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Kim B, Kim DS, Shin JG, Leem S, Cho M, Kim H, Gu KN, Seo JY, You SW, Martin AR, Park SG, Kim Y, Jeong C, Kang NG, Won HH. Mapping and annotating genomic loci to prioritize genes and implicate distinct polygenic adaptations for skin color. Nat Commun 2024; 15:4874. [PMID: 38849341 PMCID: PMC11161515 DOI: 10.1038/s41467-024-49031-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Evidence for adaptation of human skin color to regional ultraviolet radiation suggests shared and distinct genetic variants across populations. However, skin color evolution and genetics in East Asians are understudied. We quantified skin color in 48,433 East Asians using image analysis and identified associated genetic variants and potential causal genes for skin color as well as their polygenic interplay with sun exposure. This genome-wide association study (GWAS) identified 12 known and 11 previously unreported loci and SNP-based heritability was 23-24%. Potential causal genes were determined through the identification of nonsynonymous variants, colocalization with gene expression in skin tissues, and expression levels in melanocytes. Genomic loci associated with pigmentation in East Asians substantially diverged from European populations, and we detected signatures of polygenic adaptation. This large GWAS for objectively quantified skin color in an East Asian population improves understanding of the genetic architecture and polygenic adaptation of skin color and prioritizes potential causal genes.
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Affiliation(s)
- Beomsu Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Dan Say Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Joong-Gon Shin
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Sangseob Leem
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Minyoung Cho
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Hanji Kim
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Ki-Nam Gu
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Jung Yeon Seo
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Seung Won You
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, 02141, USA
| | - Sun Gyoo Park
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Yunkwan Kim
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nae Gyu Kang
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea.
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea.
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2
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Abstract
Melasma is a multifactorial dyschromia that results from exposure to external factors (such as solar radiation) and hormonal factors (such as sex hormones and pregnancy), as well as skin inflammation (such as contact dermatitis and esthetic procedures), in genetically predisposed individuals. Beyond hyperfunctional melanocytes, skin with melasma exhibits a series of structural and functional alterations in the epidermis, basement membrane, and upper dermis that interact to elicit and sustain a focal hypermelanogenic phenotype. Evolution in the knowledge of the genetic basis of melasma and the cutaneous response to solar radiation, as well as the roles of endocrine factors, antioxidant system, endothelium proliferation, fibroblast senescence, mast cell degranulation, autophagy deficits of the melanocyte, and the paracrine regulation of melanogenesis, will lead to the development of new treatments and preventive strategies. This review presents current knowledge on these aspects of the pathogenesis of melasma and discusses the effects of specific treatments and future research on these issues.
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3
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GWAS Identifies Multiple Genetic Loci for Skin Color in Korean Women. J Invest Dermatol 2021; 142:1077-1084. [PMID: 34648798 DOI: 10.1016/j.jid.2021.08.440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
Human skin color is largely determined by genetic factors. Recent GWASs have reported several genetic variants associated with skin color, mostly in European and African populations. In this study, we performed GWAS in 17,019 Korean women to identify genetic variants associated with facial skin color, quantitatively measured as CIELAB color index. We identified variants in three, one, and six genomic loci associated with facial skin color index L∗, a∗, and b∗ values, respectively, and replicated the associations (combined analysis P-value < 5.0 × 10-8). The significant loci included variants in known genes (OCA2 rs74653330, BNC2 rs16935073, rs72620727 near KITLG, and SLC6A17 rs6689641) and to our knowledge previously unreported genes (SCARB1 rs10846744, SYN2 rs12629034, and LINC00486 rs6543678). This is GWAS to elucidate genetic variants of facial skin color in a Korean female population. Further functional characterizations of the investigated genes are warranted to elucidate their contribution to skin pigmentation-related traits.
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Time to removal of sutures from the palmar surface of the hand in dark-skinned patients: Results in a prospective cohort of 146 hands. HAND SURGERY & REHABILITATION 2021; 41:142-148. [PMID: 34600132 DOI: 10.1016/j.hansur.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/25/2021] [Accepted: 09/08/2021] [Indexed: 11/23/2022]
Abstract
The objective of this study was to estimate the time to removal of a suture from the palmar surface of a dark-skinned adult hand. A descriptive and analytical study included a cohort of 146 patients, 57% male, with a mean age of 37 ± 14 years, covering a period of 10 years. The mean time to removal of sutures on the palmar surface of the dark-skinned adult hands was 21 ± 2 days. Complete epithelialization of the suture path was the clinical indication for the ideal day for removal. After removal, closure was total in 90% of cases (132 hands) and partial in 9% (14 hands). The day of suture removal was significantly (p = 0.006) related to wound healing (complete closure). Eighty-five percent of patients without complete wound closure at suture removal had history of use of skin-lightening products. Tobacco use significantly lengthened time to suture removal (p < 0.001). There was a correlation between patient age and time to suture removal. On multivariate analysis, three factors were predictive of suture removal later than day 21: being a manual worker (44% of patients) (p 0.006), suture location in a palmar fold area (<0.001) and the age of patient, the 41-50 years (p = 0.001) and >50 years (p < 0.001).
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5
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Borg AM, Baker JE. Contemporary biomedical engineering perspective on volitional evolution for human radiotolerance enhancement beyond low-earth orbit. Synth Biol (Oxf) 2021; 6:ysab023. [PMID: 34522784 PMCID: PMC8434797 DOI: 10.1093/synbio/ysab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/15/2021] [Accepted: 09/01/2021] [Indexed: 11/14/2022] Open
Abstract
A primary objective of the National Aeronautics and Space Administration (NASA) is expansion of humankind's presence outside low-Earth orbit, culminating in permanent interplanetary travel and habitation. Having no inherent means of physiological detection or protection against ionizing radiation, humans incur capricious risk when journeying beyond low-Earth orbit for long periods. NASA has made large investments to analyze pathologies from space radiation exposure, emphasizing the importance of characterizing radiation's physiological effects. Because natural evolution would require many generations to confer resistance against space radiation, immediately pragmatic approaches should be considered. Volitional evolution, defined as humans steering their own heredity, may inevitably retrofit the genome to mitigate resultant pathologies from space radiation exposure. Recently, uniquely radioprotective genes have been identified, conferring local or systemic radiotolerance when overexpressed in vitro and in vivo. Aiding in this process, the CRISPR/Cas9 technique is an inexpensive and reproducible instrument capable of making limited additions and deletions to the genome. Although cohorts can be identified and engineered to protect against radiation, alternative and supplemental strategies should be seriously considered. Advanced propulsion and mild synthetic torpor are perhaps the most likely to be integrated. Interfacing artificial intelligence with genetic engineering using predefined boundary conditions may enable the computational modeling of otherwise overly complex biological networks. The ethical context and boundaries of introducing genetically pioneered humans are considered.
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Affiliation(s)
- Alexander M Borg
- Departments of Biomedical Engineering and Radiation Oncology, Wake Forest University, Winston-Salem, NC, USA
| | - John E Baker
- Radiation Biosciences Laboratory, Medical College of Wisconsin, Milwaukee, WI, USA
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6
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Álvarez-Varas R, Rojas-Hernández N, Heidemeyer M, Riginos C, Benítez HA, Araya-Donoso R, Reséndiz E, Lara-Uc M, Godoy DA, Muñoz-Pérez JP, Alarcón-Ruales DE, Alfaro-Shigueto J, Ortiz-Alvarez C, Mangel JC, Vianna JA, Véliz D. Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle. Proc Biol Sci 2021; 288:20210754. [PMID: 34229490 DOI: 10.1098/rspb.2021.0754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle (Chelonia mydas) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq; 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds (n = 158). Our results support genetic divergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation of C. mydas to the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.
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Affiliation(s)
- Rocío Álvarez-Varas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile.,Qarapara Tortugas Marinas Chile NGO, Santiago, Chile
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Maike Heidemeyer
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Hugo A Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | | | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Mexico
| | - Mónica Lara-Uc
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Mexico
| | - Daniel A Godoy
- Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Juan Pablo Muñoz-Pérez
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galápagos, Ecuador.,University of the Sunshine Coast USC, 90 Sippy Downs Dr, Sippy Downs, Queensland 4556, Australia
| | - Daniela E Alarcón-Ruales
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galápagos, Ecuador
| | - Joanna Alfaro-Shigueto
- ProDelphinus, Lima, Peru.,Facultad de Biología Marina, Universidad Científica del Perú, Lima, Peru
| | | | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
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7
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Jablonski NG. The evolution of human skin pigmentation involved the interactions of genetic, environmental, and cultural variables. Pigment Cell Melanoma Res 2021; 34:707-729. [PMID: 33825328 PMCID: PMC8359960 DOI: 10.1111/pcmr.12976] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
The primary biological role of human skin pigmentation is as a mediator of penetration of ultraviolet radiation (UVR) into the deep layers of skin and the cutaneous circulation. Since the origin of Homo sapiens, dark, protective constitutive pigmentation and strong tanning abilities have been favored under conditions of high UVR and represent the baseline condition for modern humans. The evolution of partly depigmented skin and variable tanning abilities has occurred multiple times in prehistory, as populations have dispersed into environments with lower and more seasonal UVR regimes, with unique complements of genes and cultural practices. The evolution of extremes of dark pigmentation and depigmentation has been rare and occurred only under conditions of extremely high or low environmental UVR, promoted by positive selection on variant pigmentation genes followed by limited gene flow. Over time, the evolution of human skin pigmentation has been influenced by the nature and course of human dispersals and modifications of cultural practices, which have modified the nature and actions of skin pigmentation genes. Throughout most of prehistory and history, the evolution of human skin pigmentation has been a contingent and non-deterministic process.
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Affiliation(s)
- Nina G. Jablonski
- Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkPAUSA
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8
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Feng Y, McQuillan MA, Tishkoff SA. Evolutionary genetics of skin pigmentation in African populations. Hum Mol Genet 2021; 30:R88-R97. [PMID: 33438000 PMCID: PMC8117430 DOI: 10.1093/hmg/ddab007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022] Open
Abstract
Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo-Mesa A, Bosch E, Calafell F, Quintana-Murci L, Comas D. The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. Mol Biol Evol 2021; 38:2804-2817. [PMID: 33713133 PMCID: PMC8233508 DOI: 10.1093/molbev/msab070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modeled in human populations.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rocio Caro-Consuegra
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Elena Bosch
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Human Genomics and Evolution, Collège de France, Paris, France
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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10
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Huang X, Wang S, Jin L, He Y. Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation. Biol Open 2021; 10:bio056523. [PMID: 33495209 PMCID: PMC7888712 DOI: 10.1242/bio.056523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023] Open
Abstract
Human pigmentation is a highly diverse and complex trait among populations and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We use genotype data of 19 genes associated with human pigmentation from 17 publicly available datasets and obtain data for 2346 individuals of six representative population groups from across the world. Our results quantify the strength of natural selection on light pigmentation not only in modern Europeans (0.0259/generation) but also in proto-Eurasians (0.00650/generation). Our results also suggest that several derived alleles associated with human dark pigmentation may be under positive directional selection in some African populations. Our study provides the first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation.This article has an associated First Person interview with the first author of the article.
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Affiliation(s)
- Xin Huang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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11
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Missaggia BO, Reales G, Cybis GB, Hünemeier T, Bortolini MC. Adaptation and co-adaptation of skin pigmentation and vitamin D genes in native Americans. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:1060-1077. [PMID: 33325159 DOI: 10.1002/ajmg.c.31873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 11/06/2022]
Abstract
We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.
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Affiliation(s)
- Bruna Oliveira Missaggia
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela B Cybis
- Statistics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cátira Bortolini
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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12
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Xu J, Fu Y, Hu Y, Yin L, Tang Z, Yin D, Zhu M, Yu M, Li X, Zhou Y, Zhao S, Liu X. Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features. J Anim Sci Biotechnol 2020; 11:115. [PMID: 33292532 PMCID: PMC7713148 DOI: 10.1186/s40104-020-00520-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/19/2020] [Indexed: 01/15/2023] Open
Abstract
Background A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color). Conclusion Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. Supplementary Information Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.
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Affiliation(s)
- Jingya Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
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13
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Markiewicz E, Idowu OC. Melanogenic Difference Consideration in Ethnic Skin Type: A Balance Approach Between Skin Brightening Applications and Beneficial Sun Exposure. Clin Cosmet Investig Dermatol 2020; 13:215-232. [PMID: 32210602 PMCID: PMC7069578 DOI: 10.2147/ccid.s245043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Human skin demonstrates a striking variation in tone and color that is evident among multiple demographic populations. Such characteristics are determined predominantly by the expression of the genes controlling the quantity and quality of melanin, which can alter significantly due to the presence of small nucleotide polymorphism affecting various steps of the melanogenesis process and generally linked to the lighter skin phenotypes. Genetically determined, constitutive skin color is additionally complemented by the facultative melanogenesis and tanning responses; with high levels of melanin and melanogenic factors broadly recognized to have a protective effect against the UVR-induced molecular damage in darker skin. Long-term sun exposure, together with a genetic makeup responsible for the ability to tan or the activity of constitutive melanogenic factors, triggers defects in pigmentation across all ethnic skin types. However, sun exposure also has well documented beneficial effects that manifest at both skin homeostasis and the systemic level, such as synthesis of vitamin D, which is thought to be less efficient in the presence of high levels of melanin or potentially linked to the polymorphism in the genes responsible for skin darkening triggered by UVR. In this review, we discuss melanogenesis in a context of constitutive pigmentation, defined by gene polymorphism in ethnic skin types, and facultative pigmentation that is not only associated with the capacity to protect the skin against photo-damage but could also have an impact on vitamin D synthesis through gene polymorphism. Modulating the activities of melanogenic genes, with the focus on the markers specifically altered by polymorphism combined with differential requirements of sun exposure in ethnic skin types, could enhance the applications of already existing skin brightening factors and provide a novel approach toward improved skin tone and health in personalized skincare.
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Affiliation(s)
- Ewa Markiewicz
- Hexis Lab Limited, The Core, Newcastle Helix, Newcastle Upon Tyne NE4 5TF, UK
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14
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Yang Z, Shi H, Ma P, Zhao S, Kong Q, Bian T, Gong C, Zhao Q, Liu Y, Qi X, Zhang X, Han Y, Liu J, Li Q, Chen H, Su B. Darwinian Positive Selection on the Pleiotropic Effects of KITLG Explain Skin Pigmentation and Winter Temperature Adaptation in Eurasians. Mol Biol Evol 2020; 35:2272-2283. [PMID: 29961894 DOI: 10.1093/molbev/msy136] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human skin color diversity is considered an adaptation to environmental conditions such as UV radiation. Investigations into the genetic bases of such adaptation have identified a group of pigmentation genes contributing to skin color diversity in African and non-African populations. Here, we present a population analysis of the pigmentation gene KITLG with previously reported signal of Darwinian positive selection in both European and East Asian populations. We demonstrated that there had been recurrent selective events in the upstream and the downstream regions of KITLG in Eurasian populations. More importantly, besides the expected selection on the KITLG variants favoring light skin in coping with the weak UV radiation at high latitude, we observed a KITLG variant showing adaptation to winter temperature. In particular, compared with UV radiation, winter temperature showed a much stronger correlation with the prevalence of the presumably adaptive KITLG allele in Asian populations. This observation was further supported by the in vitro functional test at low temperature. Consequently, the pleiotropic effects of KITLG, that is, pigmentation and thermogenesis were both targeted by natural selection that acted on different KITLG sequence variants, contributing to the adaptation of Eurasians to both UV radiation and winter temperature at high latitude areas.
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Affiliation(s)
- Zhaohui Yang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Hong Shi
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qinghong Kong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Tianhao Bian
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Chao Gong
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Qi Zhao
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Jiewei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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15
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The Evolutionary History of Human Skin Pigmentation. J Mol Evol 2019; 88:77-87. [PMID: 31363820 DOI: 10.1007/s00239-019-09902-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023]
Abstract
Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color diversity and explores the implications of recent findings about the genes associated with skin pigmentation for understanding the evolutionary forces that have shaped the current patterns of skin color variation. A major aspect of these findings is that the genetic basis of skin color is less simple than previously thought and that geographic variation in skin pigmentation was influenced by the concerted action of different types of natural selection, rather than just by selective sweeps in a few key genes.
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16
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El-Sheikh AM, Elfar NN, Mourad HA, Hewedy ESS. Relationship between Trace Elements and Premature Hair Graying. Int J Trichology 2019; 10:278-283. [PMID: 30783336 PMCID: PMC6369637 DOI: 10.4103/ijt.ijt_8_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Context: Hair is said to gray prematurely when a minimum of five gray hairs occurs before the age of 20 in fair skinned, 25 in Asians, and 30 in Africans. It may be genetically associated with autoimmune syndromes or certain environmental factors. Aims: The aim of this study was to evaluate the serum level of iron, copper, and calcium and to assess their role in premature hair graying. Subjects and Methods: This study was carried out on 60 patients with premature hair graying (PHG) and 30 age- and sex-matched healthy individuals served as a control group. The severity of PHG was assessed by the hair whitening scoring system. Serum iron, copper, and calcium concentrations were measured using Beckman Coulter instrument and spectrophotometric method. Results: There was a reduction in serum levels of iron, copper, and calcium in patients with PHG in comparison with controls. There was a statistically negative significant correlation between the severity of PHG and serum iron and calcium levels. There was a negative nonsignificant correlation between body mass index and serum iron, copper, and calcium levels. Conclusions: Serum iron, copper, and calcium levels were reduced in association with PHG and correlated with its severity. Premature graying may be an indicator that hair is not getting enough nutrients and minerals, and supplementation with these trace elements might reverse and is expected to prevent progression of canities; however, further studies are needed to find the underlying mechanism of this relationship.
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Affiliation(s)
- Alshimaa M El-Sheikh
- Department of Dermatology and Venereology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Nashwa N Elfar
- Department of Dermatology and Venereology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Heba A Mourad
- Department of Clinical Pathology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - El-Sayed S Hewedy
- Department of Dermatology and Venereology, Faculty of Medicine, Tanta University, Tanta, Egypt
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17
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Sellayah D. The Impact of Early Human Migration on Brown Adipose Tissue Evolution and Its Relevance to the Modern Obesity Pandemic. J Endocr Soc 2018; 3:372-386. [PMID: 30723844 PMCID: PMC6354082 DOI: 10.1210/js.2018-00363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/13/2018] [Indexed: 01/12/2023] Open
Abstract
Genetic factors are believed to be primarily responsible for obesity; however, an understanding of how genes for obesity have become so prevalent in modern society has proved elusive. Several theories have attempted to explain the genetic basis for obesity, but none of these appear to factor in the interethnic variation in obesity. Emerging evidence is increasingly pointing to a link between reduced basal metabolism and ineffective brown adipose tissue (BAT) thermogenesis. In fact, BAT presence and function are strongly correlated with metabolic rates and directly influence obesity susceptibility. My colleagues and I recently theorized that ancestral exposure to cold necessitated the evolution of enhanced BAT thermogenesis, which, with today’s hypercaloric and sedentary lifestyle, becomes advantageous, because thermogenesis is energetically wasteful, raising basal metabolism and burning excess calories. The opposite may be true for the descendants of heat-adapted populations. This review further reconciles global evolutionary climatic exposures with obesity demographics to understand the genetic basis for the obesity pandemic, and new insights from the most recent studies are provided, including those assessing archaic human admixture. Key genetic variants influencing BAT thermogenesis are outlined that have also been linked with climatic exposure to cold and appear to support the theory that evolutionary factors relevant to climate may have shaped the modern obesity pandemic.
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Affiliation(s)
- Dyan Sellayah
- School of Biological Sciences, University of Reading, Reading, Berkshire, United Kingdom
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18
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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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19
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Del Bino S, Duval C, Bernerd F. Clinical and Biological Characterization of Skin Pigmentation Diversity and Its Consequences on UV Impact. Int J Mol Sci 2018; 19:ijms19092668. [PMID: 30205563 PMCID: PMC6163216 DOI: 10.3390/ijms19092668] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Skin color diversity is the most variable and noticeable phenotypic trait in humans resulting from constitutive pigmentation variability. This paper will review the characterization of skin pigmentation diversity with a focus on the most recent data on the genetic basis of skin pigmentation, and the various methodologies for skin color assessment. Then, melanocyte activity and amount, type and distribution of melanins, which are the main drivers for skin pigmentation, are described. Paracrine regulators of melanocyte microenvironment are also discussed. Skin response to sun exposure is also highly dependent on color diversity. Thus, sensitivity to solar wavelengths is examined in terms of acute effects such as sunburn/erythema or induced-pigmentation but also long-term consequences such as skin cancers, photoageing and pigmentary disorders. More pronounced sun-sensitivity in lighter or darker skin types depending on the detrimental effects and involved wavelengths is reviewed.
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Affiliation(s)
- Sandra Del Bino
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
| | - Christine Duval
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
| | - Françoise Bernerd
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
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20
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Galván-Femenía I, Obón-Santacana M, Piñeyro D, Guindo-Martinez M, Duran X, Carreras A, Pluvinet R, Velasco J, Ramos L, Aussó S, Mercader JM, Puig L, Perucho M, Torrents D, Moreno V, Sumoy L, de Cid R. Multitrait genome association analysis identifies new susceptibility genes for human anthropometric variation in the GCAT cohort. J Med Genet 2018; 55:765-778. [PMID: 30166351 PMCID: PMC6252362 DOI: 10.1136/jmedgenet-2018-105437] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 12/22/2022]
Abstract
Background Heritability estimates have revealed an important contribution of SNP variants for most common traits; however, SNP analysis by single-trait genome-wide association studies (GWAS) has failed to uncover their impact. In this study, we applied a multitrait GWAS approach to discover additional factor of the missing heritability of human anthropometric variation. Methods We analysed 205 traits, including diseases identified at baseline in the GCAT cohort (Genomes For Life- Cohort study of the Genomes of Catalonia) (n=4988), a Mediterranean adult population-based cohort study from the south of Europe. We estimated SNP heritability contribution and single-trait GWAS for all traits from 15 million SNP variants. Then, we applied a multitrait-related approach to study genome-wide association to anthropometric measures in a two-stage meta-analysis with the UK Biobank cohort (n=336 107). Results Heritability estimates (eg, skin colour, alcohol consumption, smoking habit, body mass index, educational level or height) revealed an important contribution of SNP variants, ranging from 18% to 77%. Single-trait analysis identified 1785 SNPs with genome-wide significance threshold. From these, several previously reported single-trait hits were confirmed in our sample with LINC01432 (p=1.9×10−9) variants associated with male baldness, LDLR variants with hyperlipidaemia (ICD-9:272) (p=9.4×10−10) and variants in IRF4 (p=2.8×10−57), SLC45A2 (p=2.2×10−130), HERC2 (p=2.8×10−176), OCA2 (p=2.4×10−121) and MC1R (p=7.7×10−22) associated with hair, eye and skin colour, freckling, tanning capacity and sun burning sensitivity and the Fitzpatrick phototype score, all highly correlated cross-phenotypes. Multitrait meta-analysis of anthropometric variation validated 27 loci in a two-stage meta-analysis with a large British ancestry cohort, six of which are newly reported here (p value threshold <5×10−9) at ZRANB2-AS2, PIK3R1, EPHA7, MAD1L1, CACUL1 and MAP3K9. Conclusion Considering multiple-related genetic phenotypes improve associated genome signal detection. These results indicate the potential value of data-driven multivariate phenotyping for genetic studies in large population-based cohorts to contribute to knowledge of complex traits.
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Affiliation(s)
- Iván Galván-Femenía
- GenomesForLife-GCAT Lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Crta. de Can Ruti, Badalona, Catalunya, Spain
| | - Mireia Obón-Santacana
- GenomesForLife-GCAT Lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Crta. de Can Ruti, Badalona, Catalunya, Spain.,Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERESP, Barcelona, Spain
| | - David Piñeyro
- High Content Genomics and Bioinformatics Unit, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalunya, Spain
| | - Marta Guindo-Martinez
- Life Sciences - Computational Genomics, Barcelona Supercomputing Center (BSC-CNS), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
| | - Xavier Duran
- GenomesForLife-GCAT Lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Crta. de Can Ruti, Badalona, Catalunya, Spain
| | - Anna Carreras
- GenomesForLife-GCAT Lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Crta. de Can Ruti, Badalona, Catalunya, Spain
| | - Raquel Pluvinet
- High Content Genomics and Bioinformatics Unit, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalunya, Spain
| | - Juan Velasco
- GenomesForLife-GCAT Lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Crta. de Can Ruti, Badalona, Catalunya, Spain
| | - Laia Ramos
- High Content Genomics and Bioinformatics Unit, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalunya, Spain
| | - Susanna Aussó
- High Content Genomics and Bioinformatics Unit, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalunya, Spain
| | - J M Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, US.,Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, US
| | - Lluis Puig
- Blood Division, Banc de Sang i Teixits, Barcelona, Spain
| | - Manuel Perucho
- Cancer Genetics and Epigenetics Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalunya, Spain
| | - David Torrents
- Life Sciences - Computational Genomics, Barcelona Supercomputing Center (BSC-CNS), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain.,ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Catalunya, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERESP, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Lauro Sumoy
- High Content Genomics and Bioinformatics Unit, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalunya, Spain
| | - Rafael de Cid
- GenomesForLife-GCAT Lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Crta. de Can Ruti, Badalona, Catalunya, Spain
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21
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Abstract
The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here, we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations.
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Affiliation(s)
- Erin A. Brettmann
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
| | - Cristina de Guzman Strong
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
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22
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Laso-Jadart R, Harmant C, Quach H, Zidane N, Tyler-Smith C, Mehdi Q, Ayub Q, Quintana-Murci L, Patin E. The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan. Am J Hum Genet 2017; 101:977-984. [PMID: 29129317 DOI: 10.1016/j.ajhg.2017.09.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022] Open
Abstract
From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their history of admixture and natural selection remains largely undefined. Here, we studied the genome-wide diversity of the African-descent Makranis, who reside on the Arabian Sea coast of Pakistan, as well that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics, and tempo of the Indian Ocean slave trade. We show that the Makranis are the result of an admixture event between local Baluch tribes and Bantu-speaking populations from eastern or southeastern Africa; we dated this event to ∼300 years ago during the Omani Empire domination. Levels of parental relatedness, measured through runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at traits evolving under positive selection, including skin color, lactase persistence, and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group-believed to confer resistance against Plasmodium vivax infection-was recently introduced to Pakistan through the slave trade and evolved adaptively in this P. vivax malaria-endemic region. Our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations.
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23
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Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Mol Ecol 2017; 26:4700-4711. [PMID: 28734070 DOI: 10.1111/mec.14240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
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Affiliation(s)
- D Eoche-Bosy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - M Gautier
- CBGP, INRA, IRD, CIRAD, Montpellier SupAgro, Montferrier-sur-Lez, France.,IBC, Montpellier, France
| | - M Esquibet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - F Legeai
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenScale, INRIA, Rennes, France
| | - A Bretaudeau
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenOuest COre Facility, INRIA, Rennes, France
| | - O Bouchez
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - S Fournet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - E Grenier
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - J Montarry
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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24
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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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Jonnalagadda M, Bharti N, Patil Y, Ozarkar S, K SM, Joshi R, Norton H. Identifying signatures of positive selection in pigmentation genes in two South Asian populations. Am J Hum Biol 2017; 29. [PMID: 28439965 DOI: 10.1002/ajhb.23012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 04/01/2017] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations. METHODS Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL). RESULTS Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population. CONCLUSIONS These results suggest that selection may have affected these loci broadly across the region.
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Affiliation(s)
- Manjari Jonnalagadda
- Symbiosis School for Liberal Arts (SSLA), Symbiosis International University (SIU), Pune, 411014, India
| | - Neeraj Bharti
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Yatish Patil
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, Pune, 411007, India
| | - Sunitha Manjari K
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Rajendra Joshi
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
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26
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Kubota Y, Mitsukawa N, Chuma K, Akita S, Sasahara Y, Rikihisa N, Satoh K. Hyperpigmentation after surgery for a deep dermal burn of the dorsum of the hand: partial-thickness debridement followed by medium split-thickness skin grafting vs full-thickness debridement followed by thick split-thickness skin grafting. BURNS & TRAUMA 2016; 4:9. [PMID: 27574679 PMCID: PMC4964008 DOI: 10.1186/s41038-016-0039-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/31/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Early excision and skin grafting are commonly used to treat deep dermal burns (DDBs) of the dorsum of the hand. Partial-thickness debridement (PTD) is one of the most commonly used procedures for the excision of burned tissue of the dorsum of the hand. In contrast, full-thickness debridement (FTD) has also been reported. However, it is unclear whether PTD or FTD is better. METHODS In this hospital-based retrospective study, we compared the outcomes of PTD followed by a medium split-thickness skin graft (STSG) with FTD followed by a thick STSG to treat a DDB of the dorsum of the hand in Japanese patients. To evaluate postoperative pigmentation of the skin graft, quantitative analyses were performed using the red, green, and blue (RGB) and the hue, saturation, and brightness (HSB) color spaces. We have organized the manuscript in a manner compliant with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement. RESULTS Data from 11 patients were analyzed. Six hands (five patients) received grafts in the PTD group and eight hands (six patients) received grafts in the FTD group. Graft take was significantly better in the FTD group (median 98 %, interquartile range 95-99) than in the PTD group (median 90 %, interquartile range 85-90) (P < 0.01). Quantitative skin color analyses in both the RGB and HSB color spaces showed that postoperative grafted skin was significantly darker than the adjacent control area in the PTD group, but not in the FTD group. CONCLUSIONS There is a possibility that FTD followed by a thick STSG is an option that can reduce the risk of hyperpigmentation after surgery for DDB of the dorsum of the hand in Japanese patients. Further investigation is needed to clarify whether the FTD or the thick STSG or both are the factor for the control of hyperpigmentation.
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Affiliation(s)
- Yoshitaka Kubota
- Department of Plastic Surgery, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8677 Japan
| | - Nobuyuki Mitsukawa
- Department of Plastic Surgery, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8677 Japan
| | - Kumiko Chuma
- Department of Plastic Surgery, Tokyo Rosai Hospital, 4-13-21, Omoriminami, Ota-ku, Tokyo 143-0013 Japan
| | - Shinsuke Akita
- Department of Plastic Surgery, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8677 Japan
| | - Yoshitaro Sasahara
- Department of Plastic Surgery, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8677 Japan
| | - Naoaki Rikihisa
- Department of Plastic Surgery, Chiba Rosai Hospital, 2-16, Tatsumidaihigashi, Ichihara, Chiba 290-0003 Japan
| | - Kaneshige Satoh
- Department of Plastic Surgery, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, Chiba 260-8677 Japan
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Edwards M, Cha D, Krithika S, Johnson M, Cook G, Parra EJ. Iris pigmentation as a quantitative trait: variation in populations of European, East Asian and South Asian ancestry and association with candidate gene polymorphisms. Pigment Cell Melanoma Res 2015; 29:141-62. [DOI: 10.1111/pcmr.12435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/02/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Melissa Edwards
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - David Cha
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - S. Krithika
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Monique Johnson
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Gillian Cook
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Esteban J. Parra
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
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28
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Marques PI, Fonseca F, Sousa T, Santos P, Camilo V, Ferreira Z, Quesada V, Seixas S. Adaptive Evolution Favoring KLK4 Downregulation in East Asians. Mol Biol Evol 2015; 33:93-108. [PMID: 26420451 DOI: 10.1093/molbev/msv199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The human kallikrein (KLK) cluster, located at chromosome 19q13.3-13.4, encodes 15 serine proteases, including neighboring genes (KLK3, KLK2, KLK4, and KLK5) with key roles in the cascades of semen liquefaction, tooth enamel maturation, and skin desquamation. KLK2 and KLK3 were previously identified as targets of adaptive evolution in primates through different mechanisms linked to reproductive biology and, in humans, genome-wide scans of positive selection captured, a yet unexplored, evidence for KLK neutrality departure in East Asians. We perform a detailed evaluation of KLK3-KLK5 variability in the 1000 Genomes samples from East Asia, Europe, and Africa, which was sustained by our own sequencing. In East Asians, we singled out a 70-kb region surrounding KLK4 that combined unusual low levels of diversity, high frequency variants with significant levels of population differentiation (FST > 0.5) and fairly homogenous haplotypes given the large local recombination rates. Among these variants, rs1654556_G, rs198968_T, and rs17800874_A stand out for their location on putative regulatory regions and predicted functional effects, namely the introduction of several microRNA binding sites and a repressor motif. Our functional assays carried out in different cellular models showed that rs198968_T and rs17800874_A operate synergistically to reduce KLK4 expression and could be further assisted by rs1654556_G. Considering the previous findings that KLK4 inactivation causes enamel malformations in humans and mice, and that this gene is coexpressed in epidermal layers along with several substrates involved in either cell adhesion or keratinocyte differentiation, we propose KLK4 as another target of selection in East Asians correlated to tooth and epidermal morphological traits.
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Affiliation(s)
- Patrícia Isabel Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal Department of Biochemistry and Molecular Biology-IUOPA, University of Oviedo, Oviedo, Spain Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Filipa Fonseca
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Tânia Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Paulo Santos
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Vânia Camilo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Zélia Ferreira
- Department of Computational and Systems Biology, University of Pittsburgh
| | - Victor Quesada
- Department of Biochemistry and Molecular Biology-IUOPA, University of Oviedo, Oviedo, Spain
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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Medina-Gómez C, Chesi A, Heppe DHM, Zemel BS, Yin JL, Kalkwarf HJ, Hofman A, Lappe JM, Kelly A, Kayser M, Oberfield SE, Gilsanz V, Uitterlinden AG, Shepherd JA, Jaddoe VWV, Grant SFA, Lao O, Rivadeneira F. BMD Loci Contribute to Ethnic and Developmental Differences in Skeletal Fragility across Populations: Assessment of Evolutionary Selection Pressures. Mol Biol Evol 2015; 32:2961-72. [PMID: 26226985 PMCID: PMC4651235 DOI: 10.1093/molbev/msv170] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bone mineral density (BMD) is a highly heritable trait used both for the diagnosis of osteoporosis in adults and to assess bone health in children. Ethnic differences in BMD have been documented, with markedly higher levels in individuals of African descent, which partially explain disparity in osteoporosis risk across populations. To date, 63 independent genetic variants have been associated with BMD in adults of Northern-European ancestry. Here, we demonstrate that at least 61 of these variants are predictive of BMD early in life by studying their compound effect within two multiethnic pediatric cohorts. Furthermore, we show that within these cohorts and across populations worldwide the frequency of those alleles associated with increased BMD is systematically elevated in individuals of Sub-Saharan African ancestry. The amount of differentiation in the BMD genetic scores among Sub-Saharan and non-Sub-Saharan populations together with neutrality tests, suggest that these allelic differences are compatible with the hypothesis of selective pressures acting on the genetic determinants of BMD. These findings constitute an explorative contribution to the role of selection on ethnic BMD differences and likely a new example of polygenic adaptation acting on a human trait.
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Affiliation(s)
- Carolina Medina-Gómez
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Denise H M Heppe
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Babette S Zemel
- Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Jia-Lian Yin
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Heidi J Kalkwarf
- Division of General and Community Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Albert Hofman
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joan M Lappe
- Division of Endocrinology, Creighton University, Omaha, NE
| | - Andrea Kelly
- Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sharon E Oberfield
- Division of Pediatric Endocrinology, Diabetes, and Metabolism, Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - Vicente Gilsanz
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A Shepherd
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Oscar Lao
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
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30
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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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ADAM protease inhibitors reduce melanogenesis by regulating PMEL17 processing in human melanocytes. J Dermatol Sci 2015; 78:133-42. [PMID: 25818872 DOI: 10.1016/j.jdermsci.2015.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/12/2015] [Accepted: 02/27/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND ADAMs (a disintegrin and metalloprotease) are a family of proteases involved in ectodomain shedding that play a role in various biological processes such as cell adhesion and migration. ADAM10 and ADAM17 are suggested to be involved in pigmentary disorders. OBJECTIVE We examined the effect of ADAM protease inhibitors on the modulation of melanogenesis in normal human epidermal melanocytes (NHEM). METHODS NHEMs and B16F10 treated with ADAM protease inhibitors were analyzed. AlamarBlue cell proliferation assay, melanin content assay, tyrosinase activity assay, Western blotting analysis, electron microscopic analysis, and RNA interference were employed. RESULTS In NHEMs, melanin content was reduced by treatment with ADAM protease inhibitors. The inhibitors did not change the protein expression of tyrosinase, TRP-1, and MITF. In B16F10 cells, treatment of the cells with ADAM protease inhibitor diminished the α-MSH-induced increase in melanin content. Electron microscopy showed that the number of fibrillar and mature melanosomes was significantly reduced and that the vacuolar compartments were filled with dense unstructured aggregates after treatment with ADAM protease inhibitors. We therefore focused on the processing of PMEL17, a melanosomal glycoprotein that forms a fibrillar matrix on which melanin gets deposited. Proteolytic processing of PMEL17 is required to form functional fibrils during melanogenesis. Recently, γ-secretase and β-site amyloid precursor protein-cleaving enzyme 2 (BACE2) were found to cleave PMEL17. We found that ADAM protease inhibitors exerted effects on the processing of C-terminal and N-terminal fragments of PMEL17. Using BACE2 siRNA and γ-secretase inhibitor, we showed that ADAM protease inhibitor affected PMEL17 processing in a γ-secretase and BACE2-independent mechanism. CONCLUSION Several proteases, including ADAM proteases, can contribute to the formation of fibrils and their assembly into sheets in melanosomes.
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Heyer E, Quintana-Murci L. Evolutionary genetics as a tool to target genes involved in phenotypes of medical relevance. Evol Appl 2015; 2:71-80. [PMID: 25567848 PMCID: PMC3352415 DOI: 10.1111/j.1752-4571.2008.00061.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 12/04/2008] [Indexed: 12/01/2022] Open
Abstract
There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. Indeed, the evolutionary approach for inferring the action of natural selection in the human genome represents a powerful tool for predicting regions of the genome potentially associated with disease and of interest in epidemiological genetic studies. Here, we review several examples going from candidate gene studies associated with specific phenotypes, including nutrition, infectious disease and climate adaptation, to whole genome scans for natural selection. All these studies illustrate the power of the evolutionary approach in identifying regions of the genome having played a major role in human survival and adaptation.
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Affiliation(s)
- Evelyne Heyer
- MNHN, Eco-Anthropologie, UMR 5145, CNRS-MNHN-P7, Musée de l'Homme Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Unit of Human Evolutionary Genetics, CNRS URA3012 Paris Cedex, France
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Rogalla U, Rychlicka E, Derenko MV, Malyarchuk BA, Grzybowski T. Simple and cost-effective 14-loci SNP assay designed for differentiation of European, East Asian and African samples. Forensic Sci Int Genet 2015; 14:42-9. [DOI: 10.1016/j.fsigen.2014.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/27/2014] [Accepted: 09/14/2014] [Indexed: 12/19/2022]
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34
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Wade P, Deister VG, Kent M, Olarte Sierra MF, del Castillo Hernández AD. Nation and the Absent Presence of Race in Latin American Genomics. CURRENT ANTHROPOLOGY 2014. [DOI: 10.1086/677945] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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de Cerqueira CCS, Hünemeier T, Gomez-Valdés J, Ramallo V, Volasko-Krause CD, Barbosa AAL, Vargas-Pinilla P, Dornelles RC, Longo D, Rothhammer F, Bedoya G, Canizales-Quinteros S, Acuña-Alonzo V, Gallo C, Poletti G, González-José R, Salzano FM, Callegari-Jacques SM, Schuler-Faccini L, Ruiz-Linares A, Cátira Bortolini M. Implications of the admixture process in skin color molecular assessment. PLoS One 2014; 9:e96886. [PMID: 24809478 PMCID: PMC4014568 DOI: 10.1371/journal.pone.0096886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/12/2014] [Indexed: 12/19/2022] Open
Abstract
The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice.
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Affiliation(s)
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jorge Gomez-Valdés
- Laboratorio de Antropología Física, Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Virgínia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Danaê Longo
- Instituto Federal de Educação, Ciência e Tecnologia Farroupilha, Alegrete, Brazil
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Facultad de Medicina, Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
| | | | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Carla Gallo
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Francisco Mauro Salzano
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sídia Maria Callegari-Jacques
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- INAGEMP – Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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Lachance J, Tishkoff SA. Population Genomics of Human Adaptation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013; 44:123-143. [PMID: 25383060 DOI: 10.1146/annurev-ecolsys-110512-135833] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 - 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci.
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Affiliation(s)
- Joseph Lachance
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sarah A Tishkoff
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
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Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, Chaubey G, Goto R, Ho SYW, Gallego Romero I, Crivellaro F, Hudjashov G, Rai N, Metspalu M, Mascie-Taylor CGN, Pitchappan R, Singh L, Mirazon-Lahr M, Thangaraj K, Villems R, Kivisild T. The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genet 2013; 9:e1003912. [PMID: 24244186 PMCID: PMC3820762 DOI: 10.1371/journal.pgen.1003912] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/07/2013] [Indexed: 11/18/2022] Open
Abstract
Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. Human skin color is one of the most visible aspects of human diversity. The genetic basis of pigmentation in Europeans has been understood to some extent, but our knowledge about South Asians has been restricted to a handful of studies. It has been suggested that a single nucleotide difference in SLC24A5 accounts for 25–38% European-African pigmentation differences and correlates with lighter skin. This genetic variant has also been associated with skin color variation among South Asians living in the UK. Here, we report a study based on a homogenous cohort of South India. Our results confirm that SLC24A5 plays a key role in pigmentation diversity of South Asians. Country-wide screening of the variant reveals that the light skin associated allele is widespread in the Indian subcontinent and its complex patterning is shaped by a combination of processes involving selection and demographic history of the populations. By studying the variation of SLC24A5 sequences among a diverse set of individuals, we show that the light skin associated allele in South Asians is identical by descent to that found in Europeans. Our study also provides new insights into positive selection acting on the gene and the evolutionary history of light skin in humans.
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Affiliation(s)
- Chandana Basu Mallick
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- * E-mail: (CBM); (TK)
| | - Florin Mircea Iliescu
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Märt Möls
- Estonian Biocentre, Tartu, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Sarah Hill
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Rie Goto
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Irene Gallego Romero
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Federica Crivellaro
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Georgi Hudjashov
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Mait Metspalu
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | | | - Ramasamy Pitchappan
- Chettinad Academy of Research and Education, Chettinad Health City, Chennai, India
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Banaras Hindu University, Varanasi, India
| | - Marta Mirazon-Lahr
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | | | - Richard Villems
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CBM); (TK)
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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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Bhat RM, Sharma R, Pinto AC, Dandekeri S, Martis J. Epidemiological and investigative study of premature graying of hair in higher secondary and pre-university school children. Int J Trichology 2013; 5:17-21. [PMID: 23960391 PMCID: PMC3746220 DOI: 10.4103/0974-7753.114706] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Hair pigmentation is one of the most conspicuous phenotypes in humans ranging from black, brown, and blonde to red. Premature graying of hair occurs more commonly without any underlying pathology but is said to be inherited in autosomal dominant pattern. Premature graying has been shown to be associated with a few of the autoimmune disorders. A role for environmental factors and nutritional deficiencies has also been postulated. However, to date the exact etiology of premature graying has not been established. AIM The objective of our study was to conduct an epidemiological and investigative study of premature graying of hair in higher secondary and pre-university school children of the semi-urban area. MATERIALS AND METHODS A total of 35 cases and controls were investigated for various parameter such as Hemoglobin, total iron binding capacity, serum ferritin (S. Ferritin), serum calcium (S. Ca), serum iron (S. Iron), vitamin B12, and vitamin D3 after taking informed consent. Epidemiological and investigations correlation was established using the Chi-square and Mann Whitney test and P < 0.05 values were considered significant. RESULT Among the various laboratory parameters S. Ca, S. Ferritin and vitamin D3 were low in patients with premature graying of hair. There was significant high number of vitamin D3 deficient and insufficient among the cases compared to the controls. CONCLUSION According to our study S. Ca, S. Ferritin, vitamin D3 may play a role in premature graying of hair in our society.
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Affiliation(s)
- Ramesh M Bhat
- Department of Dermatology, Father Muller Medical College and Hospital, Kankanady, Mangalore, Karnataka, India
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Hider JL, Gittelman RM, Shah T, Edwards M, Rosenbloom A, Akey JM, Parra EJ. Exploring signatures of positive selection in pigmentation candidate genes in populations of East Asian ancestry. BMC Evol Biol 2013; 13:150. [PMID: 23848512 PMCID: PMC3727976 DOI: 10.1186/1471-2148-13-150] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/05/2013] [Indexed: 11/17/2022] Open
Abstract
Background Currently, there is very limited knowledge about the genes involved in normal pigmentation variation in East Asian populations. We carried out a genome-wide scan of signatures of positive selection using the 1000 Genomes Phase I dataset, in order to identify pigmentation genes showing putative signatures of selective sweeps in East Asia. We applied a broad range of methods to detect signatures of selection including: 1) Tests designed to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima’s D, Fay and Wu’s H and Fu and Li’s D* and F*), 2) Tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb) and 3) Tests based on genetic differentiation between populations (LSBL). Based on the results obtained from a genome wide analysis of 25 kb windows, we constructed an empirical distribution for each statistic across all windows, and identified pigmentation genes that are outliers in the distribution. Results Our tests identified twenty genes that are relevant for pigmentation biology. Of these, eight genes (ATRN, EDAR, KLHL7, MITF, OCA2, TH, TMEM33 and TRPM1,) were extreme outliers (top 0.1% of the empirical distribution) for at least one statistic, and twelve genes (ADAM17, BNC2, CTSD, DCT, EGFR, LYST, MC1R, MLPH, OPRM1, PDIA6, PMEL (SILV) and TYRP1) were in the top 1% of the empirical distribution for at least one statistic. Additionally, eight of these genes (BNC2, EGFR, LYST, MC1R, OCA2, OPRM1, PMEL (SILV) and TYRP1) have been associated with pigmentary traits in association studies. Conclusions We identified a number of putative pigmentation genes showing extremely unusual patterns of genetic variation in East Asia. Most of these genes are outliers for different tests and/or different populations, and have already been described in previous scans for positive selection, providing strong support to the hypothesis that recent selective sweeps left a signature in these regions. However, it will be necessary to carry out association and functional studies to demonstrate the implication of these genes in normal pigmentation variation.
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Affiliation(s)
- Jessica L Hider
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
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Abstract
An enduring goal of evolutionary biology is to understand how natural selection has shaped patterns of polymorphism and divergence within and between species and to map the genetic basis of adaptations. The rapid maturation of next-generation sequencing technology has generated a deluge of genomics data from nonhuman primates, extinct hominins, and diverse human populations. These emerging genome data sets have simultaneously broadened our understanding of human evolution and sharply defined existing gaps in knowledge about the mechanistic basis of evolutionary change. In this review, we summarize recent insights into how natural selection has influenced the human genome across different timescales. Although the path to a more comprehensive understanding of selection and adaptation in humans remains arduous, some general insights are beginning to emerge, such as the importance of adaptive regulatory evolution, the absence of pervasive classic selective sweeps, and the potential roles that selection from standing variation and polygenic adaptation have likely played in recent human evolutionary history.
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Affiliation(s)
- Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065;
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Elias PM, Williams ML. Re-appraisal of current theories for the development and loss of epidermal pigmentation in hominins and modern humans. J Hum Evol 2013; 64:687-92. [PMID: 23478159 PMCID: PMC3654079 DOI: 10.1016/j.jhevol.2013.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/04/2013] [Accepted: 02/05/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Peter M Elias
- Dermatology Service, Department of Veterans Affairs Medical Center, 4150 Clement Street, MS 190, San Francisco, CA 94121, USA.
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Fortes GG, Speller CF, Hofreiter M, King TE. Phenotypes from ancient DNA: approaches, insights and prospects. Bioessays 2013; 35:690-5. [PMID: 23703035 DOI: 10.1002/bies.201300036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes.
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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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Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA, Lopes J, Campos J, Araújo II, Anderson TM, Vilhjálmsson BJ, Nordborg M, Correia e Silva A, Shriver MD, Rocha J, Barsh GS, Tang H. Genetic architecture of skin and eye color in an African-European admixed population. PLoS Genet 2013; 9:e1003372. [PMID: 23555287 PMCID: PMC3605137 DOI: 10.1371/journal.pgen.1003372] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/22/2013] [Indexed: 11/18/2022] Open
Abstract
Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (∼44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ∼70% of the estimated heritability. Differences in skin and eye color are some of the most obvious traits that underlie human diversity, yet most of our knowledge regarding the genetic basis for these traits is based on the limited range of variation represented by individuals of European ancestry. We have studied a unique population in Cape Verde, an archipelago located off the West African coast, in which extensive mixing between individuals of Portuguese and West African ancestry has given rise to a broad range of phenotypes and ancestral genome proportions. Our results help to explain how genes work together to control the full range of pigmentary phenotypic diversity, provide new insight into the evolution of these traits, and provide a model for understanding other types of quantitative variation in admixed populations.
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Affiliation(s)
- Sandra Beleza
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- * E-mail: (SB); (GSB)
| | - Nicholas A. Johnson
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Sophie I. Candille
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Marc A. Coram
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jailson Lopes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
- Universidade de Cabo Verde (Uni-CV), Praia, Santiago, Cabo Verde
| | - Joana Campos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | | | - Tovi M. Anderson
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | | | - Mark D. Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jorge Rocha
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Gregory S. Barsh
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail: (SB); (GSB)
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
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Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon. Comp Funct Genomics 2012; 2012:628204. [PMID: 23326209 PMCID: PMC3544263 DOI: 10.1155/2012/628204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.
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Comprehensive candidate gene study highlights UGT1A and BNC2 as new genes determining continuous skin color variation in Europeans. Hum Genet 2012; 132:147-58. [PMID: 23052946 DOI: 10.1007/s00439-012-1232-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/18/2012] [Indexed: 01/09/2023]
Abstract
Natural variation in human skin pigmentation is primarily due to genetic causes rooted in recent evolutionary history. Genetic variants associated with human skin pigmentation confer risk of skin cancer and may provide useful information in forensic investigations. Almost all previous gene-mapping studies of human skin pigmentation were based on categorical skin color information known to oversimplify the continuous nature of human skin coloration. We digitally quantified skin color into hue and saturation dimensions for 5,860 Dutch Europeans based on high-resolution skin photographs. We then tested an extensive list of 14,185 single nucleotide polymorphisms in 281 candidate genes potentially involved in human skin pigmentation for association with quantitative skin color phenotypes. Confirmatory association was revealed for several known skin color genes including HERC2, MC1R, IRF4, TYR, OCA2, and ASIP. We identified two new skin color genes: genetic variants in UGT1A were significantly associated with hue and variants in BNC2 were significantly associated with saturation. Overall, digital quantification of human skin color allowed detecting new skin color genes. The variants identified in this study may also contribute to the risk of skin cancer. Our findings are also important for predicting skin color in forensic investigations.
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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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Ang KC, Ngu MS, Reid KP, Teh MS, Aida ZS, Koh DXR, Berg A, Oppenheimer S, Salleh H, Clyde MM, Md-Zain BM, Canfield VA, Cheng KC. Skin color variation in Orang Asli tribes of Peninsular Malaysia. PLoS One 2012; 7:e42752. [PMID: 22912732 PMCID: PMC3418284 DOI: 10.1371/journal.pone.0042752] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 07/10/2012] [Indexed: 01/24/2023] Open
Abstract
Pigmentation is a readily scorable and quantitative human phenotype, making it an excellent model for studying multifactorial traits and diseases. Convergent human evolution from the ancestral state, darker skin, towards lighter skin colors involved divergent genetic mechanisms in people of European vs. East Asian ancestry. It is striking that the European mechanisms result in a 10–20-fold increase in skin cancer susceptibility while the East Asian mechanisms do not. Towards the mapping of genes that contribute to East Asian pigmentation there is need for one or more populations that are admixed for ancestral and East Asian ancestry, but with minimal European contribution. This requirement is fulfilled by the Senoi, one of three indigenous tribes of Peninsular Malaysia collectively known as the Orang Asli. The Senoi are thought to be an admixture of the Negrito, an ancestral dark-skinned population representing the second of three Orang Asli tribes, and regional Mongoloid populations of Indo-China such as the Proto-Malay, the third Orang Asli tribe. We have calculated skin reflectance-based melanin indices in 492 Orang Asli, which ranged from 28 (lightest) to 75 (darkest); both extremes were represented in the Senoi. Population averages were 56 for Negrito, 42 for Proto-Malay, and 46 for Senoi. The derived allele frequencies for SLC24A5 and SLC45A2 in the Senoi were 0.04 and 0.02, respectively, consistent with greater South Asian than European admixture. Females and individuals with the A111T mutation had significantly lighter skin (p = 0.001 and 0.0039, respectively). Individuals with these derived alleles were found across the spectrum of skin color, indicating an overriding effect of strong skin lightening alleles of East Asian origin. These results suggest that the Senoi are suitable for mapping East Asian skin color genes.
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Affiliation(s)
- Khai C. Ang
- Department of Experimental Pathology & Jake Gittlen Cancer Research Foundation, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail: (KCA); (KCC)
| | - Mee S. Ngu
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Katherine P. Reid
- Department of Experimental Pathology & Jake Gittlen Cancer Research Foundation, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Mei S. Teh
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Zamzuraida S. Aida
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Danny XR. Koh
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Arthur Berg
- Department of Biostatistics & Bioinformatics, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Stephen Oppenheimer
- Institute of Cognitive and Evolutionary Anthropology, School of Anthropology and Museum Ethnography: University of Oxford, Oxford, United Kingdom
| | - Hood Salleh
- Academic Heritage Museum, Chancellery Building, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mahani M. Clyde
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Badrul M. Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Victor A. Canfield
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Keith C. Cheng
- Department of Experimental Pathology & Jake Gittlen Cancer Research Foundation, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail: (KCA); (KCC)
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