploid level, enabling offspring to escape the diploid gene pools. However, the hybrid polyploids do not show significant niche differences compared to their diploid progenitors. It is concluded that the observed absence of niche divergence has precluded further differentiation and geographical partitioning of new polyploid lineages being effectively separated from the parental lines. The predominantly apomictic reproducing polyploids are trapped in the polyploid gene pool and the ecological climatic niche space of their diploid ancestors.
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Affiliation(s)
- Charlotte L Scheriau
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Nicolai M Nuerk
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Timothy F Sharbel
- Global Institute for Food Security, Seed Developmental Biology Program, University of Saskatchewan, Canada
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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Oh SS, Du R, Zeiger AM, McGarry ME, Hu D, Thakur N, Pino-Yanes M, Galanter JM, Eng C, Nishimura KK, Huntsman S, Farber HJ, Meade K, Avila P, Serebrisky D, Bibbins-Domingo K, Lenoir MA, Ford JG, Brigino-Buenaventura E, Rodriguez-Cintron W, Thyne SM, Sen S, Rodriguez-Santana JR, Williams K, Kumar R, Burchard EG. Breastfeeding associated with higher lung function in African American youths with asthma. J Asthma 2017; 54:856-865. [PMID: 27929698 PMCID: PMC6130885 DOI: 10.1080/02770903.2016.1266496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/02/2016] [Accepted: 11/26/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVE In the United States, Puerto Ricans and African Americans have lower prevalence of breastfeeding and worse clinical outcomes for asthma compared with other racial/ethnic groups. We hypothesize that the history of breastfeeding is associated with increased forced expiratory volume in 1 second (FEV1) % predicted and reduced asthma exacerbations in Latino and African American youths with asthma. METHODS As part of the Genes-environments & Admixture in Latino Americans (GALA II) Study and the Study of African Americans, asthma, Genes & Environments (SAGE II), we conducted case-only analyses in children and adolescents aged 8-21 years with asthma from four different racial/ethnic groups: African Americans (n = 426), Mexican Americans (n = 424), mixed/other Latinos (n = 255), and Puerto Ricans (n = 629). We investigated the association between any breastfeeding in infancy and FEV1% predicted using multivariable linear regression; Poisson regression was used to determine the association between breastfeeding and asthma exacerbations. RESULTS Prevalence of breastfeeding was lower in African Americans (59.4%) and Puerto Ricans (54.9%) compared to Mexican Americans (76.2%) and mixed/other Latinos (66.9%; p < 0.001). After adjusting for covariates, breastfeeding was associated with a 3.58% point increase in FEV1% predicted (p = 0.01) and a 21% reduction in asthma exacerbations (p = 0.03) in African Americans only. CONCLUSION Breastfeeding was associated with higher FEV1% predicted in asthma and reduced number of asthma exacerbations in African American youths, calling attention to continued support for breastfeeding.
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Affiliation(s)
- Sam S Oh
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Randal Du
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
- b Department of Pharmacy , University of California San Francisco , San Francisco , CA , USA
| | - Andrew M Zeiger
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Meghan E McGarry
- c Department of Pediatrics , University of California San Francisco , San Francisco , CA , USA
| | - Donglei Hu
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Neeta Thakur
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Maria Pino-Yanes
- d Research Unit , Hospital Universitario NS de Candelaria , Santa Cruz de Tenerife , Spain
| | - Joshua M Galanter
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
- e Department of Bioengineering and Therapeutic Sciences , University of California San Franscisco , San Francisco , CA , USA
| | - Celeste Eng
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | | | - Scott Huntsman
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Harold J Farber
- f Department of Pediatrics , Baylor College of Medicine , Houston , TX , USA
- g Department of Pulmonology , Texas Children's Hospital , Houston , TX , USA
| | - Kelley Meade
- h Department of Primary Care , UCSF Benioff Children's Hospital , San Francisco , CA , USA
| | - Pedro Avila
- i Department of Medicine , Northwestern University , Evanston , IL , USA
| | - Denise Serebrisky
- j Department of Pediatric Pulmonology , Jacobi Medical Center , Bronx , NY , USA
| | - Kirsten Bibbins-Domingo
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Michael A Lenoir
- k Department of Pediatrics , Bay Area Pediatrics , Oakland , CA , USA
| | - Jean G Ford
- l Department of Epidemiology , Johns Hopkins University Bloomberg School of Public Health , Baltimore , MD , USA
| | | | | | - Shannon M Thyne
- o Department of Medicine , University of California Los Angeles David Geffen School of Medicine , Los Angeles , CA , USA
| | - Saunak Sen
- p Department of Epidemiology and Biostatistics , University of California San Francisco , San Francisco , CA , USA
| | - Jose R Rodriguez-Santana
- q Department of Pediatric Pulmonology and Critical Care , Centro de Neumología Pediátrica , San Juan , Puerto Rico
| | - Keoki Williams
- r Center for Health Policy and Health Services Research, Henry Ford Health System , Detroit , MI , USA
- s Department of Internal Medicine , Henry Ford Health System , Detroit , MI , USA
| | - Rajesh Kumar
- i Department of Medicine , Northwestern University , Evanston , IL , USA
| | - Esteban G Burchard
- a Department of Medicine , University of California San Francisco , San Francisco , CA , USA
- e Department of Bioengineering and Therapeutic Sciences , University of California San Franscisco , San Francisco , CA , USA
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Sefc KM, Mattersdorfer K, Ziegelbecker A, Neuhüttler N, Steiner O, Goessler W, Koblmüller S. Shifting barriers and phenotypic diversification by hybridisation. Ecol Lett 2017; 20:651-662. [PMID: 28384842 PMCID: PMC6555762 DOI: 10.1111/ele.12766] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/06/2017] [Indexed: 01/30/2023]
Abstract
The establishment of hybrid taxa relies on reproductive isolation from the parental forms, typically achieved by ecological differentiation. Here, we present an alternative mechanism, in which shifts in the strength and location of dispersal barriers facilitate diversification by hybridisation. Our case study concerns the highly diverse, stenotopic rock-dwelling cichlids of the African Great Lakes, many of which display geographic colour pattern variation. The littoral habitat of these fish has repeatedly been restructured in the course of ancient lake level fluctuations. Genetic data and an experimental cross support the hybrid origin of a distinct yellow-coloured variant of Tropheus moorii from ancient admixture between two allopatric, red and bluish variants. Deficient assortative mating preferences imply that reproductive isolation continues to be contingent on geographic separation. Linking paleolimnological data with the establishment of the hybrid variant, we sketch a selectively neutral diversification process governed solely by rearrangements of dispersal barriers.
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Affiliation(s)
- Kristina M. Sefc
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Karin Mattersdorfer
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | | | - Nina Neuhüttler
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Oliver Steiner
- Institute of Chemistry - Analytical Chemistry, University of Graz, Universitätsplatz 1, 8010 Graz, Austria
| | - Walter Goessler
- Institute of Chemistry - Analytical Chemistry, University of Graz, Universitätsplatz 1, 8010 Graz, Austria
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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Abstract
Biological invasions are often associated with multiple introductions and genetic admixture of previously isolated populations. In addition to enhanced evolutionary potential through increased genetic variation, admixed genotypes may benefit from heterosis, which could contribute to their increased performance and invasiveness. To deepen our understanding of the mechanisms and management strategies for biological invasions, we experimentally studied whether intraspecific admixture causes heterosis in common ragweed (Ambrosia artemisiifolia) by comparing the performance of crosses (F1) between populations relative to crosses within these populations for each range (native, introduced) under different ecologically relevant conditions (control, drought, competition, simulated herbivory). Performance of admixed genotypes was highly variable, ranging from strong heterotic effects to weak outbreeding depression. Moreover, heterosis was not uniformly observed among between-population crosses, but certain native population crosses showed considerable heterosis, especially under simulated herbivory. In contrast, heterosis was largely absent in crosses from the introduced range, possibly implying that these populations were already admixed and benefit little from further mixing. In conclusion, these results support the hypothesis that heterosis may contribute to biological invasions, and indicate the need to minimize new introductions of exotic species, even if they are already present in the introduced range.
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Affiliation(s)
- Min A. Hahn
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
- Department of BiologyIndiana UniversityBloomingtonINUSA
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Moreno DJ, Ruiz S, Ríos Á, Lopera F, Ostos H, Via M, Bedoya G. Association of GWAS Top Genes With Late-Onset Alzheimer's Disease in Colombian Population. Am J Alzheimers Dis Other Demen 2017; 32:27-35. [PMID: 28084078 PMCID: PMC10857032 DOI: 10.1177/1533317516679303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The association of variants in CLU, CR1, PICALM, BIN1, ABCA7, and CD33 genes with late-onset Alzheimer's disease (LOAD) was evaluated and confirmed through genome-wide association study. However, it is unknown whether these associations can be replicated in admixed populations. METHODS The association of 14 single-nucleotide polymorphisms in those genes was evaluated in 280 LOAD cases and 357 controls from the Colombian population. RESULTS In a multivariate analysis using age, gender, APOE∊4 status, and admixture covariates, significant associations were obtained ( P < .05) for variants in BIN1 (rs744373, odds ratio [OR]: 1.42), CLU (rs11136000, OR: 0.66), PICALM (rs541458, OR: 0.69), ABCA7 (rs3764650, OR: 1.7), and CD33 (rs3865444, OR: 1.12). Likewise, a significant interaction effect was observed between CLU and CR1 variants with APOE. CONCLUSION This study replicated the associations previously reported in populations of European ancestry and shows that APOE variants have a regulatory role on the effect that variants in other loci have on LOAD, reflecting the importance of gene-gene interactions in the etiology of neurodegenerative diseases.
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Affiliation(s)
| | - Susana Ruiz
- Grupo de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Ángela Ríos
- Grupo de Neuropsicología, Universidad Surcolombiana, Neiva, Colombia
| | - Francisco Lopera
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - Henry Ostos
- Grupo de Medicina Genómica, Universidad Surcolombiana, Neiva, Colombia
| | - Marc Via
- Psicologia Clínica i Psicobiologia and Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Gabriel Bedoya
- Grupo de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
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Ortego J, Gugger PF, Sork VL. Impacts of human-induced environmental disturbances on hybridization between two ecologically differentiated Californian oak species. New Phytol 2017; 213:942-955. [PMID: 27621132 DOI: 10.1111/nph.14182] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/04/2016] [Indexed: 05/15/2023]
Abstract
Natural hybridization, which can be involved in local adaptation and in speciation processes, has been linked to different sources of anthropogenic disturbance. Here, we use genotypic data to study range-wide patterns of genetic admixture between the serpentine-soil specialist leather oak (Quercus durata) and the widespread Californian scrub oak (Quercus berberidifolia). First, we estimated hybridization rates and the direction of gene flow. Second, we tested the hypothesis that genetic admixture increases with different sources of environmental disturbance, namely anthropogenic destruction of natural habitats and wildfire frequency estimated from long-term records of fire occurrence. Our analyses indicate considerable rates of hybridization (> 25%), asymmetric gene flow from Q. durata into Q. berberidifolia, and a higher occurrence of hybrids in areas where both species live in close parapatry. In accordance with the environmental disturbance hypothesis, we found that genetic admixture increases with wildfire frequency, but we did not find a significant effect of other sources of human-induced habitat alteration (urbanization, land clearing for agriculture) or a suite of ecological factors (climate, elevation, soil type). Our findings highlight that wildfires constitute an important source of environmental disturbance, promoting hybridization between two ecologically well-differentiated native species.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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Abstract
The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health.
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Affiliation(s)
- Elvire Berthenet
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Sam Sheppard
- Departments of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
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Klimentidis YC, Arora A, Zhou J, Kittles R, Allison DB. The Genetic Contribution of West-African Ancestry to Protection against Central Obesity in African-American Men but Not Women: Results from the ARIC and MESA Studies. Front Genet 2016; 7:89. [PMID: 27313598 PMCID: PMC4888933 DOI: 10.3389/fgene.2016.00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/01/2016] [Indexed: 11/13/2022] Open
Abstract
Over 80% of African-American (AA) women are overweight or obese. A large racial disparity between AA and European-Americans (EA) in obesity rates exists among women, but curiously not among men. Although socio-economic and/or cultural factors may partly account for this race-by-sex interaction, the potential involvement of genetic factors has not yet been investigated. Among 2814 self-identified AA in the Atherosclerosis Risk in Communities study, we estimated each individual's degree of West-African genetic ancestry using 3437 ancestry informative markers. We then tested whether sex modifies the association between West-African genetic ancestry and body mass index (BMI), waist-circumference (WC), and waist-to-hip ratio (WHR), adjusting for income and education levels, and examined associations of ancestry with the phenotypes separately in males and females. We replicated our findings in the Multi-Ethnic Study of Atherosclerosis (n = 1611 AA). In both studies, we find that West-African ancestry is negatively associated with obesity, especially central obesity, among AA men, but not among AA women (pinteraction = 4.14 × 10−5 in pooled analysis of WHR). In conclusion, our results suggest that the combination of male gender and West-African genetic ancestry is associated with protection against central adiposity, and suggest that the large racial disparity that exists among women, but not men, may be at least partly attributed to genetic factors.
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Affiliation(s)
- Yann C Klimentidis
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona Tucson, AZ, USA
| | - Amit Arora
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona Tucson, AZ, USA
| | - Jin Zhou
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona Tucson, AZ, USA
| | - Rick Kittles
- Department of Surgery, College of Medicine, University of Arizona Tucson, AZ, USA
| | - David B Allison
- Nutrition and Obesity Research Center, University of Alabama at BirminghamBirmingham, AL, USA; Office of Energetics, University of Alabama at BirminghamBirmingham, AL, USA
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Le Cam S, Perrier C, Besnard AL, Bernatchez L, Evanno G. Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years. Proc Biol Sci 2016; 282:rspb.2014.2765. [PMID: 25608883 DOI: 10.1098/rspb.2014.2765] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life-history traits in supplemented populations. Here, we investigated year-to-year changes from 1989 to 2009 in genetic admixture at 15 microsatellite loci and in phenotypic traits in an Atlantic salmon (Salmo salar) population stocked during the first decade of this period with two genetically and phenotypically distinct source populations. We detected a pattern of temporally increasing introgressive hybridization between the stocked population and both source populations. The proportion of fish returning to the river after a single winter at sea (versus several ones) was higher in fish assigned to the main source population than in local individuals. Moreover, during the first decade of the study, both single-sea-winter and multi-sea-winter (MSW) fish assigned to the main source population were smaller than local fish. During the second decade of the study, MSW fish defined as hybrids were lighter and smaller than fish from parental populations, suggesting outbreeding depression. Overall, this study suggests that supplementation with non-local individuals may alter not only the genetic diversity of wild populations but also life-history traits of adaptive significance.
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Affiliation(s)
- Sabrina Le Cam
- INRA, UMR 0985 Ecology and Health of Ecosystems, Rennes 35042, France Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes 35042, France Station Biologique de Roscoff, Place Georges Teissier, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Roscoff Cedex 29688, France Station Biologique de Roscoff, Place Georges Teissier, CNRS, UMR 7144, Roscoff Cedex 29688, France
| | - Charles Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Anne-Laure Besnard
- INRA, UMR 0985 Ecology and Health of Ecosystems, Rennes 35042, France Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes 35042, France
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Guillaume Evanno
- INRA, UMR 0985 Ecology and Health of Ecosystems, Rennes 35042, France Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes 35042, France
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Halder I, Matthews KA, Buysse DJ, Strollo PJ, Causer V, Reis SE, Hall MH. African Genetic Ancestry is Associated with Sleep Depth in Older African Americans. Sleep 2015; 38:1185-93. [PMID: 25845688 DOI: 10.5665/sleep.4888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/31/2015] [Indexed: 02/05/2023] Open
Abstract
STUDY OBJECTIVES The mechanisms that underlie differences in sleep characteristics between European Americans (EA) and African Americans (AA) are not fully known. Although social and psychological processes that differ by race are possible mediators, the substantial heritability of sleep characteristics also suggests genetic underpinnings of race differences. We hypothesized that racial differences in sleep phenotypes would show an association with objectively measured individual genetic ancestry in AAs. DESIGN Cross sectional. SETTING Community-based study. PARTICIPANTS Seventy AA adults (mean age 59.5 ± 6.7 y; 62% female) and 101 EAs (mean age 60.5 ± 7 y, 39% female). MEASUREMENTS AND RESULTS Multivariate tests were used to compare the Pittsburgh Sleep Quality Index (PSQI) and in-home polysomnographic measures of sleep duration, sleep efficiency, apnea-hypopnea index (AHI), and indices of sleep depth including percent visually scored slow wave sleep (SWS) and delta EEG power of EAs and AAs. Sleep duration, efficiency, and sleep depth differed significantly by race. Individual % African ancestry (%AF) was measured in AA subjects using a panel of 1698 ancestry informative genetic markers and ranged from 10% to 88% (mean 67%). Hierarchical linear regression showed that higher %AF was associated with lower percent SWS in AAs (β (standard error) = -4.6 (1.5); P = 0.002), and explained 11% of the variation in SWS after covariate adjustment. A similar association was observed for delta power. No association was observed for sleep duration and efficiency. CONCLUSION African genetic ancestry is associated with indices of sleep depth in African Americans. Such an association suggests that part of the racial differences in slow-wave sleep may have genetic underpinnings.
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Affiliation(s)
- Indrani Halder
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Karen A Matthews
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - Daniel J Buysse
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | | | - Victoria Causer
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Steven E Reis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Martica H Hall
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
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Diez CM, Trujillo I, Martinez-Urdiroz N, Barranco D, Rallo L, Marfil P, Gaut BS. Olive domestication and diversification in the Mediterranean Basin. New Phytol 2015; 206:436-447. [PMID: 25420413 DOI: 10.1111/nph.13181] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/06/2014] [Indexed: 05/02/2023]
Abstract
Olive (Olea europaea ssp. europaea) is the most important oil fruit crop in temperate areas, but the origin of the cultivated olive remains unclear. The existence of one or several domestication events in the Mediterranean Basin (MB) is still debated. We analyzed a dataset of 387 cultivated and wild accessions that were genotyped at 25 simple-sequence repeat (SSR) loci. The sample represented genetic diversity at the geographic extremes of the MB. We inferred relationships among samples and also applied approximate Bayesian computation to estimate the most probable demographic model of our samples. Cultivated olives clustered into three different gene pools (Q1, Q2 and Q3), corresponding loosely to the west, central and eastern MB, respectively. Q1 consisted primarily of accessions from southern Spain, retained the fingerprint of a genetic bottleneck, and was closely related to accessions from the eastern MB. Q2 showed signs of recent admixture with wild olives and may derive from a local domestication event in the central MB. Overall our results suggest that admixture shaped olive germplasm and perhaps also local domestication events.
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Affiliation(s)
- Concepcion M Diez
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA
| | - Isabel Trujillo
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Nieves Martinez-Urdiroz
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Diego Barranco
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Luis Rallo
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3. Edificio C4, Campus de Rabanales, 14014, Córdoba, Spain
| | - Pedro Marfil
- Departamento de Historia del Arte, Arqueología y Música. Facultad de Filosofía y Letras, Universidad de Córdoba, Plaza del Cardenal Salazar 3, 14071, Córdoba, Spain
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA
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Besnard G, El Bakkali A. Sequence analysis of single-copy genes in two wild olive subspecies: nucleotide diversity and potential use for testing admixture. Genome 2014; 57:145-53. [PMID: 24884690 DOI: 10.1139/gen-2014-0001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The wild olive distribution extends from the Mediterranean region to south Asia and Austral Africa. The species is also invasive, particularly in Australia. Here, we investigated the sequence variation at five nuclear single-copy genes in 41 native and invasive accessions of the Mediterranean and African olive subspecies. The nucleotide diversity was assessed and the phylogenetic relationships between alleles were depicted with haplotype networks. A Bayesian clustering method (STRUCTURE) was applied to identify the main gene pools. We found an average of 18.4 alleles per locus. Native Mediterranean and African olives only share one allele, which testifies for ancient admixture on the Red Sea hills. The presence of divergent alleles in the Mediterranean olive, as well as the identification of two main genetic clusters, suggests a complex origin with two highly differentiated gene pools from the eastern and western Mediterranean that recently admixed. In the invasive range, relatively high nucleotide diversity is observed as a consequence of the introduction of alleles from two subspecies. Our data confirm that four invasive individuals are early-generation hybrids. Finally, the utility of single-copy gene sequences in olive population genomic and phylogenetic studies is briefly discussed.
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Affiliation(s)
- G Besnard
- a CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062 Toulouse cedex 9, France
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Affiliation(s)
- Robert C Berwick
- Department of Electrical Engineering and Computer Science/Brain and Cognitive Sciences, Laboratory for Information and Decision Systems, Massachusetts Institute of Technology Cambridge, MA, USA
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Dediu D, Levinson SC. On the antiquity of language: the reinterpretation of Neandertal linguistic capacities and its consequences. Front Psychol 2013; 4:397. [PMID: 23847571 PMCID: PMC3701805 DOI: 10.3389/fpsyg.2013.00397] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 06/12/2013] [Indexed: 11/13/2022] Open
Abstract
It is usually assumed that modern language is a recent phenomenon, coinciding with the emergence of modern humans themselves. Many assume as well that this is the result of a single, sudden mutation giving rise to the full "modern package." However, we argue here that recognizably modern language is likely an ancient feature of our genus pre-dating at least the common ancestor of modern humans and Neandertals about half a million years ago. To this end, we adduce a broad range of evidence from linguistics, genetics, paleontology, and archaeology clearly suggesting that Neandertals shared with us something like modern speech and language. This reassessment of the antiquity of modern language, from the usually quoted 50,000-100,000 years to half a million years, has profound consequences for our understanding of our own evolution in general and especially for the sciences of speech and language. As such, it argues against a saltationist scenario for the evolution of language, and toward a gradual process of culture-gene co-evolution extending to the present day. Another consequence is that the present-day linguistic diversity might better reflect the properties of the design space for language and not just the vagaries of history, and could also contain traces of the languages spoken by other human forms such as the Neandertals.
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Affiliation(s)
- Dan Dediu
- Language and Genetics Department, Max Planck Institute for PsycholinguisticsNijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University NijmegenNijmegen, Netherlands
| | - Stephen C. Levinson
- Donders Institute for Brain, Cognition and Behaviour, Radboud University NijmegenNijmegen, Netherlands
- Language and Cognition Department, Max Planck Institute for PsycholinguisticsNijmegen, Netherlands
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Mann PC, Cooper ME, Ryckman KK, Comas B, Gili J, Crumley S, Bream EN, Byers HM, Piester T, Schaefer A, Christine PJ, Lawrence A, Schaa KL, Kelsey KJ, Berends SK, Gadow E, Cosentino V, Castilla EE, Camelo JL, Saleme C, Day LJ, England SK, Marazita ML, Dagle JM, Murray JC, Murray JC. Polymorphisms in the fetal progesterone receptor and a calcium-activated potassium channel isoform are associated with preterm birth in an Argentinian population. J Perinatol 2013; 33:336-40. [PMID: 23018797 PMCID: PMC3719965 DOI: 10.1038/jp.2012.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To investigate genetic etiologies of preterm birth (PTB) in Argentina through evaluation of single-nucleotide polymorphisms (SNPs) in candidate genes and population genetic admixture. STUDY DESIGN Genotyping was performed in 389 families. Maternal, paternal and fetal effects were studied separately. Mitochondrial DNA (mtDNA) was sequenced in 50 males and 50 females. Y-chromosome anthropological markers were evaluated in 50 males. RESULT Fetal association with PTB was found in the progesterone receptor (PGR, rs1942836; P=0.004). Maternal association with PTB was found in small conductance calcium activated potassium channel isoform 3 (KCNN3, rs883319; P=0.01). Gestational age associated with PTB in PGR rs1942836 at 32-36 weeks (P=0.0004). MtDNA sequencing determined 88 individuals had Amerindian consistent haplogroups. Two individuals had Amerindian Y-chromosome consistent haplotypes. CONCLUSION This study replicates single locus fetal associations with PTB in PGR, maternal association in KCNN3, and demonstrates possible effects for divergent racial admixture on PTB.
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Affiliation(s)
- Paul C. Mann
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Margaret E. Cooper
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - Kelli K. Ryckman
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Belén Comas
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Juan Gili
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Suzanne Crumley
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Elise N.A. Bream
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Heather M. Byers
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Travis Piester
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Amanda Schaefer
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Paul J. Christine
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Amy Lawrence
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Kendra L. Schaa
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | | | - Susan K. Berends
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Enrique Gadow
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina
| | - Viviana Cosentino
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina
| | - Eduardo E. Castilla
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Instituto Nacional de Genética Médica Populacional and Estudio Colaborativo Latino Americano de Malformaciones Congénitas at Laboratório de Epidemiologia de Malformações Congênitas Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jorge López Camelo
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Capital Federal, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Capital Federal, Argentina,Instituto Multidisciplinario de Biología Celular, La Plata, Buenos Aires, Argentina
| | - Cesar Saleme
- Instituto de Maternidad y Ginecología Nuestra Señora de las Mercedes, San Miguel de Tucumán, Tucumán, Argentina
| | - Lori J. Day
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, Iowa, 52242
| | - Sarah K. England
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, Iowa, 52242,Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, 52242
| | - Mary L. Marazita
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - John M. Dagle
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, 52242,Corresponding Author: Jeffrey C. Murray, MD Professor, Departments of Pediatrics, Epidemiology, and Biological Sciences University of Iowa Carver College of Medicine 500 Newton Road, 2182 ML, Iowa City, IA 52242-1181 319-335-6897 phone; 319-335-6970 fax
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Abstract
Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.
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Affiliation(s)
- Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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