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Yang Z, Chen H, Lu Y, Gao Y, Sun H, Wang J, Jin L, Chu J, Xu S. Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan. BMC Biol 2022; 20:166. [PMID: 35864541 PMCID: PMC9306206 DOI: 10.1186/s12915-022-01367-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Yunnan is located in Southwest China and consists of great cultural, linguistic, and genetic diversity. However, the genomic diversity of ethnic minorities in Yunnan is largely under-investigated. To gain insights into population history and local adaptation of Yunnan minorities, we analyzed 242 whole-exome sequencing data with high coverage (~ 100-150 ×) of Yunnan minorities representing Achang, Jingpo, Dai, and Deang, who were linguistically assumed to be derived from three ancient lineages (the tri-genealogy hypothesis), i.e., Di-Qiang, Bai-Yue, and Bai-Pu. RESULTS Yunnan minorities show considerable genetic differences. Di-Qiang populations likely migrated from the Tibetan area about 6700 years ago. Genetic divergence between Bai-Yue and Di-Qiang was estimated to be 7000 years, and that between Bai-Yue and Bai-Pu was estimated to be 5500 years. Bai-Pu is relatively isolated, but gene flow from surrounding Di-Qiang and Bai-Yue populations was also found. Furthermore, we identified genetic variants that are differentiated within Yunnan minorities possibly due to the living circumstances and habits. Notably, we found that adaptive variants related to malaria and glucose metabolism suggest the adaptation to thalassemia and G6PD deficiency resulting from malaria resistance in the Dai population. CONCLUSIONS We provided genetic evidence of the tri-genealogy hypothesis as well as new insights into the genetic history and local adaptation of the Yunnan minorities.
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Affiliation(s)
- Zhaoqing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, 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
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for 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
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for 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
| | - Jiayou Chu
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for 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.
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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2
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Positive selection in Europeans and East-Asians at the ABCA12 gene. Sci Rep 2019; 9:4843. [PMID: 30890716 PMCID: PMC6424970 DOI: 10.1038/s41598-019-40360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022] Open
Abstract
Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation. We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation. We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons and the transcription starting site of ABCA12. We found no obvious effect of rs10180970 alleles on ABCA12 gene expression. We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and present in non-Africans 45,000 years ago.
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3
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Curnoe D, Datan I, Goh HM, Sauffi MS. Femur associated with the Deep Skull from the West Mouth of the Niah Caves (Sarawak, Malaysia). J Hum Evol 2019; 127:133-148. [PMID: 30777354 DOI: 10.1016/j.jhevol.2018.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023]
Abstract
The skeletal remains of Pleistocene anatomically modern humans are rare in island Southeast Asia. Moreover, continuing doubts over the dating of most of these finds has left the arrival time for the region's earliest inhabitants an open question. The unique biogeography of island Southeast Asia also raises questions about the physical and cultural adaptations of early anatomically modern humans, especially within the setting of rainforest inhabitation. Within this context the Deep Skull from the West Mouth of the Niah Caves continues to figure prominently owing to its relative completeness and the greater certainty surrounding its geological age. Recovered along with this partial cranium in 1958 were several postcranial bones including a partial femur which until now has received little attention. Here we provide a description and undertake a comparison of the Deep Skull femur finding it to be very small in all of its cross-sectional dimensions. We note a number of size and shape similarities to the femora of Indigenous Southeast Asians, especially Aeta people from the Philippines. We estimate its stature to have been roughly 145-146 cm and body mass around 35 kg, confirming similarities to Aeta females. Its extreme gracility indicated by low values for a range of biomechanical parameters taken midshaft meets expectations for a very small (female) Paleolithic East Asian. Interestingly, the second moment of area about the mediolateral axis is enlarged relative to the second moment of area about the anteroposterior axis, which could potentially signal a difference in activity levels or lifestyle compared with other Paleolithic femora. However, it might also be the result of sexual dimorphism in these parameters as well as possibly reflecting changes associated with aging.
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Affiliation(s)
- Darren Curnoe
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Palaeontology, Geobiology and Earth Archives Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Ipoi Datan
- Sarawak Museum Department, Jalan Barak, Kuching, Sarawak, 93000, Malaysia
| | - Hsiao Mei Goh
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Palaeontology, Geobiology and Earth Archives Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia; Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Mohammed S Sauffi
- Sarawak Museum Department, Jalan Barak, Kuching, Sarawak, 93000, Malaysia
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4
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Mohd-Assaad N, McDonald BA, Croll D. Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen. Genome Biol Evol 2018; 10:1315-1332. [PMID: 29722810 PMCID: PMC5972619 DOI: 10.1093/gbe/evy087] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/29/2022] Open
Abstract
Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
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5
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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6
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Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TNB, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY. Characterising private and shared signatures of positive selection in 37 Asian populations. Eur J Hum Genet 2017; 25:499-508. [PMID: 28098149 DOI: 10.1038/ejhg.2016.181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.
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Affiliation(s)
- Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Philip J Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Suthat Fucharoen
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Worachart Lert-Itthiporn
- Faculty of Science, Molecular Medicine Graduate Programme, Mahidol University, Bangkok, Thailand.,Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kwanrutai Chin-Inmanu
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tran Nguyen Bich Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Katie Anders
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | | | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, YinchuanChina
| | - Yeun-Jun Chung
- Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University Medical College, Seoul, Korea
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE), Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | | | - RickTwee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sarah J Dunstan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cameron Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Institute of Personalized Genomics and Gene Therapy (IPGG), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
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7
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Ågren J, Oakley CG, Lundemo S, Schemske DW. Adaptive divergence in flowering time among natural populations of
Arabidopsis thaliana
: Estimates of selection and QTL mapping. Evolution 2016; 71:550-564. [DOI: 10.1111/evo.13126] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Jon Ågren
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre Uppsala University Norbyvägen 18 D SE‐752 36 Uppsala Sweden
| | | | - Sverre Lundemo
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre Uppsala University Norbyvägen 18 D SE‐752 36 Uppsala Sweden
- WWF Norway Postboks 6784, St. Olavs Plass 0130 Oslo Norway
| | - Douglas W. Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station Michigan State University East Lansing Michigan 48824
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8
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Bankoff RJ, Perry GH. Hunter-gatherer genomics: evolutionary insights and ethical considerations. Curr Opin Genet Dev 2016; 41:1-7. [PMID: 27400119 DOI: 10.1016/j.gde.2016.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 10/21/2022]
Abstract
Hunting and gathering societies currently comprise only a small proportion of all human populations. However, the geographic and environmental diversity of modern hunter-gatherer groups, their inherent dependence on ecological resources, and their connection to patterns of behavior and subsistence that represent the vast majority of human history provide opportunities for scientific research to deliver major insights into the evolutionary history of our species. We review recent evolutionary genomic studies of hunter-gatherers, focusing especially on those that identify and functionally characterize phenotypic adaptations to local environments. We also call attention to specific ethical issues that scientists conducting hunter-gatherer genomics research ought to consider, including potential social and economic tensions between traditionally mobile hunter-gatherers and the land ownership-based nation-states by which they are governed, and the implications of genomic-based evidence of long-term evolutionary associations with particular habitats.
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Affiliation(s)
- Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Intercollege Program in Bioethics, Pennsylvania State University, University Park, PA 16802, USA.
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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9
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Detecting signatures of positive selection associated with musical aptitude in the human genome. Sci Rep 2016; 6:21198. [PMID: 26879527 PMCID: PMC4754774 DOI: 10.1038/srep21198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/19/2016] [Indexed: 01/18/2023] Open
Abstract
Abilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude.
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10
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Huang N, Wen Y, Guo X, Li Z, Dai J, Ni B, Yu J, Lin Y, Zhou W, Yao B, Jiang Y, Sha J, Conrad DF, Hu Z. A Screen for Genomic Disorders of Infertility Identifies MAST2 Duplications Associated with Nonobstructive Azoospermia in Humans. Biol Reprod 2015. [PMID: 26203179 DOI: 10.1095/biolreprod.115.131185] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Since the cytogenetic identification of azoospermia factor regions 40 years ago, the Y chromosome has dominated research on the genetics of male infertility. We hypothesized that hotspots of structural rearrangement, which are dispersed across the genome, may mediate rare, recurrent copy number variations (CNVs), leading to severe infertility. We tested this hypothesis by contrasting patterns of rare CNVs in 970 Han Chinese men with idiopathic nonobstructive azoospermia and 1661 ethnicity-matched controls. Our results strongly support our previous claim that sperm production is modulated by genetic variation across the entire genome. The X chromosome in particular was enriched for loci modulating spermatogenesis--rare X-linked deletions larger than 100 kb were twice as common in patients compared with controls (odds ratio [OR] = 2.05, P = 0.01). At rearrangement hotspots across the genome, we observed a 2.4-fold enrichment of singleton CNVs in patients (P < 0.02), and we identified 117 testis genes, such as SYCE1, contained within 47 hotspots that may plausibly mediate genomic disorders of fertility. In our discovery sample we observed 3 case-specific duplications of the autosomal gene MAST2, and in a replication phase we found another 11 duplications in 1457 patients and 1 duplication in 1590 controls (P < 5 × 10(-5), combined data). With a large, polygenic genetic basis, new ways of establishing the pathogenicity of rare, large-effect mutations will be needed to fully reap the benefit of genome data in the management of azoospermia.
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Affiliation(s)
- Ni Huang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Yang Wen
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuejiang Guo
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Zheng Li
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juncheng Dai
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bixian Ni
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jun Yu
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuan Lin
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wen Zhou
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bing Yao
- Department of Andrology, Nanjing Jinling Hospital, Nanjing, China
| | - Yue Jiang
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Zhibin Hu
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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11
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Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Hum Genet 2015; 134:375-92. [PMID: 25634076 DOI: 10.1007/s00439-014-1525-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/25/2014] [Indexed: 10/24/2022]
Abstract
The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
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12
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Boettcher PJ, Hoffmann I, Baumung R, Drucker AG, McManus C, Berg P, Stella A, Nilsen LB, Moran D, Naves M, Thompson MC. Genetic resources and genomics for adaptation of livestock to climate change. Front Genet 2015; 5:461. [PMID: 25646122 PMCID: PMC4298221 DOI: 10.3389/fgene.2014.00461] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/15/2014] [Indexed: 01/30/2023] Open
Affiliation(s)
- Paul J Boettcher
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations Rome, Italy
| | - Irene Hoffmann
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations Rome, Italy
| | - Roswitha Baumung
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations Rome, Italy
| | - Adam G Drucker
- In Situ and On Farm Conservation, Bioversity International Maccarese, Italy
| | | | - Peer Berg
- NordGen Farm Animals, Nordic Genetic Resource Center Ås, Norway
| | - Alessandra Stella
- Parco Tecnologico Padano Lodi, Italy ; Institute of Agricultural Biology and Biotechnology, National Research Council Milan, Italy
| | - Linn B Nilsen
- Plant Production and Protection Division, Food and Agriculture Organization of the United Nations Rome, Italy ; NADEL - Center for Development and Cooperation, Swiss Federal Institute of Technology in Zürich Zürich, Switzerland
| | - Dominic Moran
- Sustainable Rural Systems, Scotland's Rural College Edinburgh, UK
| | - Michel Naves
- UR143, Unité de Recherches Zootechniques, Institut National de la Recherche Agronomique Petit-Bourg, Guadeloupe, France
| | - Mary C Thompson
- In Situ and On Farm Conservation, Bioversity International Maccarese, Italy ; Basque Center for Climate Change Bilbao, Spain
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13
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Koh XH, Liu X, Teo YY. Can evidence from genome-wide association studies and positive natural selection surveys be used to evaluate the thrifty gene hypothesis in East Asians? PLoS One 2014; 9:e110974. [PMID: 25337808 PMCID: PMC4206456 DOI: 10.1371/journal.pone.0110974] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 09/17/2014] [Indexed: 12/02/2022] Open
Abstract
Body fat deposition and distribution differ between East Asians and Europeans, and for the same level of obesity, East Asians are at higher risks of Type 2 diabetes (T2D) and other metabolic disorders. This observation has prompted the reclassifications of body mass index thresholds for the definitions of “overweight” and “obese” in East Asians. However, the question remains over what evolutionary mechanisms have driven the differences in adiposity morphology between two population groups that shared a common ancestor less than 80,000 years ago. The Thrifty Gene hypothesis has been suggested as a possible explanation, where genetic factors that allowed for efficient food-energy conversion and storage are evolutionarily favoured by conferring increased chances of survival and fertility. Here, we leveraged on the existing findings from genome-wide association studies and large-scale surveys of positive natural selection to evaluate whether there is currently any evidence to support the Thrifty Gene hypothesis. We first assess whether the existing genetic associations with obesity and T2D are located in genomic regions that are reported to be under positive selection, and if so, whether the risk alleles sit on the extended haplotype forms. In addition, we interrogate whether these risk alleles are the derived forms that differ from the ancestral alleles, and whether there is significant evidence of population differentiation at these SNPs between East Asian and European populations. Our systematic survey did not yield conclusive evidence to support the Thrifty Gene hypothesis as a possible explanation for the differences observed between East Asians and Europeans.
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Affiliation(s)
- Xuan-Han Koh
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- * E-mail:
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14
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The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia. Hum Genet 2014; 133:1169-85. [DOI: 10.1007/s00439-014-1459-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/29/2014] [Indexed: 12/12/2022]
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15
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Liu X, Saw WY, Ali M, Ong RTH, Teo YY. Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium. BMC Genomics 2014; 15:332. [PMID: 24885517 PMCID: PMC4035063 DOI: 10.1186/1471-2164-15-332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/25/2014] [Indexed: 11/22/2022] Open
Abstract
Background The HUGO Pan-Asian SNP Consortium (PASNP) has generated a genetic resource of almost 55,000 autosomal single nucleotide polymorphisms (SNPs) across more than 1,800 individuals from 73 urban and indigenous populations in Asia. This has offered valuable insights into the correlation between the genetic ancestry of these populations with major linguistic systems and geography. Here, we attempt to understand whether adaptation to local climate, diet and environment partly explains the genetic variation present in these populations by investigating the genomic signatures of positive selection. Results To evaluate the impact to the selection analyses due to the considerably lower SNP density as compared to other population genetics resources such as the International HapMap Project (HapMap) or the Singapore Genome Variation Project, we evaluated the extent of haplotype phasing switch errors and the consistency of selection signals from three haplotype-based approaches (iHS, XP-EHH, haploPS) when the HapMap data is thinned to a similar density as PASNP. We subsequently applied haploPS to detect and characterize positive selection in the PASNP populations, identifying 59 genomics regions that were selected in at least one PASNP populations. A cluster analysis on the basis of these 59 signals showed that indigenous populations such as the Negrito from Malaysia and Philippines, the China Hmong, and the Taiwan Ami and Atayal shared more of these signals. We also reported evidence of a positive selection signal encompassing the beta globin gene in the Taiwan Ami and Atayal that was distinct from the signal in the HapMap Africans, suggesting the possibility of convergent evolution at this locus due to malarial selection. Conclusions We established that the lower SNP content of the PASNP data conferred weaker ability to detect signatures of positive selection, but the availability of the new approach haploPS retained modest power. Out of all the populations in PASNP, we identified only 59 signals, suggesting a strong need for high-density population-level genotyping data or sequencing data in order to achieve a comprehensive survey of positive selection in Asian populations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-332) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, MD3 16 Medical Drive, Singapore 117597, Singapore.
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