1
|
Kamitaki N, Hujoel MLA, Mukamel RE, Gebara E, McCarroll SA, Loh PR. A sequence of SVA retrotransposon insertions in ASIP shaped human pigmentation. Nat Genet 2024:10.1038/s41588-024-01841-4. [PMID: 39048794 DOI: 10.1038/s41588-024-01841-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Retrotransposons comprise about 45% of the human genome1, but their contributions to human trait variation and evolution are only beginning to be explored2,3. Here, we find that a sequence of SVA retrotransposon insertions in an early intron of the ASIP (agouti signaling protein) gene has probably shaped human pigmentation several times. In the UK Biobank (n = 169,641), a recent 3.3-kb SVA insertion polymorphism associated strongly with lighter skin pigmentation (0.22 [0.21-0.23] s.d.; P = 2.8 × 10-351) and increased skin cancer risk (odds ratio = 1.23 [1.18-1.27]; P = 1.3 × 10-28), appearing to underlie one of the strongest common genetic influences on these phenotypes within European populations4-6. ASIP expression in skin displayed the same association pattern, with the SVA insertion allele exhibiting 2.2-fold (1.9-2.6) increased expression. This effect had an unusual apparent mechanism: an earlier, nonpolymorphic, human-specific SVA retrotransposon 3.9 kb upstream appeared to have caused ASIP hypofunction by nonproductive splicing, which the new (polymorphic) SVA insertion largely eliminated. Extended haplotype homozygosity indicated that the insertion allele has risen to allele frequencies up to 11% in European populations over the past several thousand years. These results indicate that a sequence of retrotransposon insertions contributed to a species-wide increase, then a local decrease, of human pigmentation.
Collapse
Affiliation(s)
- Nolan Kamitaki
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Margaux L A Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward Gebara
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
2
|
Pu Y, Pu S, Chen Y, Kong Q, Liu X, Zhao Q, Xu K, Liu J, Li M, Xu X, Qiao X, Su B, Chen J, Yang Z. Weakened tanning ability is an important mechanism for evolutionary skin lightening in East Asians. J Genet Genomics 2024; 51:703-713. [PMID: 38461943 DOI: 10.1016/j.jgg.2024.03.001] [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: 02/28/2024] [Revised: 03/03/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024]
Abstract
The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments. East Asians are ideal populations for studying skin color evolution because of the complex environment of East Asia. Here, we report a strong selection signal for the pigmentation gene phenylalanine hydroxylase (PAH) in light-skinned Han Chinese individuals. The intron mutation rs10778203 in PAH is enriched in East Asians and is significantly associated with skin color of the back of the hand in Han Chinese males (P < 0.05). In vitro luciferase and transcription factor binding assays show that the ancestral allele of rs10778203 could bind to SMAD2 and has a significant enhancer activity for PAH. However, the derived T allele (the major allele in East Asians) of rs10778203 decreases the binding activity of transcription factors and enhancer activity. Meanwhile, the derived T allele of rs10778203 shows a weaker ultraviolet radiation response in A375 cells and zebrafish embryos. Furthermore, rs10778203 decreases melanin production in transgenic zebrafish embryos after ultraviolet B (UVB) treatment. Collectively, PAH is a potential pigmentation gene that regulates skin tanning ability. Natural selection has enriched the adaptive allele, resulting in weakened tanning ability in East Asians, suggesting a unique genetic mechanism for evolutionary skin lightening in East Asians.
Collapse
Affiliation(s)
- Youwei Pu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyu Pu
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanyan Chen
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qinghong Kong
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xuyang Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qi Zhao
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ke Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jiuming Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mengyuan Li
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xiaoyu Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xiaoyang Qiao
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jing Chen
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Yilmaz F, Karageorgiou C, Kim K, Pajic P, Scheer K, Beck CR, Torregrossa AM, Lee C, Gokcumen O. Paleolithic Gene Duplications Primed Adaptive Evolution of Human Amylase Locus Upon Agriculture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.27.568916. [PMID: 38077078 PMCID: PMC10705236 DOI: 10.1101/2023.11.27.568916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Starch digestion is a cornerstone of human nutrition. The amylase genes code for the starch-digesting amylase enzyme. Previous studies suggested that the salivary amylase (AMY1) gene copy number increased in response to agricultural diets. However, the lack of nucleotide resolution of the amylase locus hindered detailed evolutionary analyses. Here, we have resolved this locus at nucleotide resolution in 98 present-day humans and identified 30 distinct haplotypes, revealing that the coding sequences of all amylase gene copies are evolving under negative selection. The phylogenetic reconstruction suggested that haplotypes with three AMY1 gene copies, prevalent across all continents and constituting about 70% of observed haplotypes, originated before the out-of-Africa migrations of ancestral modern humans. Using thousands of unique 25 base pair sequences across the amylase locus, we showed that additional AMY1 gene copies existed in the genomes of four archaic hominin genomes, indicating that the initial duplication of this locus may have occurred as far back 800,000 years ago. We similarly analyzed 73 ancient human genomes dating from 300 - 45,000 years ago and found that the AMY1 copy number variation observed today existed long before the advent of agriculture (~10,000 years ago), predisposing this locus to adaptive increase in the frequency of higher amylase copy number with the spread of agriculture. Mechanistically, the common three-copy haplotypes seeded non-allelic homologous recombination events that appear to be occurring at one of the fastest rates seen for tandem repeats in the human genome. Our study provides a comprehensive population-level understanding of the genomic structure of the amylase locus, identifying the mechanisms and evolutionary history underlying its duplication and copy number variability in relation to the onset of agriculture.
Collapse
|
5
|
Liu J, Bitsue HK, Yang Z. Skin colour: A window into human phenotypic evolution and environmental adaptation. Mol Ecol 2024; 33:e17369. [PMID: 38713101 DOI: 10.1111/mec.17369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.
Collapse
Affiliation(s)
- Jiuming Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Habtom K Bitsue
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
6
|
Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e15. [PMID: 38516374 PMCID: PMC10955370 DOI: 10.1017/ehs.2024.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.
Collapse
Affiliation(s)
| | - Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
7
|
Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet 2024; 56:258-272. [PMID: 38200130 PMCID: PMC11005318 DOI: 10.1038/s41588-023-01626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
Collapse
Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Xie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Human Phenome Institute, School of Life Science, Fudan University, Shanghai, China
| | - Joshua Saskin
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Chao Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN); Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Elena Oancea
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
8
|
Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. Nature 2024; 625:312-320. [PMID: 38200293 PMCID: PMC10781624 DOI: 10.1038/s41586-023-06705-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2023] [Indexed: 01/12/2024]
Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
Collapse
Affiliation(s)
- Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alma S Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Ruairidh Macleod
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- UCL Genetics Institute, University College London, London, UK
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Leo Speidel
- UCL Genetics Institute, University College London, London, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Aaron J Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
| |
Collapse
|
9
|
Wang X, Hivert V, Groot S, Wang Y, Yengo L, McGrath JJ, Kemper KE, Visscher PM, Wray NR, Revez JA. Cross-ancestry analyses identify new genetic loci associated with 25-hydroxyvitamin D. PLoS Genet 2023; 19:e1011033. [PMID: 37963177 PMCID: PMC10684098 DOI: 10.1371/journal.pgen.1011033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 11/28/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
Vitamin D status-a complex trait influenced by environmental and genetic factors-is tightly associated with skin colour and ancestry. Yet very few studies have investigated the genetic underpinnings of vitamin D levels across diverse ancestries, and the ones that have, relied on small sample sizes, resulting in inconclusive results. Here, we conduct genome-wide association studies (GWAS) of 25 hydroxyvitamin D (25OHD)-the main circulating form of vitamin D-in 442,435 individuals from four broad genetically-determined ancestry groups represented in the UK Biobank: European (N = 421,867), South Asian (N = 9,983), African (N = 8,306) and East Asian (N = 2,279). We identify a new genetic determinant of 25OHD (rs146759773) in individuals of African ancestry, which was not detected in previous analysis of much larger European cohorts due to low minor allele frequency. We show genome-wide significant evidence of dominance effects in 25OHD that protect against vitamin D deficiency. Given that key events in the synthesis of 25OHD occur in the skin and are affected by pigmentation levels, we conduct GWAS of 25OHD stratified by skin colour and identify new associations. Lastly, we test the interaction between skin colour and variants associated with variance in 25OHD levels and identify two loci (rs10832254 and rs1352846) whose association with 25OHD differs in individuals of distinct complexions. Collectively, our results provide new insights into the complex relationship between 25OHD and skin colour and highlight the importance of diversity in genomic studies. Despite the much larger rates of vitamin D deficiency that we and others report for ancestry groups with dark skin (e.g., South Asian), our study highlights the importance of considering ancestral background and/or skin colour when assessing the implications of low vitamin D.
Collapse
Affiliation(s)
- Xiaotong Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Valentin Hivert
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Shiane Groot
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - John J. McGrath
- National Centre for Register-Based Research, Aarhus University, Aarhus V, Denmark
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn E. Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M. Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Joana A. Revez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
10
|
Wang K, Prüfer K, Krause-Kyora B, Childebayeva A, Schuenemann VJ, Coia V, Maixner F, Zink A, Schiffels S, Krause J. High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry. CELL GENOMICS 2023; 3:100377. [PMID: 37719142 PMCID: PMC10504632 DOI: 10.1016/j.xgen.2023.100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/10/2023] [Accepted: 07/13/2023] [Indexed: 09/19/2023]
Abstract
The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.
Collapse
Affiliation(s)
- Ke Wang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Science, Fudan University, Shanghai 200438, China
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, 24118 Kiel, Germany
| | | | - Verena J. Schuenemann
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland
- Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - Valentina Coia
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Frank Maixner
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Albert Zink
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| |
Collapse
|
11
|
Hanly JJ, Francescutti CM, Loh LS, Corning OBWH, Long DJ, Nakatani MA, Porter AH, Martin A. Genetics of yellow-orange color variation in a pair of sympatric sulphur butterflies. Cell Rep 2023; 42:112820. [PMID: 37481719 DOI: 10.1016/j.celrep.2023.112820] [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: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023] Open
Abstract
Continuous color polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits. Here we investigated continuous color variation in Colias eurytheme and Colias philodice, two species of sulphur butterflies that hybridize in sympatry. Using quantitative trait locus (QTL) analysis and high-throughput color quantification, we found two interacting large-effect loci affecting orange-to-yellow chromaticity. Knockouts of red Malpighian tubules (red), likely involved in endosomal maturation, result in depigmented wing scales. Additionally, the transcription factor bric-a-brac can act as a modulator of orange pigmentation. We also describe the QTL architecture of other continuously varying traits, together supporting a large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the range of possible genetic architectures that can underpin a continuously varying trait and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye.
Collapse
Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC, USA; Smithsonian Tropical Research Institute, Gamboa, Panama.
| | | | - Ling S Loh
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Olaf B W H Corning
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Derek J Long
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Marshall A Nakatani
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Adam H Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA.
| |
Collapse
|
12
|
Bajpai VK, Swigut T, Mohammed J, Naqvi S, Arreola M, Tycko J, Kim TC, Pritchard JK, Bassik MC, Wysocka J. A genome-wide genetic screen uncovers determinants of human pigmentation. Science 2023; 381:eade6289. [PMID: 37561850 PMCID: PMC10901463 DOI: 10.1126/science.ade6289] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 06/28/2023] [Indexed: 08/12/2023]
Abstract
Skin color, one of the most diverse human traits, is determined by the quantity, type, and distribution of melanin. In this study, we leveraged the light-scattering properties of melanin to conduct a genome-wide screen for regulators of melanogenesis. We identified 169 functionally diverse genes that converge on melanosome biogenesis, endosomal transport, and gene regulation, of which 135 represented previously unknown associations with pigmentation. In agreement with their melanin-promoting function, the majority of screen hits were up-regulated in melanocytes from darkly pigmented individuals. We further unraveled functions of KLF6 as a transcription factor that regulates melanosome maturation and pigmentation in vivo, and of the endosomal trafficking protein COMMD3 in modulating melanosomal pH. Our study reveals a plethora of melanin-promoting genes, with broad implications for human variation, cell biology, and medicine.
Collapse
Affiliation(s)
- Vivek K. Bajpai
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- School of Chemical, Biological, and Materials Engineering, The University of Oklahoma, Norman, OK, 73019, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Martin Arreola
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Tayne C. Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
- Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
13
|
Veilleux CC, Garrett EC, Pajic P, Saitou M, Ochieng J, Dagsaan LD, Dominy NJ, Perry GH, Gokcumen O, Melin AD. Human subsistence and signatures of selection on chemosensory genes. Commun Biol 2023; 6:683. [PMID: 37400713 DOI: 10.1038/s42003-023-05047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/15/2023] [Indexed: 07/05/2023] Open
Abstract
Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.
Collapse
Affiliation(s)
- Carrie C Veilleux
- Department of Anatomy, Midwestern University, 19555 N 59th Ave, Glendale, AZ, 85308, USA.
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
| | - Eva C Garrett
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA, 02215, USA
| | - Petar Pajic
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Marie Saitou
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Joseph Ochieng
- Department of Anatomy, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lilia D Dagsaan
- National Commission for Indigenous Peoples, Botolan, Philippines
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH, 03755, USA
| | - George H Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, 410 Carpenter Building, University Park, PA, 16802, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.
| |
Collapse
|
14
|
Thawabteh AM, Jibreen A, Karaman D, Thawabteh A, Karaman R. Skin Pigmentation Types, Causes and Treatment-A Review. Molecules 2023; 28:4839. [PMID: 37375394 DOI: 10.3390/molecules28124839] [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: 05/05/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Human skin pigmentation and melanin synthesis are incredibly variable, and are impacted by genetics, UV exposure, and some drugs. Patients' physical appearance, psychological health, and social functioning are all impacted by a sizable number of skin conditions that cause pigmentary abnormalities. Hyperpigmentation, where pigment appears to overflow, and hypopigmentation, where pigment is reduced, are the two major classifications of skin pigmentation. Albinism, melasma, vitiligo, Addison's disease, and post-inflammatory hyperpigmentation, which can be brought on by eczema, acne vulgaris, and drug interactions, are the most common skin pigmentation disorders in clinical practice. Anti-inflammatory medications, antioxidants, and medications that inhibit tyrosinase, which prevents the production of melanin, are all possible treatments for pigmentation problems. Skin pigmentation can be treated orally and topically with medications, herbal remedies, and cosmetic products, but a doctor should always be consulted before beginning any new medicine or treatment plan. This review article explores the numerous types of pigmentation problems, their causes, and treatments, as well as the 25 plants, 4 marine species, and 17 topical and oral medications now on the market that have been clinically tested to treat skin diseases.
Collapse
Affiliation(s)
- Amin Mahmood Thawabteh
- Faculty of Pharmacy, Nursing and Health Professions, Birzeit University, Ramallah 00972, Palestine
- General Safety Section, General Services Department, Birzeit University, Bir Zeit 71939, Palestine
| | - Alaa Jibreen
- Research and Development Department, Beit Jala Pharmaceutical Co., Ltd., Beit Jala 97300, Palestine
| | - Donia Karaman
- Pharmaceutical Sciences Department, Faculty of Pharmacy, Al-Quds University, Jerusalem 20002, Palestine
| | - Alà Thawabteh
- Medical Imaging Department, Faculty of Health Profession, Al-Quds University, Jerusalem 20002, Palestine
| | - Rafik Karaman
- Pharmaceutical Sciences Department, Faculty of Pharmacy, Al-Quds University, Jerusalem 20002, Palestine
- Department of Sciences, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| |
Collapse
|
15
|
Ang KC, Canfield VA, Foster TC, Harbaugh TD, Early KA, Harter RL, Reid KP, Leong SL, Kawasawa Y, Liu D, Hawley JW, Cheng KC. Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population. eLife 2023; 12:e77514. [PMID: 37294081 PMCID: PMC10371226 DOI: 10.7554/elife.77514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/08/2023] [Indexed: 06/10/2023] Open
Abstract
Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago Territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was -8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of -6 and -4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24-29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.
Collapse
Affiliation(s)
- Khai C Ang
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Victor A Canfield
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Tiffany C Foster
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Thaddeus D Harbaugh
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Kathryn A Early
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Rachel L Harter
- Department of Pathology, Penn State College of MedicineHersheyUnited States
| | - Katherine P Reid
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Shou Ling Leong
- Department of Family & Community Medicine, Penn State College of MedicineHersheyUnited States
| | - Yuka Kawasawa
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
- Institute of Personalized Medicine, Penn State College of MedicineHersheyUnited States
| | - Dajiang Liu
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Public Health Sciences, Penn State College of MedicineHersheyUnited States
| | | | - Keith C Cheng
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
| |
Collapse
|
16
|
Sun X, Niu Q, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Xu L, Ren H. Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers. Genes (Basel) 2023; 14:1183. [PMID: 37372363 DOI: 10.3390/genes14061183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.
Collapse
Affiliation(s)
- Xiaoyan Sun
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Qunhao Niu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Jiang
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Jie Li
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Cancan Chen
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Liangjia Liu
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hangxing Ren
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| |
Collapse
|
17
|
Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, Ranciaro A, Hirbo J, Beggs W, Thomas N, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi A, Folkunang C, Meskel DW, Belay G, Song YS, Tishkoff SA. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 2023; 186:923-939.e14. [PMID: 36868214 PMCID: PMC10568978 DOI: 10.1016/j.cell.2023.01.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
Abstract
We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from "ghost" populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.
Collapse
Affiliation(s)
- Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey P Spence
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neil Thomas
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, P.O. Box 9790, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana
| | - Alfred Njamnshi
- Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Charles Folkunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Dawit Wolde Meskel
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
18
|
Lucock MD. The evolution of human skin pigmentation: A changing medley of vitamins, genetic variability, and UV radiation during human expansion. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:252-271. [PMID: 36790744 PMCID: PMC10083917 DOI: 10.1002/ajpa.24564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 04/12/2023]
Abstract
This review examines putative, yet likely critical evolutionary pressures contributing to human skin pigmentation and subsequently, depigmentation phenotypes. To achieve this, it provides a synthesis of ideas that frame contemporary thinking, without limiting the narrative to pigmentation genes alone. It examines how geography and hence the quality and quantity of UV exposure, pigmentation genes, diet-related genes, vitamins, anti-oxidant nutrients, and cultural practices intersect and interact to facilitate the evolution of human skin color. The article has a strong focus on the vitamin D-folate evolutionary model, with updates on the latest biophysical research findings to support this paradigm. This model is examined within a broad canvas that takes human expansion out of Africa and genetic architecture into account. A thorough discourse on the biology of melanization is provided (includes relationship to BH4 and DNA damage repair), with the relevance of this to the UV sensitivity of folate and UV photosynthesis of vitamin D explained in detail, including the relevance of these vitamins to reproductive success. It explores whether we might be able to predict vitamin-related gene polymorphisms that pivot metabolism to the prevailing UVR exposome within the vitamin D-folate evolutionary hypothesis context. This is discussed in terms of a primary adaptive phenotype (pigmentation/depigmentation), a secondary adaptive phenotype (flexible metabolic phenotype based on vitamin-related gene polymorphism profile), and a tertiary adaptive strategy (dietary anti-oxidants to support the secondary adaptive phenotype). Finally, alternative evolutionary models for pigmentation are discussed, as are challenges to future research in this area.
Collapse
Affiliation(s)
- Mark D. Lucock
- School of Environmental & Life SciencesUniversity of NewcastleOurimbahNew South WalesAustralia
| |
Collapse
|
19
|
Markiewicz E, Idowu OC. Evaluation of Personalized Skincare Through in-silico Gene Interactive Networks and Cellular Responses to UVR and Oxidative Stress. Clin Cosmet Investig Dermatol 2022; 15:2221-2243. [PMID: 36284733 PMCID: PMC9588296 DOI: 10.2147/ccid.s383790] [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: 07/26/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Abstract
Purpose Personalized approaches in dermatology are designed to match the specific requirements based on the individual genetic makeup. One major factor accounting for the differences in skin phenotypes is single nucleotide polymorphism (SNP) within several genes with diverse roles that extend beyond skin tone and pigmentation. Therefore, the cellular sensitivities to the environmental stress and damage linked to extrinsic aging could also underlie the individual characteristics of the skin and dictate the unique skin care requirements. This study aimed to identify the likely biomarkers and molecular signatures expressed in skin cells of different ethnic backgrounds, which could aid further the design of personalized skin products based on specific demands. Methods Using data mining and in-silico modeling, the association of SNP-affected genes with three major skin types of European, Asian and African origin was analyzed and compared within the structure-function gene interaction networks. Cultured dermal fibroblasts were subsequently subjected to ultraviolet radiation and oxidative stress and analyzed for DNA damage and senescent markers. The protective applications of two cosmetic ingredients, Resveratrol and Quercetin, were validated in both cellular and in-silico models. Results Each skin type was characterized by the presence of SNPs in the genes controlling facultative and constitutive pigmentation, which could also underlie the major differences in responses to photodamage, such as oxidative stress, inflammation, and barrier homeostasis. Skin-type-specific dermal fibroblasts cultured in-vitro demonstrated distinctive sensitivities to ultraviolet radiation and oxidative stress, which could be modulated further by the bioactive compounds with the predicted capacities to interact with some of the genes in the in-silico models. Conclusion Evaluation of the SNP-affected gene networks and likely sensitivities of skin cells, defined as low threshold levels to extrinsic stress factors, can provide a valuable tool for the design and formulation of personalized skin products that match more accurately diverse ethnic backgrounds.
Collapse
Affiliation(s)
- Ewa Markiewicz
- Hexis Lab, The Catalyst, Newcastle Helix, Newcastle upon Tyne, UK
| | - Olusola C Idowu
- Hexis Lab, The Catalyst, Newcastle Helix, Newcastle upon Tyne, UK,Correspondence: Olusola C Idowu, HexisLab Limited, The Catalyst, Newcastle Helix, Newcastle upon Tyne, NE4 5TG, UK, Tel +44 1394 825487, Email
| |
Collapse
|
20
|
Abstract
Strong ultraviolet (UV) radiation at high altitude imposes a serious selective pressure, which may induce skin pigmentation adaptation of indigenous populations. We conducted skin pigmentation phenotyping and genome-wide analysis of Tibetans in order to understand the underlying mechanism of adaptation to UV radiation. We observe that Tibetans have darker baseline skin color compared with lowland Han Chinese, as well as an improved tanning ability, suggesting a two-level adaptation to boost their melanin production. A genome-wide search for the responsible genes identifies GNPAT showing strong signals of positive selection in Tibetans. An enhancer mutation (rs75356281) located in GNPAT intron 2 is enriched in Tibetans (58%) but rare in other world populations (0 to 18%). The adaptive allele of rs75356281 is associated with darker skin in Tibetans and, under UVB treatment, it displays higher enhancer activities compared with the wild-type allele in in vitro luciferase assays. Transcriptome analyses of gene-edited cells clearly show that with UVB treatment, the adaptive variant of GNPAT promotes melanin synthesis, likely through the interactions of CAT and ACAA1 in peroxisomes with other pigmentation genes, and they act synergistically, leading to an improved tanning ability in Tibetans for UV protection.
Collapse
|
21
|
van Eeden G, Uren C, Pless E, Mastoras M, van der Spuy GD, Tromp G, Henn BM, Möller M. The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans. Genome Biol 2022; 23:172. [PMID: 35945619 PMCID: PMC9361568 DOI: 10.1186/s13059-022-02744-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Recombination maps are important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. Results We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans. Conclusions Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02744-5.
Collapse
Affiliation(s)
- Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Evlyn Pless
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Mira Mastoras
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Gian D van der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.,SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.,SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. .,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.
| |
Collapse
|
22
|
Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck. Genes (Basel) 2022; 13:genes13071271. [PMID: 35886054 PMCID: PMC9322730 DOI: 10.3390/genes13071271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/04/2022] Open
Abstract
Beak color diversity is a broadly occurring phenomenon in birds. Here, we used ducks to identify candidate genes for yellow, black, and spotted beaks. For this, an F2 population consisting of 275 ducks was genotyped using whole genome resequencing containing 12.6 M single-nucleotide polymorphisms (SNPs) and three beak colors. Genome-wide association studies (GWAS) was used to identify the candidate and potential SNPs for three beak colors in ducks (yellow, spotted, and black). The results showed that 2753 significant SNPs were associated with black beaks, 7462 with yellow, and 17 potential SNPs with spotted beaks. Based on SNP annotation, MITF, EDNRB2, members of the POU family, and the SLC superfamily were the candidate genes regulating pigmentation. Meanwhile, isoforms MITF-M and EDNRB2 were significantly different between black and yellow beaks. MITF and EDNRB2 likely play a synergistic role in the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. This study provides new insights into genetic factors that may influence the diversity of beak color.
Collapse
Affiliation(s)
- Qixin Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Correspondence: (H.B.); (G.C.); Tel.: +86-18796608824 (H.B.); +86-17851975060 (G.C.)
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-18796608824 (H.B.); +86-17851975060 (G.C.)
| |
Collapse
|
23
|
Yair S, Coop G. Population differentiation of polygenic score predictions under stabilizing selection. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200416. [PMID: 35430887 PMCID: PMC9014188 DOI: 10.1098/rstb.2020.0416] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/08/2022] [Indexed: 12/15/2022] Open
Abstract
Given the many small-effect loci uncovered by genome-wide association studies (GWAS), polygenic scores have become central to genomic medicine, and have found application in diverse settings including evolutionary studies of adaptation. Despite their promise, polygenic scores have been found to suffer from limited portability across human populations. This at first seems in conflict with the observation that most common genetic variation is shared among populations. We investigate one potential cause of this discrepancy: stabilizing selection on complex traits. Counterintuitively, while stabilizing selection constrains phenotypic evolution, it accelerates the loss and fixation of alleles underlying trait variation within populations (GWAS loci). Thus even when populations share an optimum phenotype, stabilizing selection erodes the variance contributed by their shared GWAS loci, such that predictions from GWAS in one population explain less of the phenotypic variation in another. We develop theory to quantify how stabilizing selection is expected to reduce the prediction accuracy of polygenic scores in populations not represented in GWAS samples. In addition, we find that polygenic scores can substantially overstate average genetic differences of phenotypes among populations. We emphasize stabilizing selection around a common optimum as a useful null model to connect patterns of allele frequency and polygenic score differentiation. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.
Collapse
Affiliation(s)
- Sivan Yair
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Graham Coop
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| |
Collapse
|
24
|
Gopalan S, Smith SP, Korunes K, Hamid I, Ramachandran S, Goldberg A. Human genetic admixture through the lens of population genomics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200410. [PMID: 35430881 PMCID: PMC9014191 DOI: 10.1098/rstb.2020.0410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
Collapse
Affiliation(s)
- Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Katharine Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
- Data Science Initiative, Brown University, Providence, RI 02912, USA
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| |
Collapse
|
25
|
Dabas P, Jain S, Khajuria H, Nayak BP. Forensic DNA phenotyping: Inferring phenotypic traits from crime scene DNA. J Forensic Leg Med 2022; 88:102351. [DOI: 10.1016/j.jflm.2022.102351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/01/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
|
26
|
Dadzie OE, Sturm RA, Fajuyigbe D, Petit A, Jablonski NG. The Eumelanin Human Skin Colour Scale: A Proof-of-Concept Study. Br J Dermatol 2022; 187:99-104. [PMID: 35349165 DOI: 10.1111/bjd.21277] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND At present there is no standard nomenclature for describing the diversity of human constitutive skin colour. OBJECTIVES To develop a standard nomenclature for describing human constitutive skin colour. METHODS Monthly focus group discussions by a multi-disciplinary group of specialists over a 7-month period. Topics covered were: 1) Limitations and unmet needs of current nomenclature(s) pertaining to human cutaneous diversity; 2) Practical considerations about the function and role of any proposed nomenclature pertaining to human cutaneous diversity; 3) Review of the cellular basis and current molecular genetic understanding of variation in human skin pigmentation; 4) In vivo methods to evaluate human skin pigmentation. In addition, a preliminary review of the published literature was undertaken to collate data on published skin reflectance measurements, notably melanin index (MI) values for well-referenced human populations. RESULTS Development of a 5-point scale to describe the full spectrum of human constitutive skin colour, termed The Eumelanin Human Skin Colour Scale. The nomenclature of the scale uses Eumelanin, the dominant chromophore of human skin, as a central descriptive word. The categories of the scale (nomenclature and MI values) are: Eumelanin Low (EML)- <25; Eumelanin Intermediate Low (EMIL)- 25-<50; Eumelanin Intermediate (EMI)- 50-<75; Eumelanin Intermediate High (EMIH)- 75-<100; Eumelanin High (EH)- ≥100. CONCLUSIONS The Eumelanin Human Skin Colour Scale enables the complete range of human constitutive skin colour to be described in an objective, equitable and understandable manner. In future, this scale can be used as the basis for developing other scales that address the specific functional aspects of human skin, such as response to ultraviolet radiation.
Collapse
Affiliation(s)
- Ophelia E Dadzie
- Department of Dermatology, The Hillingdon Hospitals NHS Foundation Trust, Uxbridge, UK.,Department of Cellular Pathology, Northwest London Pathology, imperial College London NHS Trust, London, UK
| | - Rick A Sturm
- Dermatology Research Centre, The University of Queensland, Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia
| | | | - Antoine Petit
- Service de Dermatologie, APHP Hôpital Saint Louis, Paris, France
| | - Nina G Jablonski
- Department of Anthropology, The Pennsylvania State University, Sate College, Pennsylvania, USA
| |
Collapse
|
27
|
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]
|
28
|
Dreier MR, de la Serna IL. SWI/SNF Chromatin Remodeling Enzymes in Melanoma. EPIGENOMES 2022; 6:epigenomes6010010. [PMID: 35323214 PMCID: PMC8947417 DOI: 10.3390/epigenomes6010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
Collapse
|
29
|
Zhang C, Hansen MEB, Tishkoff SA. Advances in integrative African genomics. Trends Genet 2022; 38:152-168. [PMID: 34740451 PMCID: PMC8752515 DOI: 10.1016/j.tig.2021.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
There has been a rapid increase in human genome sequencing in the past two decades, resulting in the identification of millions of previously unknown genetic variants. However, African populations are under-represented in sequencing efforts. Additional sequencing from diverse African populations and the construction of African-specific reference genomes is needed to better characterize the full spectrum of variation in humans. However, sequencing alone is insufficient to address the molecular and cellular mechanisms underlying variable phenotypes and disease risks. Determining functional consequences of genetic variation using multi-omics approaches is a fundamental post-genomic challenge. We discuss approaches to close the knowledge gaps about African genomic diversity and review advances in African integrative genomic studies and their implications for precision medicine.
Collapse
Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
30
|
Pośpiech E, Teisseyre P, Mielniczuk J, Branicki W. Predicting Physical Appearance from DNA Data-Towards Genomic Solutions. Genes (Basel) 2022; 13:genes13010121. [PMID: 35052461 PMCID: PMC8774670 DOI: 10.3390/genes13010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.
Collapse
Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
- Central Forensic Laboratory of the Police, 00-583 Warsaw, Poland
- Correspondence: ; Tel.: +48-126-645-024
| |
Collapse
|
31
|
Schurz H, Glanzmann B, Bowker N, van Toorn R, Solomons R, Schoeman J, van Helden PD, Kinnear CJ, Hoal EG, Möller M. Deciphering Genetic Susceptibility to Tuberculous Meningitis. Front Neurol 2022; 13:820168. [PMID: 35401413 PMCID: PMC8993185 DOI: 10.3389/fneur.2022.820168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculous meningitis (TBM) is the most severe form of extrapulmonary tuberculosis (TB) that arises when a caseating meningeal granuloma discharges its contents into the subarachnoid space. It accounts for ~1% of all disease caused by Mycobacterium tuberculosis and the age of peak incidence is from 2-4 years. The exact pathogenesis of TBM is still not fully understood and the mechanism(s) by which the bacilli initially invade the blood-brain-barrier are still to be elucidated. This study investigated the involvement of the host genome in TBM susceptibility, by considering common variants (minor allele frequency (MAF) >5%) using microarray genotyping and rare variants (MAF <1%) via exome sequencing. A total of 123 TBM cases, 400 pulmonary TB (pTB) cases and 477 healthy controls were genotyped on the MEGA array. A genome-wide association study (GWAS) comparing 114 TBM cases to 395 healthy controls showed no association with TBM susceptibility. A second analysis comparing 114 TBM cases to 382 pTB cases was conducted to investigate variants associated with different TB phenotypes. No significant associations were found with progression from pTB to TBM. Ten TBM cases and 10 healthy controls were exome sequenced. Gene set association tests SKAT-O and SKAT Common Rare were used to assess the association of rare SNPs and the cumulative effect of both common and rare SNPs with susceptibility to TBM, respectively. Ingenuity Pathway Analysis (IPA) of the top-hits of the SKAT-O analysis showed that NOD2 and CYP4F2 are both important in TBM pathogenesis and highlighted these as targets for future study. For the SKAT Common Rare analysis Centriolar Coiled-Coil Protein 110 (CCP110) was nominally associated (p = 5.89x10-6) with TBM susceptibility. In addition, several top-hit genes ascribed to the development of the central nervous system (CNS) and innate immune system regulation were identified. Exome sequencing and GWAS of our TBM cohort has identified a single previously undescribed association of CCP110 with TBM susceptibility. These results advance our understanding of TBM in terms of both variants and genes that influence susceptibility. In addition, several candidate genes involved in innate immunity have been identified for further genotypic and functional investigation.
Collapse
Affiliation(s)
- Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC Genomics Centre, Cape Town, South Africa
| | - Nicholas Bowker
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ronald van Toorn
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Regan Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Johan Schoeman
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Paul D. van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Craig J. Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC Genomics Centre, Cape Town, South Africa
| | - Eileen G. Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- *Correspondence: Marlo Möller
| |
Collapse
|
32
|
Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, Lu D, Lu Y, Mokhtar SS, Rahman TA, Hoh BP, Xu S. Genetic connections and convergent evolution of tropical indigenous peoples in Asia. Mol Biol Evol 2021; 39:6481554. [PMID: 34940850 PMCID: PMC8826522 DOI: 10.1093/molbev/msab361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
Collapse
Affiliation(s)
- Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinan Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Sihan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Thuhairah Abdul Rahman
- Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Boon-Peng Hoh
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, UCSI Heights 56000 Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
33
|
Vicente M, Lankheet I, Russell T, Hollfelder N, Coetzee V, Soodyall H, Jongh MD, Schlebusch CM. Male-biased migration from East Africa introduced pastoralism into southern Africa. BMC Biol 2021; 19:259. [PMID: 34872534 PMCID: PMC8650298 DOI: 10.1186/s12915-021-01193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introduced West African-related genetic ancestry into the area. Present-day Khoekhoe-speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most other historical Khoekhoe populations have, however, disappeared over the last few centuries and their contribution to the genetic structure of present-day populations is not well understood. In our study, we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking Hessequa herders from the southern Cape region of what is now South Africa. RESULTS We generated genome-wide data from 162 individuals and mitochondrial DNA data of a subset of 87 individuals, sampled in the Western Cape Province, South Africa, where the Hessequa population once lived. Using available comparative data from Khoe-speaking and related groups, we aligned genetic date estimates and admixture proportions to the archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We identified several Afro-Asiatic-speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. We also found that the East African pastoralist expansion was heavily male-biased, akin to a pastoralist migration previously observed on the genetic level in ancient Europe, by which Pontic-Caspian Steppe pastoralist groups represented by the Yamnaya culture spread across the Eurasian continent during the late Neolithic/Bronze Age. CONCLUSION We propose that pastoralism in southern Africa arrived through male-biased migration of an East African Afro-Asiatic-related group(s) who introduced new subsistence and livestock practices to local southern African hunter-gatherers. Our results add to the understanding of historical human migration and mobility in Africa, connected to the spread of food-producing and livestock practices.
Collapse
Affiliation(s)
- Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Imke Lankheet
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Thembi Russell
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | - Nina Hollfelder
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Vinet Coetzee
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Academy of Science of South Africa, Pretoria, South Africa
| | - Michael De Jongh
- Department of Anthropology and Archaeology, University of South Africa, Pretoria, South Africa
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa.
- SciLife Lab, Uppsala, Sweden.
| |
Collapse
|
34
|
A large Canadian cohort provides insights into the genetic architecture of human hair colour. Commun Biol 2021; 4:1253. [PMID: 34737440 PMCID: PMC8568909 DOI: 10.1038/s42003-021-02764-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Hair colour is a polygenic phenotype that results from differences in the amount and ratio of melanins located in the hair bulb. Genome-wide association studies (GWAS) have identified many loci involved in the pigmentation pathway affecting hair colour. However, most of the associated loci overlap non-protein coding regions and many of the molecular mechanisms underlying pigmentation variation are still not understood. Here, we conduct GWAS meta-analyses of hair colour in a Canadian cohort of 12,741 individuals of European ancestry. By performing fine-mapping analyses we identify candidate causal variants in pigmentation loci associated with blonde, red and brown hair colour. Additionally, we observe colocalization of several GWAS hits with expression and methylation quantitative trait loci (QTLs) of cultured melanocytes. Finally, transcriptome-wide association studies (TWAS) further nominate the expression of EDNRB and CDK10 as significantly associated with hair colour. Our results provide insights on the mechanisms regulating pigmentation biology in humans.
Collapse
|
35
|
Saitou M, Masuda N, Gokcumen O. Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Mol Biol Evol 2021; 39:6413645. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
Collapse
Affiliation(s)
- Marie Saitou
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Currently at the Faculty of Biosciences, Norwegian University of Life Sciences, Universitetstunet 3, 1430 Ås, Norway.,Dept. of Medicine, The University of Chicago. Section of Genetic Medicine, 5841 S. Maryland Ave., Chicago, IL, 60637-1447, USA
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State University of New York, Buffalo, NY 14260-5030, USA
| | - Omer Gokcumen
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA
| |
Collapse
|
36
|
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.
Collapse
|
37
|
Lucock MD, Jones PR, Veysey M, Thota R, Garg M, Furst J, Martin C, Yates Z, Scarlett CJ, Jablonski NG, Chaplin G, Beckett EL. Biophysical evidence to support and extend the vitamin D-folate hypothesis as a paradigm for the evolution of human skin pigmentation. Am J Hum Biol 2021; 34:e23667. [PMID: 34418235 DOI: 10.1002/ajhb.23667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To test the "vitamin D-folate hypothesis for the evolution of human skin pigmentation." METHODS Total ozone mapping spectrometer (TOMS) satellite data were used to examine surface UV-irradiance in a large (n = 649) Australian cross-sectional study population. Genetic analysis was used to score vitamin D- and folate-related gene polymorphisms (n = 22), along with two pigmentation gene variants (IRF4-rs12203592/HERC2-rs12913832). Red cell folate and vitamin D3 were measured by immunoassay and HPLC, respectively. RESULTS Ultraviolet radiation (UVR) and pigmentation genes interact to modify blood vitamin levels; Light skin IRF4-TT genotype has greatest folate loss while light skin HERC2-GG genotype has greatest vitamin D3 synthesis (reflected in both TOMS and seasonal data). UV-wavelength exhibits a dose-response relationship in folate loss within light skin IRF4-TT genotype (305 > 310 > 324 > 380 nm). Significant vitamin D3 photosynthesis only occurs within light skin HERC2-GG genotype, and is maximal at 305 nm. Three dietary antioxidants (vitamins C, E, and β-carotene) interact with UVR and pigmentation genes preventing oxidative loss of labile reduced folate vitamers, with greatest benefit in light skin IRF4-TT subjects. The putative photosensitiser, riboflavin, did not sensitize red cell folate to UVR and actually afforded protection. Four genes (5xSNPs) influenced blood vitamin levels when stratified by pigmentation genotype; MTHFR-rs1801133/rs1801131, TS-rs34489327, CYP24A-rs17216707, and VDR-ApaI-rs7975232. Lightest IRF4-TT/darkest HERC2-AA genotype combination (greatest folate loss/lowest vitamin D3 synthesis) has 0% occurrence. The opposing, commonest (39%) compound genotype (darkest IRF4-CC/lightest HERC2-GG) permits least folate loss and greatest synthesis of vitamin D3 . CONCLUSION New biophysical evidence supports the vitamin D-folate hypothesis for evolution of skin pigmentation.
Collapse
Affiliation(s)
- Mark D Lucock
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Patrice R Jones
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | | | - Rohith Thota
- Nutraceuticals Research Group, University of Newcastle, Callaghan, New South Wales, Australia.,Metabolism and Nutrition, Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Manohar Garg
- Nutraceuticals Research Group, University of Newcastle, Callaghan, New South Wales, Australia
| | - John Furst
- Maths and Physical Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Charlotte Martin
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Zoe Yates
- Biomedical Sciences and Pharmacy, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Christopher J Scarlett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Nina G Jablonski
- Anthropology Department, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Chaplin
- Anthropology Department, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Emma L Beckett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| |
Collapse
|
38
|
Allouche J, Rachmin I, Adhikari K, Pardo LM, Lee JH, McConnell AM, Kato S, Fan S, Kawakami A, Suita Y, Wakamatsu K, Igras V, Zhang J, Navarro PP, Lugo CM, Noonan HR, Christie KA, Itin K, Mujahid N, Lo JA, Won CH, Evans CL, Weng QY, Wang H, Osseiran S, Lovas A, Németh I, Cozzio A, Navarini AA, Hsiao JJ, Nguyen N, Kemény LV, Iliopoulos O, Berking C, Ruzicka T, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Acuna-Alonso V, Gallo C, Poletti G, Bedoya G, Rothhammer F, Ito S, Schiaffino MV, Chao LH, Kleinstiver BP, Tishkoff S, Zon LI, Nijsten T, Ruiz-Linares A, Fisher DE, Roider E. NNT mediates redox-dependent pigmentation via a UVB- and MITF-independent mechanism. Cell 2021; 184:4268-4283.e20. [PMID: 34233163 PMCID: PMC8349839 DOI: 10.1016/j.cell.2021.06.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/09/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022]
Abstract
Ultraviolet (UV) light and incompletely understood genetic and epigenetic variations determine skin color. Here we describe an UV- and microphthalmia-associated transcription factor (MITF)-independent mechanism of skin pigmentation. Targeting the mitochondrial redox-regulating enzyme nicotinamide nucleotide transhydrogenase (NNT) resulted in cellular redox changes that affect tyrosinase degradation. These changes regulate melanosome maturation and, consequently, eumelanin levels and pigmentation. Topical application of small-molecule inhibitors yielded skin darkening in human skin, and mice with decreased NNT function displayed increased pigmentation. Additionally, genetic modification of NNT in zebrafish alters melanocytic pigmentation. Analysis of four diverse human cohorts revealed significant associations of skin color, tanning, and sun protection use with various single-nucleotide polymorphisms within NNT. NNT levels were independent of UVB irradiation and redox modulation. Individuals with postinflammatory hyperpigmentation or lentigines displayed decreased skin NNT levels, suggesting an NNT-driven, redox-dependent pigmentation mechanism that can be targeted with NNT-modifying topical drugs for medical and cosmetic purposes.
Collapse
Affiliation(s)
- Jennifer Allouche
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, The Open University, Milton Keynes, MK7 6AA, UK; Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Luba M Pardo
- Department of Dermatology, Erasmus Medical Center, 3015 Rotterdam, the Netherlands
| | - Ju Hee Lee
- Department of Dermatology and Cutaneous Biology Research Institute, Yonsei University College of Medicine, 03722 Seoul, Korea
| | - Alicia M McConnell
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Shinichiro Kato
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Immunology, Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yusuke Suita
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Vivien Igras
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jianming Zhang
- National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| | - Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Haley R Noonan
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kathleen A Christie
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Kaspar Itin
- Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland
| | - Nisma Mujahid
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Boston University School of Medicine, Boston, MA 02118, USA; University of Utah, Department of Dermatology, Salt Lake City, UT 84132, USA
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Chong Hyun Won
- Department of Dermatology, Asan Medical Center, Ulsan University College of Medicine, 05505 Seoul, Korea
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Qing Yu Weng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hequn Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sam Osseiran
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alyssa Lovas
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - István Németh
- Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary
| | - Antonio Cozzio
- Department of Dermatology, Venerology, and Allergology, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Alexander A Navarini
- Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland
| | - Jennifer J Hsiao
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nhu Nguyen
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lajos V Kemény
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary
| | - Othon Iliopoulos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Carola Berking
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich Alexander University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Thomas Ruzicka
- Department of Dermatology and Allergy, University Hospital Munich, Ludwig Maximilian University, 80337 Munich, Germany
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn U912OACD, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City 04510, Mexico
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000009, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 1027, Chile
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Maria Vittoria Schiaffino
- Internal Medicine, Diabetes and Endocrinology Unit, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Tamar Nijsten
- Department of Dermatology, Erasmus Medical Center, 3015 Rotterdam, the Netherlands
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; UMR 7268, CNRS-EFS-ADES, Aix-Marseille University, Marseille 13005, France
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Elisabeth Roider
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland; Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary.
| |
Collapse
|
39
|
Irving-Pease EK, Muktupavela R, Dannemann M, Racimo F. Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution? Front Genet 2021; 12:703541. [PMID: 34422004 PMCID: PMC8371751 DOI: 10.3389/fgene.2021.703541] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.
Collapse
Affiliation(s)
- Evan K. Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasa Muktupavela
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael Dannemann
- Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Nina G. Jablonski
- Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| |
Collapse
|
41
|
Zhang W, Zeng W, Jiang A, He Z, Shen X, Dong X, Feng J, Lu H. Global, regional and national incidence, mortality and disability-adjusted life-years of skin cancers and trend analysis from 1990 to 2019: An analysis of the Global Burden of Disease Study 2019. Cancer Med 2021; 10:4905-4922. [PMID: 34105887 PMCID: PMC8290243 DOI: 10.1002/cam4.4046] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/08/2021] [Accepted: 05/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Information about global and local epidemiology and trends of skin cancers is limited, which increases the difficulty of cutaneous cancer control. METHODS To estimate the global spatial patterns and temporal trends of skin cancer burden. Based on the GBD 2019, we collected and analyzed numbers and age-standardized rates (ASR) of skin cancer incidence, disability-adjusted life years (DALYs) and mortality (ASIR, ASDR, and ASMR) in 204 countries from 1990 through 2019 were estimated by age, sex, subtype (malignant skin melanoma [MSM], squamous-cell carcinoma [SCC], and basal-cell carcinoma [BCC]), Socio-demographic Index (SDI), region, and country. Temporal trends in ASR were also analyzed using estimated annual percentage change. RESULTS Globally, in 2019, there were 4.0 million BCC, 2.4 million SCC, and 0.3 million MSM. There were approximately 62.8 thousand deaths and 1.7 million DALYs due to MSM, and 56.1 thousand deaths and 1.2 million DALYs were attributed to SCC, respectively. The men had higher ASR of skin cancer burden than women. The age-specific rates of global skin cancer burden were higher in the older adults, increasing trends observed from 55 years old. Geographically, the numbers and ASR of skin cancers varied greatly across countries, with the largest burden of ASIR in high SDI regions. However, an unexpected increase was observed in some regions from 1990 to 2019, such as East Asia, and Sub-Saharan Africa. Although there was a slight decrease of the ASMR and ASDR, the global ASIR of MSM dramatically increased, 1990-2019. Also, there was a remarkable increase in ASR of BCC and SCC burden. CONCLUSIONS Skin cancer remains a major global public health threat. Reducing morbidity and mortality strategies such as primary and secondary prevention should be reconsidered, especially in the most prevalent and unexpected increased regions, especially for those areas with the greatest proportions of their population over age 55.
Collapse
Affiliation(s)
- Wei Zhang
- Department of DermatologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
- Department of ImmunologyBasic Medical SchoolGuizhou Medical UniversityGuiyangChina
| | - Wen Zeng
- Department of DermatologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Aofei Jiang
- School of ManagementDalian Polytechnic UniversityDalianChina
| | - Zhi He
- Department of DermatologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Xiaoping Shen
- Department of DermatologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Xian Dong
- Department of DermatologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Jianglong Feng
- Department of PathologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Hongguang Lu
- Department of DermatologyAffiliated Hospital of Guizhou Medical UniversityGuiyangChina
- Department of ImmunologyBasic Medical SchoolGuizhou Medical UniversityGuiyangChina
| |
Collapse
|
42
|
Dato S, Crocco P, Rambaldi Migliore N, Lescai F. Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging. Front Genet 2021; 12:689824. [PMID: 34178042 PMCID: PMC8225294 DOI: 10.3389/fgene.2021.689824] [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: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Aging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration. Recent Advances In this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today. Critical Issues Although the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types. Future Directions We critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.
Collapse
Affiliation(s)
- Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | | | - Francesco Lescai
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| |
Collapse
|
43
|
Lin M, Park DS, Zaitlen NA, Henn BM, Gignoux CR. Admixed Populations Improve Power for Variant Discovery and Portability in Genome-Wide Association Studies. Front Genet 2021; 12:673167. [PMID: 34108994 PMCID: PMC8181458 DOI: 10.3389/fgene.2021.673167] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) are primarily conducted in single-ancestry settings. The low transferability of results has limited our understanding of human genetic architecture across a range of complex traits. In contrast to homogeneous populations, admixed populations provide an opportunity to capture genetic architecture contributed from multiple source populations and thus improve statistical power. Here, we provide a mechanistic simulation framework to investigate the statistical power and transferability of GWAS under directional polygenic selection or varying divergence. We focus on a two-way admixed population and show that GWAS in admixed populations can be enriched for power in discovery by up to 2-fold compared to the ancestral populations under similar sample size. Moreover, higher accuracy of cross-population polygenic score estimates is also observed if variants and weights are trained in the admixed group rather than in the ancestral groups. Common variant associations are also more likely to replicate if first discovered in the admixed group and then transferred to an ancestral population, than the other way around (across 50 iterations with 1,000 causal SNPs, training on 10,000 individuals, testing on 1,000 in each population, p = 3.78e-6, 6.19e-101, ∼0 for FST = 0.2, 0.5, 0.8, respectively). While some of these FST values may appear extreme, we demonstrate that they are found across the entire phenome in the GWAS catalog. This framework demonstrates that investigation of admixed populations harbors significant advantages over GWAS in single-ancestry cohorts for uncovering the genetic architecture of traits and will improve downstream applications such as personalized medicine across diverse populations.
Collapse
Affiliation(s)
- Meng Lin
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Danny S Park
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, San Francisco, CA, United States
| | - Noah A Zaitlen
- Department of Neurology and Computational Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California, Davis, Davis, CA, United States
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| |
Collapse
|
44
|
Le L, Sirés-Campos J, Raposo G, Delevoye C, Marks MS. Melanosome biogenesis in the pigmentation of mammalian skin. Integr Comp Biol 2021; 61:1517-1545. [PMID: 34021746 DOI: 10.1093/icb/icab078] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Melanins, the main pigments of the skin and hair in mammals, are synthesized within membrane-bound organelles of melanocytes called melanosomes. Melanosome structure and function are determined by a cohort of resident transmembrane proteins, many of which are expressed only in pigment cells, that localize specifically to melanosomes. Defects in the genes that encode melanosome-specific proteins or components of the machinery required for their transport in and out of melanosomes underlie various forms of ocular or oculocutaneous albinism, characterized by hypopigmentation of the hair, skin and eyes and by visual impairment. We review major components of melanosomes, including the enzymes that catalyze steps in melanin synthesis from tyrosine precursors, solute transporters that allow these enzymes to function, and structural proteins that underlie melanosome shape and melanin deposition. We then review the molecular mechanisms by which these components are biosynthetically delivered to newly forming melanosomes-many of which are shared by other cell types that generate cell type-specific lysosome-related organelles. We also highlight unanswered questions that need to be addressed by future investigation.
Collapse
Affiliation(s)
- Linh Le
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA USA.,Department of Pathology & Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA USA
| | - Julia Sirés-Campos
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, 75005, France
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, 75005, France
| | - Cédric Delevoye
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, 75005, France
| | - Michael S Marks
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA USA.,Department of Pathology & Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| |
Collapse
|
45
|
Svensson E, Günther T, Hoischen A, Hervella M, Munters AR, Ioana M, Ridiche F, Edlund H, van Deuren RC, Soficaru A, de-la-Rua C, Netea MG, Jakobsson M. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr Biol 2021; 31:2973-2983.e9. [PMID: 34010592 DOI: 10.1016/j.cub.2021.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
Collapse
Affiliation(s)
- Emma Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mihai Ioana
- Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rosanne C van Deuren
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Andrei Soficaru
- "Francisc J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| |
Collapse
|
46
|
Abstract
Some of the genes responsible for the evolution of light skin pigmentation in Europeans show signals of positive selection in present-day populations. Recently, genome-wide association studies have highlighted the highly polygenic nature of skin pigmentation. It is unclear whether selection has operated on all of these genetic variants or just a subset. By studying variation in over a thousand ancient genomes from West Eurasia covering 40,000 y, we are able to study both the aggregate behavior of pigmentation-associated variants and the evolutionary history of individual variants. We find that the evolution of light skin pigmentation in Europeans was driven by frequency changes in a relatively small fraction of the genetic variants that are associated with variation in the trait today. Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.
Collapse
|
47
|
Chen Y, André M, Adhikari K, Blin M, Bonfante B, Mendoza-Revilla J, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, de Cerqueira CCS, Hünemeier T, Ramallo V, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Tobin DJ, Wang S, Faux P, Ruiz-Linares A. A genome-wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans. Br J Dermatol 2021; 185:988-998. [PMID: 33959940 DOI: 10.1111/bjd.20436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans. OBJECTIVES To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America. METHODS Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome. RESULTS Genome-wide significant association was observed at four genome regions: two were associated with wrinkling (in 1p13·3 and 21q21·2), one with mole count (in 1q32·3) and one with both wrinkling and mole count (in 5p13·2). Associated SNPs in 5p13·2 and in 1p13·3 are intronic within SLC45A2 and VAV3, respectively, while SNPs in 1q32·3 are near the SLC30A1 gene, and those in 21q21·2 occur in a gene desert. Analyses of SNPs in IRF4 and MC1R are consistent with a role of these genes in skin ageing. CONCLUSIONS We replicate the association of wrinkling with variants in SLC45A2, IRF4 and MC1R reported in Europeans. We identify VAV3 and SLC30A1 as two novel candidate genes impacting on wrinkling and mole count, respectively. We provide the first evidence that SLC45A2 influences mole count, in addition to variants in this gene affecting melanoma risk in Europeans.
Collapse
Affiliation(s)
- Y Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
| | - M André
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - K Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, UK.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - M Blin
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - B Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - J Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú.,Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, 75015, France
| | - M Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - S Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - J C Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - M Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - V Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - V Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - C Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - W Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - R B Lozano
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, 07745, Germany
| | - P Everardo-Martínez
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico
| | - J Gómez-Valdés
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico
| | - H Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, MC, 4510, Mexico
| | | | - T Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - V Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil.,Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - R Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - L Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - M-C Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - V Acuña-Alonzo
- National Institute of Anthropology and History, Mexico City, MC, 6600, Mexico
| | - S Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, MC, 4510, Mexico
| | - C Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - G Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - G Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - F Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000000, Chile
| | - D Balding
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - D J Tobin
- The Charles Institute of Dermatology, University College Dublin, Dublin, Ireland
| | - S Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, University of the Chinese Academy of Sciences, Shanghai, 200031, China
| | - P Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France
| | - A Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China.,UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille, 13005, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| |
Collapse
|
48
|
Shi X, Wu J, Lang X, Wang C, Bai Y, Riley DG, Liu L, Ma X. Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PeerJ 2021; 9:e11122. [PMID: 33986980 PMCID: PMC8086576 DOI: 10.7717/peerj.11122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
Background Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation. Methods Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds. Results Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.
Collapse
Affiliation(s)
- Xiaolei Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Jianping Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Xia Lang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Cailian Wang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China.,Key Laboratory for Sheep, Goat, and Cattle Germplasm and Straw Feed in Gansu Province, Lanzhou, Gansu Province, China
| | - Yan Bai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - David Greg Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Lishan Liu
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xiaoming Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| |
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
Palmal S, Adhikari K, Mendoza-Revilla J, Fuentes-Guajardo M, Silva de Cerqueira CC, Bonfante B, Chacón-Duque JC, Sohail A, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, Hünemeier T, Ramallo V, Parolin ML, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Faux P, Ruiz-Linares A. Prediction of eye, hair and skin colour in Latin Americans. Forensic Sci Int Genet 2021; 53:102517. [PMID: 33865096 DOI: 10.1016/j.fsigen.2021.102517] [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] [Received: 11/30/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.
Collapse
Affiliation(s)
- Sagnik Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú; Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | | | - Betty Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anood Sohail
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Claudia Jaramillo
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan; GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City 6600, Mexico; Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | | | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil; Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | | | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Arica 1000000, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Pierre Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France.
| | - Andrés Ruiz-Linares
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China.
| |
Collapse
|