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Goli RC, Chishi KG, Ganguly I, Singh S, Dixit S, Rathi P, Diwakar V, Sree C C, Limbalkar OM, Sukhija N, Kanaka K. Global and Local Ancestry and its Importance: A Review. Curr Genomics 2024; 25:237-260. [PMID: 39156729 PMCID: PMC11327809 DOI: 10.2174/0113892029298909240426094055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 08/20/2024] Open
Abstract
The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.
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Affiliation(s)
| | - Kiyevi G. Chishi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Indrajit Ganguly
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S.P. Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vikas Diwakar
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Chandana Sree C
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
- Central Tasar Research and Training Institute, Ranchi, 835303, Jharkhand, India
| | - K.K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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Montag A. [The history of skin color is the history of mankind!]. DERMATOLOGIE (HEIDELBERG, GERMANY) 2023; 74:75-79. [PMID: 36593352 DOI: 10.1007/s00105-022-05101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.
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Affiliation(s)
- Andreas Montag
- Praxis für Haut und Geschlechtskrankheiten, Allergologie, Phlebologie, Reisemedizin, Schweriner Str. 17, 22143, Hamburg, Deutschland.
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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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Weasel L. How Neanderthals became White: The introgression of race into contemporary human evolutionary genomics. Am Nat 2022; 200:129-139. [DOI: 10.1086/720130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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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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Mata X, Renaud G, Mollereau C. The repertoire of family A-peptide GPCRs in archaic hominins. Peptides 2019; 122:170154. [PMID: 31560950 DOI: 10.1016/j.peptides.2019.170154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 12/30/2022]
Abstract
Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. We then searched in the literature the functional changes, phenotypes and risk of disease possibly associated with the detected variants. Our survey suggests that Neanderthal and Denisovan hominins were likely prone to lower risk of obesity, to enhanced platelet aggregation in response to thrombin, to better response to infection, to less anxiety and aggressiveness and to favorable sociability. While some archaic variants were likely advantageous in the past, they might be responsible for maladaptive disorders today in the context of modern life and/or specific regional distribution. For example, an archaic haplotype in the neuromedin receptor 2 is susceptible to confer risk of diabetic nephropathy in type 1 diabetes in present-day Europeans. Paying attention to the pharmacological properties of some of the archaic variants described in this study may be helpful to understand the variability of therapeutic efficacy between individuals or ethnic groups.
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Affiliation(s)
- Xavier Mata
- Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Catherine Mollereau
- Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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Hohl DM, Bezus B, Ratowiecki J, Catanesi CI. Genetic and phenotypic variability of iris color in Buenos Aires population. Genet Mol Biol 2018; 41:50-58. [PMID: 29658972 PMCID: PMC5901501 DOI: 10.1590/1678-4685-gmb-2017-0175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/31/2017] [Indexed: 11/21/2022] Open
Abstract
The aim of this work was to describe the phenotypic and genotypic variability related to iris color for the population of Buenos Aires province (Argentina), and to assess the usefulness of current methods of analysis for this country. We studied five Single Nucleotide Polymorphisms (SNPs) included in the IrisPlex kit, in 118 individuals, and we quantified eye color with Digital Iris Analysis Tool. The markers fit Hardy-Weinberg equilibrium for the whole sample, but not for rs12913832 within the group of brown eyes (LR=8.429; p=0.004). We found a remarkable association of HERC2 rs12913832 GG with blue color (p < 0.01) but the other markers did not show any association with iris color. The results for the Buenos Aires population differ from those of other populations of the world for these polymorphisms (p < 0,01). The differences we found might respond to the admixed ethnic composition of Argentina; therefore, methods of analysis used in European populations should be carefully applied when studying the population of Argentina. These findings reaffirm the importance of this investigation in the Argentinian population for people identification based on iris color.
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Affiliation(s)
- Diana María Hohl
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Brenda Bezus
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina
| | - Julia Ratowiecki
- Centro de Estudios Médicos e Investigaciones Clínicas CEMIC CONICET, Buenos Aires, Argentina
| | - Cecilia Inés Catanesi
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
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10
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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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Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil. Leg Med (Tokyo) 2017; 25:43-51. [DOI: 10.1016/j.legalmed.2016.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/05/2016] [Accepted: 12/30/2016] [Indexed: 01/28/2023]
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12
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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Abstract
The well-documented latitudinal clines of genes affecting human skin color presumably arise from the need for protection from intense ultraviolet radiation (UVR) vs. the need to use UVR for vitamin D synthesis. Sampling 751 subjects from a broad range of latitudes and skin colors, we investigated possible multilocus correlated adaptation of skin color genes with the vitamin D receptor gene (VDR), using a vector correlation metric and network method called BlocBuster. We discovered two multilocus networks involving VDR promoter and skin color genes that display strong latitudinal clines as multilocus networks, even though many of their single gene components do not. Considered one by one, the VDR components of these networks show diverse patterns: no cline, a weak declining latitudinal cline outside of Africa, and a strong in- vs. out-of-Africa frequency pattern. We confirmed these results with independent data from HapMap. Standard linkage disequilibrium analyses did not detect these networks. We applied BlocBuster across the entire genome, showing that our networks are significant outliers for interchromosomal disequilibrium that overlap with environmental variation relevant to the genes’ functions. These results suggest that these multilocus correlations most likely arose from a combination of parallel selective responses to a common environmental variable and coadaptation, given the known Mendelian epistasis among VDR and the skin color genes.
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Hu Y, Ding Q, He Y, Xu S, Jin L. Reintroduction of a Homocysteine Level-Associated Allele into East Asians by Neanderthal Introgression. Mol Biol Evol 2015; 32:3108-13. [PMID: 26392408 DOI: 10.1093/molbev/msv176] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In this study, we present an analysis of Neanderthal introgression at the dipeptidase 1 gene, DPEP1. A Neanderthal origin for the putative introgressive haplotypes was demonstrated using an established three-step approach. This introgression was under positive natural selection, reached a frequency of >50%, and introduced a homocysteine level- and pigmentation-associated allele (rs460879-T) into East Asians. However, the same allele was also found in non-East Asians, but not from Neanderthal introgression. It is likely that rs460879-T was lost in East Asians and was reintroduced subsequently through Neanderthal introgression. Our findings suggest that Neanderthal introgression could reintroduce an important previously existing allele into populations where the allele had been lost. This study sheds new light on understanding the contribution of Neanderthal introgression to the adaptation of non-Africans.
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Affiliation(s)
- Ya Hu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qiliang Ding
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China Department of Molecular Biology and Genetics, Cornell University
| | - Yungang He
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Shuhua Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
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15
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Rifkin RF, Dayet L, Queffelec A, Summers B, Lategan M, d’Errico F. Evaluating the Photoprotective Effects of Ochre on Human Skin by In Vivo SPF Assessment: Implications for Human Evolution, Adaptation and Dispersal. PLoS One 2015; 10:e0136090. [PMID: 26353012 PMCID: PMC4564224 DOI: 10.1371/journal.pone.0136090] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022] Open
Abstract
Archaeological indicators of cognitively modern behaviour become increasingly prevalent during the African Middle Stone Age (MSA). Although the exploitation of ochre is viewed as a key feature of the emergence of modern human behaviour, the uses to which ochre and ochre-based mixtures were put remain ambiguous. Here we present the results of an experimental study exploring the efficacy of ochre as a topical photoprotective compound. This is achieved through the in vivo calculation of the sun protection factor (SPF) values of ochre samples obtained from Ovahimba women (Kunene Region, Northern Namibia) and the Palaeozoic Bokkeveld Group deposits of the Cape Supergroup (Western Cape Province, South Africa). We employ visible spectroscopy, energy-dispersive X-ray fluorescence (ED-XRF), X-ray diffraction (XRD) and granulometric analyses to characterise ochre samples. The capacity of ochre to inhibit the susceptibility of humans to the harmful effects of exposure to ultraviolet radiation (UVR) is confirmed and the mechanisms implicated in the efficacy of ochre as a sunscreen identified. It is posited that the habitual application of ochre may have represented a crucial innovation for MSA humans by limiting the adverse effects of ultraviolet exposure. This may have facilitated the colonisation of geographic regions largely unfavourable to the constitutive skin colour of newly arriving populations.
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Affiliation(s)
- Riaan F. Rifkin
- Institute for Archaeology, History, Culture and Religion, University of Bergen, Bergen, Norway
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Laure Dayet
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche, University of Bordeaux, Pessac, France
| | - Alain Queffelec
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche, University of Bordeaux, Pessac, France
| | - Beverley Summers
- Photobiology Laboratory, Department of Pharmacy, University of Limpopo, Medunsa, South Africa
| | - Marlize Lategan
- Photobiology Laboratory, Department of Pharmacy, University of Limpopo, Medunsa, South Africa
| | - Francesco d’Errico
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche, University of Bordeaux, Pessac, France
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16
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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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17
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Skoglund P, Malmström H, Omrak A, Raghavan M, Valdiosera C, Günther T, Hall P, Tambets K, Parik J, Sjögren KG, Apel J, Willerslev E, Storå J, Götherström A, Jakobsson M. Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 2014; 344:747-50. [PMID: 24762536 DOI: 10.1126/science.1253448] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.
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Affiliation(s)
- Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Helena Malmström
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Cristina Valdiosera
- Department of Archaeology, Environment and Community Planning, La Trobe University, Melbourne VIC 3086, Australia
| | - Torsten Günther
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Kristiina Tambets
- Evolutionary Biology Group, Estonian Biocentre and University of Tartu, Tartu 51010, Estonia
| | - Jüri Parik
- Evolutionary Biology Group, Estonian Biocentre and University of Tartu, Tartu 51010, Estonia
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, 405 30, Sweden
| | - Jan Apel
- Department of Archaeology and Ancient History, Lund University, Lund, 221 00, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Jan Storå
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden.
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden. Science for Life Laboratory, Uppsala University, Uppsala 752 36, Sweden.
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18
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Affiliation(s)
- John Hawks
- Department of Anthropology, University of Wisconsin, Madison, Wisconsin 53706;
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19
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Draus-Barini J, Walsh S, Pośpiech E, Kupiec T, Głąb H, Branicki W, Kayser M. Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains. INVESTIGATIVE GENETICS 2013; 4:3. [PMID: 23317428 PMCID: PMC3551694 DOI: 10.1186/2041-2223-4-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/14/2012] [Indexed: 11/10/2022]
Abstract
UNLABELLED BACKGROUND DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person's externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions. METHODS Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system. RESULTS Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general Władysław Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction. CONCLUSIONS Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.
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Affiliation(s)
| | - Susan Walsh
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ewelina Pośpiech
- Department of Genetics and Evolution, Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland
| | - Tomasz Kupiec
- Institute of Forensic Research, Section of Forensic Genetics, Kraków, Poland
| | - Henryk Głąb
- Department of Anthropology, Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland
| | - Wojciech Branicki
- Institute of Forensic Research, Section of Forensic Genetics, Kraków, Poland.,Department of Genetics and Evolution, Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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20
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Disotell TR. Archaic human genomics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149 Suppl 55:24-39. [PMID: 23124308 DOI: 10.1002/ajpa.22159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.
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Affiliation(s)
- Todd R Disotell
- Center for Study of Human Origins, Department of Anthropology, New York University, New York, NY 10003, USA.
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21
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Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science 2012; 338:222-6. [PMID: 22936568 DOI: 10.1126/science.1224344] [Citation(s) in RCA: 1083] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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Affiliation(s)
- Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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