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Liu J, Bitsue HK, Yang Z. Skin colour: A window into human phenotypic evolution and environmental adaptation. Mol Ecol 2024; 33:e17369. [PMID: 38713101 DOI: 10.1111/mec.17369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.
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Affiliation(s)
- Jiuming Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Habtom K Bitsue
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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2
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A large Canadian cohort provides insights into the genetic architecture of human hair colour. Commun Biol 2021; 4:1253. [PMID: 34737440 PMCID: PMC8568909 DOI: 10.1038/s42003-021-02764-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Hair colour is a polygenic phenotype that results from differences in the amount and ratio of melanins located in the hair bulb. Genome-wide association studies (GWAS) have identified many loci involved in the pigmentation pathway affecting hair colour. However, most of the associated loci overlap non-protein coding regions and many of the molecular mechanisms underlying pigmentation variation are still not understood. Here, we conduct GWAS meta-analyses of hair colour in a Canadian cohort of 12,741 individuals of European ancestry. By performing fine-mapping analyses we identify candidate causal variants in pigmentation loci associated with blonde, red and brown hair colour. Additionally, we observe colocalization of several GWAS hits with expression and methylation quantitative trait loci (QTLs) of cultured melanocytes. Finally, transcriptome-wide association studies (TWAS) further nominate the expression of EDNRB and CDK10 as significantly associated with hair colour. Our results provide insights on the mechanisms regulating pigmentation biology in humans.
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3
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Le L, Escobar IE, Ho T, Lefkovith AJ, Latteri E, Haltaufderhyde KD, Dennis MK, Plowright L, Sviderskaya EV, Bennett DC, Oancea E, Marks MS. SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation. Mol Biol Cell 2020; 31:2687-2702. [PMID: 32966160 PMCID: PMC7927184 DOI: 10.1091/mbc.e20-03-0200] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
SLC45A2 encodes a putative transporter expressed primarily in pigment cells. SLC45A2 mutations cause oculocutaneous albinism type 4 (OCA4) and polymorphisms are associated with pigmentation variation, but the localization, function, and regulation of SLC45A2 and its variants remain unknown. We show that SLC45A2 localizes to a cohort of mature melanosomes that only partially overlaps with the cohort expressing the chloride channel OCA2. SLC45A2 expressed ectopically in HeLa cells localizes to lysosomes and raises lysosomal pH, suggesting that in melanocytes SLC45A2 expression, like OCA2 expression, results in the deacidification of maturing melanosomes to support melanin synthesis. Interestingly, OCA2 overexpression compensates for loss of SLC45A2 expression in pigmentation. Analyses of SLC45A2- and OCA2-deficient mouse melanocytes show that SLC45A2 likely functions later during melanosome maturation than OCA2. Moreover, the light skin-associated SLC45A2 allelic F374 variant restores only moderate pigmentation to SLC45A2-deficient melanocytes due to rapid proteasome-dependent degradation resulting in lower protein expression levels in melanosomes than the dark skin-associated allelic L374 variant. Our data suggest that SLC45A2 maintains melanosome neutralization that is initially orchestrated by transient OCA2 activity to support melanization at late stages of melanosome maturation, and that a common allelic variant imparts reduced activity due to protein instability.
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Affiliation(s)
- Linh Le
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Iliana E Escobar
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Tina Ho
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ariel J Lefkovith
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily Latteri
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
| | - Kirk D Haltaufderhyde
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Megan K Dennis
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Biology Department, Marist College, Poughkeepsie, NY 12601
| | - Lynn Plowright
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena V Sviderskaya
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Dorothy C Bennett
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Michael S Marks
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
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4
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Abstract
Human skin and hair color are visible traits that can vary dramatically within and across ethnic populations. The genetic makeup of these traits-including polymorphisms in the enzymes and signaling proteins involved in melanogenesis, and the vital role of ion transport mechanisms operating during the maturation and distribution of the melanosome-has provided new insights into the regulation of pigmentation. A large number of novel loci involved in the process have been recently discovered through four large-scale genome-wide association studies in Europeans, two large genetic studies of skin color in Africans, one study in Latin Americans, and functional testing in animal models. The responsible polymorphisms within these pigmentation genes appear at different population frequencies, can be used as ancestry-informative markers, and provide insight into the evolutionary selective forces that have acted to create this human diversity.
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Affiliation(s)
- William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia;
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5
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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6
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Okamura K, Hayashi M, Nakajima O, Kono M, Abe Y, Hozumi Y, Suzuki T. A 4‐bp deletion promoter variant (rs984225803) is associated with mild
OCA
4 among Japanese patients. Pigment Cell Melanoma Res 2018; 32:79-84. [DOI: 10.1111/pcmr.12727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/11/2018] [Accepted: 07/13/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Ken Okamura
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Masahiro Hayashi
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Osamu Nakajima
- Faculty of MedicineResearch Center for Molecular GeneticsInstitute for Promotion of Medical Science ResearchYamagata University Yamagata Japan
| | - Michihiro Kono
- Department of DermatologyNagoya University Graduate School of Medicine Nagoya Japan
| | - Yuko Abe
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Yutaka Hozumi
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Tamio Suzuki
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
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7
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Deng L, Xu S. Adaptation of human skin color in various populations. Hereditas 2017; 155:1. [PMID: 28701907 PMCID: PMC5502412 DOI: 10.1186/s41065-017-0036-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/02/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine. DISCUSSION Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies. CONCLUSION Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.
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Affiliation(s)
- Lian Deng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China.,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438 China
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8
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Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z, Groß M, Sell C, Blöcher J, Kirsanow K, Rohland N, Rieger B, Kaiser E, Schier W, Pozdniakov D, Khokhlov A, Georges M, Wilde S, Powell A, Heyer E, Currat M, Reich D, Samashev Z, Parzinger H, Molodin VI, Burger J. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat Commun 2017; 8:14615. [PMID: 28256537 PMCID: PMC5337992 DOI: 10.1038/ncomms14615] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/13/2017] [Indexed: 01/10/2023] Open
Abstract
During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.
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Affiliation(s)
- Martina Unterländer
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Friso Palstra
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aleksandr Pilipenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Zuzana Hofmanová
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Melanie Groß
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Christian Sell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Karola Kirsanow
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin Rieger
- Molecular Genetics and Genome Analysis Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Elke Kaiser
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Wolfram Schier
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Dimitri Pozdniakov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara 443099, Russian Federation
| | - Myriam Georges
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Sandra Wilde
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Adam Powell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany
| | - Evelyne Heyer
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Mathias Currat
- Dépt. de Génétique & Evolution, Unité d'anthropologie, Université de Genève, 1205 Genève, Suisse
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zainolla Samashev
- Branch of Margulan Institute of Archaeology, Astana 010000, Kazakhstan
| | | | - Vyacheslav I. Molodin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
| | - Joachim Burger
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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9
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Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil. Leg Med (Tokyo) 2017; 25:43-51. [DOI: 10.1016/j.legalmed.2016.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/05/2016] [Accepted: 12/30/2016] [Indexed: 01/28/2023]
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10
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Kita R, Fraser HB. Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin. PLoS Genet 2016; 12:e1006382. [PMID: 27760139 PMCID: PMC5070784 DOI: 10.1371/journal.pgen.1006382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022] Open
Abstract
Sun-exposure is a key environmental variable in the study of human evolution. Several skin-pigmentation genes serve as classical examples of positive selection, suggesting that sun-exposure has significantly shaped worldwide genomic variation. Here we investigate the interaction between genetic variation and sun-exposure, and how this impacts gene expression regulation. Using RNA-Seq data from 607 human skin samples, we identified thousands of transcripts that are differentially expressed between sun-exposed skin and non-sun-exposed skin. We then tested whether genetic variants may influence each individual’s gene expression response to sun-exposure. Our analysis revealed 10 sun-exposure-dependent gene expression quantitative trait loci (se-eQTLs), including genes involved in skin pigmentation (SLC45A2) and epidermal differentiation (RASSF9). The allele frequencies of the RASSF9 se-eQTL across diverse populations correlate with the magnitude of solar radiation experienced by these populations, suggesting local adaptation to varying levels of sunlight. These results provide the first examples of sun-exposure-dependent regulatory variation and suggest that this variation has contributed to recent human adaptation. Varying levels of sun-exposure across the world have significantly shaped human evolution. Previous analyses have found several skin pigmentation genes with evidence of strong evolutionary pressures throughout human history, manifesting as large differences in the frequency of genomic variants across populations. But even within populations, individuals respond differently to sun-exposure, suggesting variation in addition to the major differences in skin pigmentation across populations. Here we investigated whether genetic variants associate with response to sun-exposure within Europeans. To measure the response we analyzed gene expression in sun-exposed and non-sun-exposed skin, and identified ten genetic variants that associated with the sun-exposure response of nearby genes. One of these genetic variants, which associated with the sun-exposure response of the gene RASSF9, showed evidence of adaptation in humans in response to solar radiation. Together this evidence suggests that the regulation of gene expression is influenced by sun-exposure and that the sun-exposure dependent effect on RASSF9 expression may have had an effect on human fitness. To our knowledge, this is the first example of an environment-dependent regulatory variant with evidence of adaptation in humans.
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Affiliation(s)
- Ryosuke Kita
- Department of Biology, Stanford University, Stanford California
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford California
- * E-mail:
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11
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Lesch BJ, Silber SJ, McCarrey JR, Page DC. Parallel evolution of male germline epigenetic poising and somatic development in animals. Nat Genet 2016; 48:888-94. [PMID: 27294618 DOI: 10.1038/ng.3591] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
Changes in gene regulation frequently underlie changes in morphology during evolution, and differences in chromatin state have been linked with changes in anatomical structure and gene expression across evolutionary time. Here we assess the relationship between evolution of chromatin state in germ cells and evolution of gene regulatory programs governing somatic development. We examined the poised (H3K4me3/H3K27me3 bivalent) epigenetic state in male germ cells from five mammalian and one avian species. We find that core genes poised in germ cells from multiple amniote species are ancient regulators of morphogenesis that sit at the top of transcriptional hierarchies controlling somatic tissue development, whereas genes that gain poising in germ cells from individual species act downstream of core poised genes during development in a species-specific fashion. We propose that critical regulators of animal development gained an epigenetically privileged state in germ cells, manifested in amniotes by H3K4me3/H3K27me3 poising, early in metazoan evolution.
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Affiliation(s)
| | - Sherman J Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, Missouri, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, USA
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12
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Key FM, Fu Q, Romagné F, Lachmann M, Andrés AM. Human adaptation and population differentiation in the light of ancient genomes. Nat Commun 2016; 7:10775. [PMID: 26988143 PMCID: PMC4802047 DOI: 10.1038/ncomms10775] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 01/24/2023] Open
Abstract
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. Detecting the targets of positive selection in the human genome is challenging. Here, the authors combine modern and ancient genomes to show that alleles strongly differentiated between Africans and Europeans mediated local adaptation in European populations, and were mostly contributed by ancient hunter-gatherers.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,Department of Genetics, Harvard Medical School, Boston 02115, Massachusetts, USA
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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Jonnalagadda M, Norton H, Ozarkar S, Kulkarni S, Ashma R. Association of genetic variants with skin pigmentation phenotype among populations of west Maharashtra, India. Am J Hum Biol 2016; 28:610-8. [PMID: 26918427 DOI: 10.1002/ajhb.22836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/23/2015] [Accepted: 01/07/2016] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES South Asians exhibit extensive variation in skin melanin index (MI) which is observed across the broader region of South Asia as well as within restricted geographic regions. However, the genetic variants associated with variation in the skin pigmentation phenotype are poorly understood in these populations. The present study examines the association between MI measures and genetic variants from 5 candidate pigmentation genes among 533 individuals representing 6 populations of West Maharashtra. METHODS Associations between five single nucleotide polymorphisms (SNPs) known to play a role in pigmentation (rs1426654-SLC24A5, rs1042602-TYR, rs16891982-SLC45A2, rs6058017-ASIP, and rs642742-KITLG) and MI measures were tested using standard one-way analysis of variance (ANOVA) within each population. Multiple linear regression was used to test the effects of these SNPs in the full West Maharashtra sample using sex, age, and population or social group as covariates. RESULTS rs1426654 showed significant association with MI in all six study populations (P < 0.01). Association tests using sex, age, and population as covariates showed rs1426654 and rs1042602 to be significantly (P < 0.01) associated with lighter skin pigmentation in West Maharashtra as a whole. By contrast, when social group was added as a covariate instead of population, rs1426654, rs1042602, and rs16891982 were significantly (P < 0.01) associated with lighter skin pigmentation. CONCLUSIONS Only rs1426654 is significantly associated with MI in each individual population; however, rs1426654, rs1042602, and rs16891982 are significantly associated with pigmentation in the broader West Maharashtra region after controlling for population and social group, with rs1426654 (SLC24A5) explaining the majority of the observed variation. Am. J. Hum. Biol. 28:610-618, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Manjari Jonnalagadda
- Department of Anthropology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India
| | - Shaunak Kulkarni
- Department of Anthropology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India.
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Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
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Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
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Rishishwar L, Conley AB, Wigington CH, Wang L, Valderrama-Aguirre A, Jordan IK. Ancestry, admixture and fitness in Colombian genomes. Sci Rep 2015. [PMID: 26197429 PMCID: PMC4508918 DOI: 10.1038/srep12376] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%–96.7%), followed by Native American (average = 18.1%, range = 2.1%–33.3%) and African (average = 7.3%, range = 0.2%–38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.
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Affiliation(s)
- Lavanya Rishishwar
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA [2] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [3] BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia
| | - Andrew B Conley
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Lu Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Augusto Valderrama-Aguirre
- 1] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [2] Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia [3] Regenerar - Center of Excellence for Regenerative and Personalized Medicine, Cali, Valle del Cauca, Colombia
| | - I King Jordan
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA [2] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [3] BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia
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Maroñas O, Phillips C, Söchtig J, Gomez-Tato A, Cruz R, Alvarez-Dios J, de Cal MC, Ruiz Y, Fondevila M, Carracedo Á, Lareu MV. Development of a forensic skin colour predictive test. Forensic Sci Int Genet 2014; 13:34-44. [DOI: 10.1016/j.fsigen.2014.06.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 11/29/2022]
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Adaptations to local environments in modern human populations. Curr Opin Genet Dev 2014; 29:1-8. [PMID: 25129844 DOI: 10.1016/j.gde.2014.06.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 06/30/2014] [Indexed: 12/11/2022]
Abstract
After leaving sub-Saharan Africa around 50000-100000 years ago, anatomically modern humans have quickly occupied extremely diverse environments. Human populations were exposed to further environmental changes resulting from cultural innovations, such as the spread of farming, which gave rise to new selective pressures related to pathogen exposures and dietary shifts. In addition to changing the frequency of individual adaptive alleles, natural selection may also shape the overall genetic architecture of adaptive traits. Here, we review recent advances in understanding the genetic architecture of adaptive human phenotypes based on insights from the studies of lactase persistence, skin pigmentation and high-altitude adaptation. These adaptations evolved in parallel in multiple human populations, providing a chance to investigate independent realizations of the evolutionary process. We suggest that the outcome of adaptive evolution is often highly variable even under similar selective pressures. Finally, we highlight a growing need for detecting adaptations that did not follow the classical sweep model and for incorporating new sources of genetic evidence such as information from ancient DNA.
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López S, García Ó, Yurrebaso I, Flores C, Acosta-Herrera M, Chen H, Gardeazabal J, Careaga JM, Boyano MD, Sánchez A, Ratón-Nieto JA, Sevilla A, Smith-Zubiaga I, de Galdeano AG, Martinez-Cadenas C, Izagirre N, de la Rúa C, Alonso S. The interplay between natural selection and susceptibility to melanoma on allele 374F of SLC45A2 gene in a South European population. PLoS One 2014; 9:e104367. [PMID: 25093503 PMCID: PMC4122405 DOI: 10.1371/journal.pone.0104367] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022] Open
Abstract
We aimed to study the selective pressures interacting on SLC45A2 to investigate the interplay between selection and susceptibility to disease. Thus, we enrolled 500 volunteers from a geographically limited population (Basques from the North of Spain) and by resequencing the whole coding region and intron 5 of the 34 most and the 34 least pigmented individuals according to the reflectance distribution, we observed that the polymorphism Leu374Phe (L374F, rs16891982) was statistically associated with skin color variability within this sample. In particular, allele 374F was significantly more frequent among the individuals with lighter skin. Further genotyping an independent set of 558 individuals of a geographically wider population with known ancestry in the Spanish population also revealed that the frequency of L374F was significantly correlated with the incident UV radiation intensity. Selection tests suggest that allele 374F is being positively selected in South Europeans, thus indicating that depigmentation is an adaptive process. Interestingly, by genotyping 119 melanoma samples, we show that this variant is also associated with an increased susceptibility to melanoma in our populations. The ultimate driving force for this adaptation is unknown, but it is compatible with the vitamin D hypothesis. This shows that molecular evolution analysis can be used as a useful technology to predict phenotypic and biomedical consequences in humans.
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Affiliation(s)
- Saioa López
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Óscar García
- Ertzaintza Forensic Unit, Erandio, Bizkaia, Spain
| | | | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Tenerife, Spain
- Applied Genomics Group (G2A), Genetics Laboratory, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - Marialbert Acosta-Herrera
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Tenerife, Spain
- Research Unit, Universitary Hospital Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Hua Chen
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jesús Gardeazabal
- Dermatology Service, BioCruces Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Jesús María Careaga
- Dermatology Service, BioCruces Health Research Institute, Basurto University Hospital, Bilbao, Bizkaia, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Ana Sánchez
- Dermatology Service, BioCruces Health Research Institute, Basurto University Hospital, Bilbao, Bizkaia, Spain
| | - Juan Antonio Ratón-Nieto
- Dermatology Service, BioCruces Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Arrate Sevilla
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Isabel Smith-Zubiaga
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Alicia García de Galdeano
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | | | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Concepción de la Rúa
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
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Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. Proc Natl Acad Sci U S A 2014; 111:4832-7. [PMID: 24616518 DOI: 10.1073/pnas.1316513111] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y.
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20
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Hudjashov G, Villems R, Kivisild T. Global patterns of diversity and selection in human tyrosinase gene. PLoS One 2013; 8:e74307. [PMID: 24040225 PMCID: PMC3770694 DOI: 10.1371/journal.pone.0074307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/31/2013] [Indexed: 01/09/2023] Open
Abstract
Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.
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Affiliation(s)
- Georgi Hudjashov
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
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Lucotte G, Yuasa I. Near fixation of 374l allele frequencies of the skin pigmentation gene SLC45A2 in Africa. Biochem Genet 2013; 51:655-65. [PMID: 23660638 DOI: 10.1007/s10528-013-9595-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 11/28/2012] [Indexed: 11/27/2022]
Abstract
The L374F polymorphism of the SLC45A2 gene, encoding the membrane-associated transporter protein that plays an important role in melanin synthesis, has been suggested to be associated with skin color in human populations. In this study, the detailed distribution of the 374f and 374l alleles has been investigated in 2,581 unrelated subjects from 36 North, East, West, and Central African populations. We found once more the highly significant (p < 0.001) correlation coefficient (r = 0.957) cline of 374f frequencies with degrees of latitude in European and North African populations. Almost all the African populations located below 16° of latitude are fixed for the 374l allele. Peul, Toucouleur, and Soninké populations have 374l allele frequencies of 0.06, 0.03, and 0.03, respectively.
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Affiliation(s)
- Gérard Lucotte
- Institute of Molecular Anthropology, 44 Monge Street, 75005, Paris, France,
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22
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Liu F, Wen B, Kayser M. Colorful DNA polymorphisms in humans. Semin Cell Dev Biol 2013; 24:562-75. [PMID: 23587773 DOI: 10.1016/j.semcdb.2013.03.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/26/2013] [Indexed: 10/26/2022]
Abstract
In this review article we summarize current knowledge on how variation on the DNA level influences human pigmentation including color variation of iris, hair, and skin. We review recent progress in the field of human pigmentation genetics by focusing on the genes and DNA polymorphisms discovered to be involved in determining human pigmentation traits, their association with diseases particularly skin cancers, and their power to predict human eye, hair, and skin colors with potential utilization in forensic investigations.
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Affiliation(s)
- Fan Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Vasseur E, Quintana-Murci L. The impact of natural selection on health and disease: uses of the population genetics approach in humans. Evol Appl 2013; 6:596-607. [PMID: 23789027 PMCID: PMC3684741 DOI: 10.1111/eva.12045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/13/2012] [Indexed: 01/09/2023] Open
Abstract
Investigations of the legacy of natural selection in the human genome have proved particularly informative, pinpointing functionally important regions that have participated in our genetic adaptation to the environment. Furthermore, genetic dissection of the intensity and type of selection acting on human genes can be used to predict involvement in different forms and severities of human diseases. We review here the progress made in population genetics studies toward understanding the effects of selection, in its different forms and intensities, on human genome diversity. We discuss some outstanding, robust examples of genes and biological functions subject to strong dietary, climatic and pathogen selection pressures. We also explore the possible relationship between cancer and natural selection, a topic that has been largely neglected because cancer is generally seen as a late-onset disease. Finally, we discuss how the present-day incidence of some diseases of modern societies may represent a by-product of past adaptation to other selective forces and changes in lifestyle. This perspective thus illustrates the value of adopting a population genetics approach in delineating the biological mechanisms that have played a major evolutionary role in the way humans have genetically adapted to different environments and lifestyles over time.
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Affiliation(s)
- Estelle Vasseur
- Institut Pasteur, Unit of Human Evolutionary Genetics 75015, Paris, France ; Centre National de la Recherche Scientifique, URA 3012 75015, Paris, France ; Centre National de la Recherche Scientifique, UMR 5174, Evolution et Diversité Biologique 31062, Toulouse, France ; Université de Toulouse 31062, Toulouse, France
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Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
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Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
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Beleza S, Santos AM, McEvoy B, Alves I, Martinho C, Cameron E, Shriver MD, Parra EJ, Rocha J. The timing of pigmentation lightening in Europeans. Mol Biol Evol 2012; 30:24-35. [PMID: 22923467 DOI: 10.1093/molbev/mss207] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes. To provide a temporal framework for the evolution of lighter pigmentation, we used forward Monte Carlo simulations coupled with a rejection sampling algorithm to estimate the time of onset of selective sweeps and selection coefficients at four genes associated with this trait in Europeans: KITLG, TYRP1, SLC24A5, and SLC45A2. Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one single-nucleotide polymorphism in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration, whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe. We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci.
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Affiliation(s)
- Sandra Beleza
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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Rees JL, Harding RM. Understanding the Evolution of Human Pigmentation: Recent Contributions from Population Genetics. J Invest Dermatol 2012; 132:846-53. [DOI: 10.1038/jid.2011.358] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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de Gruijter JM, Lao O, Vermeulen M, Xue Y, Woodwark C, Gillson CJ, Coffey AJ, Ayub Q, Mehdi SQ, Kayser M, Tyler-Smith C. Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing. INVESTIGATIVE GENETICS 2011; 2:24. [PMID: 22133426 PMCID: PMC3287149 DOI: 10.1186/2041-2223-2-24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/01/2011] [Indexed: 01/21/2023]
Abstract
Background Numerous genome-wide scans conducted by genotyping previously ascertained single-nucleotide polymorphisms (SNPs) have provided candidate signatures for positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it is unclear how well the signatures discovered by such haplotype-based test statistics can be reproduced in tests based on full resequencing data. Four genes (oculocutaneous albinism II (OCA2), tyrosinase-related protein 1 (TYRP1), dopachrome tautomerase (DCT), and KIT ligand (KITLG)) implicated in human skin-color variation, have shown evidence for positive selection in Europeans and East Asians in previous SNP-scan data. In the current study, we resequenced 4.7 to 6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians, and South Asians. Results Applying all commonly used neutrality-test statistics for allele frequency distribution to the newly generated sequence data provided conflicting results regarding evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. Although some tests were marginally significant for some populations and genes, none of them were significant after multiple-testing correction. Combined P values for each gene-population pair did not improve these results. Application of Approximate Bayesian Computation Markov chain Monte Carlo based to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes, providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection, as previously detected with sequence-based and some haplotype-based tests. Conclusions Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.
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Affiliation(s)
- Johanna Maria de Gruijter
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands.,Netherlands Forensic Institute, Postbus 24044, The Hague, 2490 AA, The Netherlands
| | - Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Mark Vermeulen
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Yali Xue
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Cara Woodwark
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Christopher J Gillson
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Alison J Coffey
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Qasim Ayub
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - S Qasim Mehdi
- Sindh Institute of Urology and Transplantation (SIUT) Karachi, Civil Hospital Karachi 74200, Pakistan
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Chris Tyler-Smith
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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Ibarrola-Villava M, Fernandez LP, Alonso S, Boyano MD, Peña-Chilet M, Pita G, Aviles JA, Mayor M, Gomez-Fernandez C, Casado B, Martin-Gonzalez M, Izagirre N, De la Rua C, Asumendi A, Perez-Yarza G, Arroyo-Berdugo Y, Boldo E, Lozoya R, Torrijos-Aguilar A, Pitarch A, Pitarch G, Sanchez-Motilla JM, Valcuende-Cavero F, Tomas-Cabedo G, Perez-Pastor G, Diaz-Perez JL, Gardeazabal J, de Lizarduy IM, Sanchez-Diez A, Valdes C, Pizarro A, Casado M, Carretero G, Botella-Estrada R, Nagore E, Lazaro P, Lluch A, Benitez J, Martinez-Cadenas C, Ribas G. A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene. PLoS One 2011; 6:e19271. [PMID: 21559390 PMCID: PMC3084811 DOI: 10.1371/journal.pone.0019271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/25/2011] [Indexed: 11/19/2022] Open
Abstract
As the incidence of Malignant Melanoma (MM) reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2) and rs2069398 (SILV/CKD2), were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls). A novel SNP located on the SLC45A2 gene (rs35414) was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001). None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively) had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls). Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.
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Affiliation(s)
- Maider Ibarrola-Villava
- Servicio de Oncologia Medica y Hematologia, Fundacion Hospital Clinico Universitario-INCLIVA, Valencia, Spain
- Programa Genetica Humana, CNIO, Madrid, Spain
| | | | - Santos Alonso
- Department of Genetica, Antropologia Fisica y Fisiologia Animal, Universidad del Pais Vasco, Leioa, Spain
| | - M. Dolores Boyano
- Department of Biologia Celular e Histologia, Universidad del Pais Vasco, Leioa, Spain
| | - Maria Peña-Chilet
- Servicio de Oncologia Medica y Hematologia, Fundacion Hospital Clinico Universitario-INCLIVA, Valencia, Spain
| | | | - Jose A. Aviles
- Department of Dermatologia, Hospital Gregorio Marañon, Madrid, Spain
| | - Matias Mayor
- Department of Dermatologia, Hospital La Paz, Madrid, Spain
| | | | - Beatriz Casado
- Department of Dermatologia, Hospital La Paz, Madrid, Spain
| | | | - Neskuts Izagirre
- Department of Genetica, Antropologia Fisica y Fisiologia Animal, Universidad del Pais Vasco, Leioa, Spain
| | - Concepcion De la Rua
- Department of Genetica, Antropologia Fisica y Fisiologia Animal, Universidad del Pais Vasco, Leioa, Spain
| | - Aintzane Asumendi
- Department of Biologia Celular e Histologia, Universidad del Pais Vasco, Leioa, Spain
| | - Gorka Perez-Yarza
- Department of Biologia Celular e Histologia, Universidad del Pais Vasco, Leioa, Spain
| | - Yoana Arroyo-Berdugo
- Department of Biologia Celular e Histologia, Universidad del Pais Vasco, Leioa, Spain
| | - Enrique Boldo
- Unidad de Cirugia Oncologica, Hospital Provincial Castellon, Castellon, Spain
| | - Rafael Lozoya
- Unidad de Cirugia Oncologica, Hospital Provincial Castellon, Castellon, Spain
| | | | - Ana Pitarch
- Servicio de Dermatologia, Hospital General Castellon, Castellon, Spain
| | - Gerard Pitarch
- Servicio de Dermatologia, Hospital General Castellon, Castellon, Spain
| | | | | | | | - Gemma Perez-Pastor
- Servicio de Dermatologia, Hospital La Plana, Vila-real, Castellon, Spain
| | | | | | | | | | - Carlos Valdes
- Servicio de Dermatologia, Hospital de Basurto, Bilbao, Spain
| | - Angel Pizarro
- Department of Dermatologia, Hospital La Paz, Madrid, Spain
| | - Mariano Casado
- Department of Dermatologia, Hospital La Paz, Madrid, Spain
| | - Gregorio Carretero
- Department of Dermatologia, Hospital Dr Negrin, Las Palmas de Gran Canaria, Spain
| | | | | | - Pablo Lazaro
- Department of Dermatologia, Hospital Gregorio Marañon, Madrid, Spain
| | - Ana Lluch
- Servicio de Oncologia Medica y Hematologia, Fundacion Hospital Clinico Universitario-INCLIVA, Valencia, Spain
| | | | | | - Gloria Ribas
- Servicio de Oncologia Medica y Hematologia, Fundacion Hospital Clinico Universitario-INCLIVA, Valencia, Spain
- Programa Genetica Humana, CNIO, Madrid, Spain
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29
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Casto AM, Feldman MW. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet 2011; 7:e1001266. [PMID: 21253569 PMCID: PMC3017115 DOI: 10.1371/journal.pgen.1001266] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 12/02/2010] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human fitness, including many immunological, metabolic, cardiovascular, and behavioral phenotypes. Given the polygenic nature of complex traits, selection may exert its influence on them by altering allele frequencies at many associated loci, a possibility which has yet to be explored empirically. Here we use 38 different measures of allele frequency variation and 8 iHS scores to characterize over 1,300 GWAS SNPs in 53 globally distributed human populations. We apply these same techniques to evaluate SNPs grouped by trait association. We find that groups of SNPs associated with pigmentation, blood pressure, infectious disease, and autoimmune disease traits exhibit unusual allele frequency patterns and elevated iHS scores in certain geographical locations. We also find that GWAS SNPs have generally elevated scores for measures of allele frequency variation and for iHS in Eurasia and East Asia. Overall, we believe that our results provide evidence for selection on several complex traits that has caused changes in allele frequencies and/or elevated iHS scores at a number of associated loci. Since GWAS SNPs collectively exhibit elevated allele frequency measures and iHS scores, selection on complex traits may be quite widespread. Our findings are most consistent with this selection being either positive or negative, although the relative contributions of the two are difficult to discern. Our results also suggest that trait-SNP associations identified in Eurasian samples may not be present in Africa, Oceania, and the Americas, possibly due to differences in linkage disequilibrium patterns. This observation suggests that non-Eurasian and non-East Asian sample populations should be included in future GWAS.
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Affiliation(s)
- Amanda M Casto
- Department of Genetics, Stanford University, Stanford, California, United States of America.
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Wu DD, Jin W, Hao XD, Tang NLS, Zhang YP. Evidence for positive selection on the Osteogenin (BMP3) gene in human populations. PLoS One 2010; 5:e10959. [PMID: 20532035 PMCID: PMC2881034 DOI: 10.1371/journal.pone.0010959] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 05/10/2010] [Indexed: 01/18/2023] Open
Abstract
Background Human skeletal system has evolved rapidly since the dispersal of modern humans from Africa, potentially driven by selection and adaptation. Osteogenin (BMP3) plays an important role in skeletal development and bone osteogenesis as an antagonist of the osteogenic bone morphogenetic proteins, and negatively regulates bone mineral density. Methodology/Principal Findings Here, we resequenced the BMP3 gene from individuals in four geographically separated modern human populations. Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality. The prevalent haplotypes of the first exon region in Europeans demonstrated features of long-range haplotype homogeneity. In contrast with findings in European, the derived allele SNP Arg192Gln shows higher extended haplotype homozygosity in East Asian. The worldwide allele frequency distribution of SNP shows not only a high-derived allele frequency in Asians, but also in Americans, which is suggestive of functional adaptation. Conclusions/Significance In conclusion, we provide evidence for recent positive selection operating upon a crucial gene in skeletal development, which may provide new insight into the evolution of the skeletal system and bone development.
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Affiliation(s)
- Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Wei Jin
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Xiao-Dan Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Nelson Leung Sang Tang
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
- Laboratory for Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- * E-mail:
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31
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Lucotte G, Mercier G, Diéterlen F, Yuasa I. A Decreasing Gradient of 374F Allele Frequencies in the Skin Pigmentation Gene SLC45A2, from the North of West Europe to North Africa. Biochem Genet 2009; 48:26-33. [DOI: 10.1007/s10528-009-9289-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2008] [Accepted: 09/24/2008] [Indexed: 11/29/2022]
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32
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Juzeniene A, Setlow R, Porojnicu A, Steindal AH, Moan J. Development of different human skin colors: A review highlighting photobiological and photobiophysical aspects. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:93-100. [DOI: 10.1016/j.jphotobiol.2009.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 02/10/2009] [Accepted: 04/24/2009] [Indexed: 12/14/2022]
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33
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Soejima M, Munkhtulga L, Iwamoto S, Koda Y. Genetic variation ofFUT3in Ghanaians, Caucasians, and Mongolians. Transfusion 2009; 49:959-66. [DOI: 10.1111/j.1537-2995.2008.02069.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Hiroshige K, Soejima M, Nishioka T, Kamimura S, Koda Y. Simple and sensitive method for identification of human DNA by allele-specific polymerase chain reaction of FOXP2. J Forensic Sci 2009; 54:857-61. [PMID: 19457146 DOI: 10.1111/j.1556-4029.2009.01063.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The forkhead box P2 (FOXP2) gene is specifically involved in speech and language development in humans. The sequence is well conserved among many vertebrate species but has accumulated amino acid changes in the human lineage. The aim of this study was to develop a simple method to discriminate between human and nonhuman vertebrate DNA in forensic specimens by amplification of a human-specific genomic region. In the present study, we designed an allele-specific polymerase chain reaction (PCR) using primers to amplify smaller than 70-bp regions of FOXP2 to identify DNA as being of human or nonhuman, including ape, origin. PCR amplification was also successfully performed using fluorescence-labeled primers, and this method allows a single PCR reaction with a genomic DNA sample as small as 0.01 ng. This system also identified the presence of human DNA in two blood stains stored for 20 and 38 years. The results suggested the potential usefulness of FOXP2 as an identifier of human DNA in forensic samples.
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Affiliation(s)
- Kenichi Hiroshige
- Forensic Science Laboratory, Fukuoka Prefectural Police Headquarters, 7-7 Higashikoen, Hakata-ku, Fukuoka 812-8576, Japan
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Abstract
The genetic basis underlying normal variation in the pigmentary traits of skin, hair and eye colour has been the subject of intense research directed at understanding the diversity seen both between and within human populations. A combination of approaches have been used including comparative genomics of candidate genes and the identification of regions of the human genome under positive selection, together with genome-wide and specific allele association studies. Independent selection for different pigmentation gene sets has been found between Asian, European and African populations. Several genome-wide association studies for pigmentation have now been conducted and identified single nucleotide polymorphism (SNP) markers in known, TYR, TYRP1, OCA2, SLC45A2, SLC24A5, MC1R, ASIP, KITLG and previously unknown SLC24A4, IRF4, TPCN2, candidate genes. The contribution of SNP polymorphisms present in populations from South Asia have been tested and alleles found at TYR, SLC45A2 and SLC24A5 can largely account for differences between those of darkest and lightest skin reflectance using a simple additive model. Skin and hair colour associations in Europeans are found within a range of pigmentation gene alleles, whereas blue-brown eye colour can be explained by a single SNP proposed to regulate OCA2 expression. Functional testing of variant alleles has begun to connect phenotype correlations with biological differences. Variant MC1R alleles show direct correlations between the biochemical signalling properties of the encoded receptor and the red-hair fair skin pigmentation phenotype. Direct testing of a range of clonal melanocyte cultures derived from donor skin tissue characterized for three causal SNPs within SLC45A2, SLC24A5 and OCA2 has assessed their impact on melanin content and tyrosinase enzyme activity. From a culmination of genetic and functional studies, it is apparent that a number of genes impacting melanosome biogenesis or the melanin biosynthetic pathway are candidates to explain the diversity seen in human pigmentation.
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Affiliation(s)
- Richard A Sturm
- Melanogenix Group, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.
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36
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Fernandez LP, Milne RL, Pita G, Floristan U, Sendagorta E, Feito M, Avilés JA, Martin-Gonzalez M, Lázaro P, Benítez J, Ribas G. Pigmentation-related genes and their implication in malignant melanoma susceptibility. Exp Dermatol 2009; 18:634-42. [PMID: 19320733 DOI: 10.1111/j.1600-0625.2009.00846.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human pigmentation appears to be one of the main modulators of individual risk of developing malignant melanoma (MM). A large number of genes are known to be involved in rare pigmentary disorders and explain most of the variation in pigmentation phenotypes seen in human populations. This Spanish case-control study included 205 patients with melanoma and 245 control subjects. Thirty-one single nucleotide polymorphisms (SNPs) in genes that had been mainly associated with congenital pigmentation syndromes (ADTB3A, ATRN, CHS1, EDNRB, HPS, KIT, MGRN1, MITF, MLANA, MYO5A, MYO7A, OA1, OCA2, PAX3 and SOX10) were selected. We found that the variant allele of OCA2 R419Q (rs1800407) was associated with increased risk of MM (OR 1.55, 95% CI 1.04-2.31, P = 0.03). This effect on melanoma risk appeared to be stronger among individuals with solar lentigines, or at least 50 nevi. We also describe, for the first time, an association with the variant S1666C (rs2276288) in the MYO7A gene (OR 1.35; 95% CI 1.04-1.76; P = 0.03). Again, this association appeared to be stronger in several phenotypic groups such as individuals with fair skin and those with childhood sunburns. We also found that several variants in the pigmentation genes considered were associated with intermediate phenotypic characteristics. Our findings highlight the potential importance of pigmentation genes in sporadic MM susceptibility.
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Affiliation(s)
- Lara P Fernandez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid E-28029, Spain
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37
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Sequence Analysis of Human TRPV6 Suggests Positive Selection Outside Africa. Biochem Genet 2009; 47:147-53. [DOI: 10.1007/s10528-009-9222-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2008] [Accepted: 07/29/2008] [Indexed: 11/27/2022]
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38
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Hofer T, Ray N, Wegmann D, Excoffier L. Large Allele Frequency Differences between Human Continental Groups are more Likely to have Occurred by Drift During range Expansions than by Selection. Ann Hum Genet 2009; 73:95-108. [PMID: 19040659 DOI: 10.1111/j.1469-1809.2008.00489.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- T Hofer
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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39
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Guedj M, Bourillon A, Combadières C, Rodero M, Dieudé P, Descamps V, Dupin N, Wolkenstein P, Aegerter P, Lebbe C, Basset-Seguin N, Prum B, Saiag P, Grandchamp B, Soufir N. Variants of the MATP/SLC45A2 gene are protective for melanoma in the French population. Hum Mutat 2008; 29:1154-60. [PMID: 18683857 DOI: 10.1002/humu.20823] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study, we investigated whether variants in three key pigmentation genes-MC1R, MATP/SLC45A2, and OCA2--were involved in melanoma predisposition. A cohort comprising 1,019 melanoma patients (MelanCohort) and 1,466 Caucasian controls without skin cancers were studied. A total of 10 polymorphisms, including five functional MC1R alleles (p.Asp84Glu, p.Arg142His, p.Arg151Cys, p.Arg160Trp, and p.Asp294His), two nonsynonymous SLC45A2 variants (p.Phe374Leu and p.Glu272Lys), and three intronic OCA2 variants previously shown to be strongly associated with eye color (rs7495174 T>C, rs4778241 G>T, and rs4778138 T>C) were genotyped. As expected, MC1R variants were closely associated with melanoma risk (P value <2.20.10(-16); odds ratio [OR]=2.29 [95% confidence interval, CI=1.85-2.82 and OR=3.3 [95% CI=2.00-5.45], for the presence of one or two variants, respectively). Interestingly, the SLC45A2 variant p.Phe374Leu was significantly and strongly protective for melanoma (P-value=2.12.10(-15); OR=0.35 [95% CI=0.26-0.46] and OR=0.32 [95% CI=0.24-0.43], considering the genotypes Phe/Leu and Leu/Leu, respectively). MC1R and SLC45A2 variants had additive effects on melanoma risk, and after adjusting for pigmentation characteristics, the risk was persistent, even though both genes had a strong impact on pigmentation. Future studies may show whether genetic information could provide a useful complement to physical examination in predicting melanoma risk.
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Affiliation(s)
- Mickaël Guedj
- Laboratoire Statistique et Génome, UMR CNRS 8071, INRA 1152, Université d'Evry Val d'Essonne, Evry, France
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40
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Fernandez LP, Milne RL, Pita G, Avilés JA, Lázaro P, Benítez J, Ribas G. SLC45A2: a novel malignant melanoma-associated gene. Hum Mutat 2008; 29:1161-7. [PMID: 18563784 DOI: 10.1002/humu.20804] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human pigmentation appears to be one of the strongest risk factors for malignant melanoma (MM). In humans, there is a long list of genes known to be involved in rare pigmentary disorders such as albinism. These genes explain most of the variation in pigmentation phenotypes seen in human populations, and they do this by regulating the level of synthesis, chemical composition, packaging, and distribution of melanin. This Spanish case-control study included 131 consecutive melanoma patients and 245 control subjects frequency-matched for sex and age. A total of 23 SNPs in six candidate genes (ASP, OCA2, TYR, TYRP1, SILV, and SLC45A) belonging to the pigmentation pathway were genotyped. We found that the variant allele of c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 (membrane associated transporter previously known as MATP) was associated with protection from MM (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing). This association was validated by the consistent link observed with dark hair, dark skin, dark eye color, and the presence of solar lentigins and childhood sunburns. This is the first time SLC45A2 has been described as a melanoma susceptibility gene in a light-skinned population.
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Affiliation(s)
- L P Fernandez
- Human Genetics Group, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
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41
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Pavlidis P, Hutter S, Stephan W. A population genomic approach to map recent positive selection in model species. Mol Ecol 2008; 17:3585-98. [PMID: 18627454 DOI: 10.1111/j.1365-294x.2008.03852.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on nearly complete genome sequences from a variety of organisms data on naturally occurring genetic variation on the scale of hundreds of loci to entire genomes have been collected in recent years. In parallel, new statistical tests have been developed to infer evidence of recent positive selection from these data and to localize the target regions of selection in the genome. These methods have now been successfully applied to Drosophila melanogaster, humans, mice and a few plant species. In genomic regions of normal recombination rates, the targets of positive selection have been mapped down to the level of individual genes.
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Affiliation(s)
- P Pavlidis
- Department of Biology, Section of Evolutionary Biology, University of Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany.
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42
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Association of the SLC45A2 gene with physiological human hair colour variation. J Hum Genet 2008; 53:966-971. [PMID: 18806926 DOI: 10.1007/s10038-008-0338-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
Abstract
Pigmentation is a complex physical trait with multiple genes involved. Several genes have already been associated with natural differences in human pigmentation. The SLC45A2 gene encoding a transporter protein involved in melanin synthesis is considered to be one of the most important genes affecting human pigmentation. Here we present results of an association study conducted on a population of European origin, where the relationship between two non-synonymous polymorphisms in the SLC45A2 gene - rs26722 (E272K) and rs16891982 (L374F) - and different pigmentation traits was examined. The study revealed a significant association between both variable sites and normal variation in hair colour. Only L374F remained significantly associated with hair colour when both SNPs were included in a logistic regression model. No association with other pigmentation traits was detected in this population sample. Our results indicate that the rare allele L374 significantly increases the possibility of having black hair colour (OR = 7.05) and thus may be considered as a future marker for black hair colour prediction.
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44
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Johansson Å, Gyllensten U. Identification of local selective sweeps in human populations since the exodus from Africa. Hereditas 2008; 145:126-37. [DOI: 10.1111/j.0018-0661.2008.02054.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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45
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Bryk J, Hardouin E, Pugach I, Hughes D, Strotmann R, Stoneking M, Myles S. Positive selection in East Asians for an EDAR allele that enhances NF-kappaB activation. PLoS One 2008; 3:e2209. [PMID: 18493316 PMCID: PMC2374902 DOI: 10.1371/journal.pone.0002209] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 04/07/2008] [Indexed: 12/18/2022] Open
Abstract
Genome-wide scans for positive selection in humans provide a promising approach to establish links between genetic variants and adaptive phenotypes. From this approach, lists of hundreds of candidate genomic regions for positive selection have been assembled. These candidate regions are expected to contain variants that contribute to adaptive phenotypes, but few of these regions have been associated with phenotypic effects. Here we present evidence that a derived nonsynonymous substitution (370A) in EDAR, a gene involved in ectodermal development, was driven to high frequency in East Asia by positive selection prior to 10,000 years ago. With an in vitro transfection assay, we demonstrate that 370A enhances NF-kappaB activity. Our results suggest that 370A is a positively selected functional genetic variant that underlies an adaptive human phenotype.
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Affiliation(s)
- Jarosław Bryk
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Emilie Hardouin
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rainer Strotmann
- Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sean Myles
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail:
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Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M. Identification and analysis of genomic regions with large between-population differentiation in humans. Ann Hum Genet 2008; 72:99-110. [PMID: 18184145 DOI: 10.1111/j.1469-1809.2007.00390.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that show large differences between populations are expected to be associated with genomic regions exhibiting large allele frequency differences between populations. Thus, from genome-wide polymorphism data genomic regions with large allele frequency differences between populations can be identified, and evaluated as candidates for large between-population phenotypic differences. Here we use allele frequency data from approximately 1.5 million SNPs from three human populations, and present an algorithm that identifies genomic regions containing SNPs with extreme Fst. We demonstrate that our candidate regions have reduced heterozygosity in Europeans and Chinese relative to African-Americans, and are likely enriched with genes that have experienced positive natural selection. We identify genes that are likely responsible for phenotypes known to differ dramatically between human populations and present several candidates worthy of future investigation. Our list of high Fst genomic regions is a first step in identifying the genetic variants that contribute to large phenotypic differences between populations, many of which have likely experienced positive natural selection. Our approach based on between population differences can compliment traditional within population linkage and association studies to uncover novel genotype-phenotype relationships.
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Affiliation(s)
- S Myles
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig,
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Alonso S, Izagirre N, Smith-Zubiaga I, Gardeazabal J, Díaz-Ramón JL, Díaz-Pérez JL, Zelenika D, Boyano MD, Smit N, de la Rúa C. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans. BMC Evol Biol 2008; 8:74. [PMID: 18312627 PMCID: PMC2292700 DOI: 10.1186/1471-2148-8-74] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 02/29/2008] [Indexed: 12/31/2022] Open
Abstract
Background The observed correlation between ultraviolet light incidence and skin color, together with the geographical apportionment of skin reflectance among human populations, suggests an adaptive value for the pigmentation of the human skin. We have used Affymetrix U133a v2.0 gene expression microarrays to investigate the expression profiles of a total of 9 melanocyte cell lines (5 from lightly pigmented donors and 4 from darkly pigmented donors) plus their respective unirradiated controls. In order to reveal signatures of selection in loci with a bearing on skin pigmentation in humans, we have resequenced between 4 to 5 kb of the proximal regulatory regions of three of the most differently expressed genes, in the expectation that variation at regulatory regions might account for intraespecific morphological diversity, as suggested elsewhere. Results Contrary to our expectations, expression profiles did not cluster the cells into unirradiated versus irradiated melanocytes, or into lightly pigmented versus darkly pigmented melanocytes. Instead, expression profiles correlated with the presence of Bovine Pituitary Extract (known to contain α-MSH) in the media. This allowed us to differentiate between melanocytes that are synthesizing melanin and those that are not. TYR, TYRP1 and DCT were among the five most differently expressed genes between these two groups. Population genetic analyses of sequence haplotypes of the proximal regulatory flanking-regions included Tajima's D, HEW and DHEW neutrality tests analysis. These were complemented with EHH tests (among others) in which the significance was obtained by a novel approach using extensive simulations under the coalescent model with recombination. We observe strong evidence for positive selection for TYRP1 alleles in Africans and for DCT and TYRP1 in Asians. However, the overall picture reflects a complex pattern of selection, which might include overdominance for DCT in Europeans. Conclusion Diversity patterns clearly evidence adaptive selection in pigmentation genes in Africans and Asians. In Europeans, the evidence is more complex, and both directional and balancing selection may be involved in light skin. As a result, different non-African populations may have acquired light skin by alternative ways, and so light skin, and perhaps dark skin too, may be the result of convergent evolution.
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Affiliation(s)
- Santos Alonso
- Dept, Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain.
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Suzuki Y, Pasch A, Bonny O, Mohaupt MG, Hediger MA, Frey FJ. Gain-of-function haplotype in the epithelial calcium channel TRPV6 is a risk factor for renal calcium stone formation. Hum Mol Genet 2008; 17:1613-8. [DOI: 10.1093/hmg/ddn048] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rescue from oculocutaneous albinism type 4 using medaka slc45a2 cDNA driven by its own promoter. Genetics 2008; 178:761-9. [PMID: 18245373 DOI: 10.1534/genetics.107.073387] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Patients and vertebrate mutants with oculocutaneous albinism type 4 (OCA4) have mutations in the solute carrier family 45 member 2 (slc45a2) gene. However, there is no empirical evidence for this gene-phenotype relationship. There is a unique OCA4 mutant in medaka (b) that exhibits albinism only in the skin, but the mechanism underlying this phenotype is also unknown. In this study, we rescued medaka OCA4 phenotypes, in both the eyes and the skin, by micro-injection of an slc45a2-containing genomic fragment or slc45a2 cDNA driven by its own 0.9-kb promoter. We also identified a spontaneous nucleotide change of 339 bp in the promoter as the b mutation. There are multiple transcription start sites in medaka slc45a2, as in its human ortholog, and only the shortest and eye-specific mRNA is transcribed with the b mutation. Interestingly, we further revealed a conserved pyrimidine (Py)-rich sequence of approximately 10 bp in the promoter by medaka-pufferfish comparative genomics and verified that it plays an indispensable role for expression of slc45a2 in the skin. Further studies of the 0.9-kb promoter identified in this study should provide insights into the cis/trans-regulatory mechanisms underlying the ocular and cutaneous expression of slc45a2.
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Fujimoto A, Kimura R, Ohashi J, Omi K, Yuliwulandari R, Batubara L, Mustofa MS, Samakkarn U, Settheetham-Ishida W, Ishida T, Morishita Y, Furusawa T, Nakazawa M, Ohtsuka R, Tokunaga K. A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. Hum Mol Genet 2007; 17:835-43. [PMID: 18065779 DOI: 10.1093/hmg/ddm355] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hair morphology is one of the most differentiated traits among human populations. However, genetic backgrounds of hair morphological differences among populations have not been clarified yet. In addition, little is known about the evolutionary forces that have acted on hair morphology. To identify hair morphology-determining genes, the levels of local genetic differentiation in 170 genes that are related to hair morphogenesis were evaluated by using data from the International HapMap project. Among highly differentiated genes, ectodysplasin A receptor (EDAR) harboring an Asian-specific non-synonymous single nucleotide polymorphism (1540T/C, 370Val/Ala) was identified as a strong candidate. Association studies between genotypes and hair morphology revealed that the Asian-specific 1540C allele is associated with increase in hair thickness. Reporter gene assays suggested that 1540T/C affects the activity of the downstream transcription factor NF-kappaB. It was inferred from geographic distribution of 1540T/C and the long-range haplotype test that 1540C arose after the divergence of Asians from Europeans and its frequency has rapidly increased in East Asian populations. These findings lead us to conclude that EDAR is a major genetic determinant of Asian hair thickness and the 1540C allele spread through Asian populations due to recent positive selection.
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Affiliation(s)
- Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo, Tokyo, Japan
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