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Çubukcu H, Kılınç GM. Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA. Mamm Genome 2024; 35:461-473. [PMID: 39028337 DOI: 10.1007/s00335-024-10053-4] [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: 03/22/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.
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Affiliation(s)
- Hande Çubukcu
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey.
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2
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Burt CH. Polygenic Indices (a.k.a. Polygenic Scores) in Social Science: A Guide for Interpretation and Evaluation. SOCIOLOGICAL METHODOLOGY 2024; 54:300-350. [PMID: 39091537 PMCID: PMC11293310 DOI: 10.1177/00811750241236482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Polygenic indices (PGI)-the new recommended label for polygenic scores (PGS) in social science-are genetic summary scales often used to represent an individual's liability for a disease, trait, or behavior based on the additive effects of measured genetic variants. Enthusiasm for linking genetic data with social outcomes and the inclusion of premade PGIs in social science datasets have facilitated increased uptake of PGIs in social science research-a trend that will likely continue. Yet, most social scientists lack the expertise to interpret and evaluate PGIs in social science research. Here, we provide a primer on PGIs for social scientists focusing on key concepts, unique statistical genetic considerations, and best practices in calculation, estimation, reporting, and interpretation. We summarize our recommended best practices as a checklist to aid social scientists in evaluating and interpreting studies with PGIs. We conclude by discussing the similarities between PGIs and standard social science scales and unique interpretative considerations.
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3
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Harris KD, Greenbaum G. DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data. Nucleic Acids Res 2024; 52:W54-W60. [PMID: 38742634 PMCID: PMC11223807 DOI: 10.1093/nar/gkae373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.
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Affiliation(s)
- Keith D Harris
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Givat Ram, 9190401 Jerusalem, Israel
| | - Gili Greenbaum
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Givat Ram, 9190401 Jerusalem, Israel
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4
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Benítez-Burraco A, Moran S. Editorial: The adaptive value of languages: non-linguistic causes of language diversity, volume II. Front Psychol 2024; 15:1387290. [PMID: 38510301 PMCID: PMC10951400 DOI: 10.3389/fpsyg.2024.1387290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
| | - Steven Moran
- Department of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Department of Anthropology, University of Miami, Coral Gables, FL, United States
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5
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Barouch A, Mathov Y, Meshorer E, Yakir B, Carmel L. Reconstructing DNA methylation maps of ancient populations. Nucleic Acids Res 2024; 52:1602-1612. [PMID: 38261973 PMCID: PMC10939417 DOI: 10.1093/nar/gkad1232] [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: 01/11/2023] [Revised: 12/09/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Studying premortem DNA methylation from ancient DNA (aDNA) provides a proxy for ancient gene activity patterns, and hence valuable information on evolutionary changes in gene regulation. Due to statistical limitations, current methods to reconstruct aDNA methylation maps are constrained to high-coverage shotgun samples, which comprise a small minority of available ancient samples. Most samples are sequenced using in-situ hybridization capture sequencing which targets a predefined set of genomic positions. Here, we develop methods to reconstruct aDNA methylation maps of samples that were not sequenced using high-coverage shotgun sequencing, by way of pooling together individuals to obtain a DNA methylation map that is characteristic of a population. We show that the resulting DNA methylation maps capture meaningful biological information and allow for the detection of differential methylation across populations. We offer guidelines on how to carry out comparative studies involving ancient populations, and how to control the rate of falsely discovered differentially methylated regions. The ability to reconstruct DNA methylation maps of past populations allows for the development of a whole new frontier in paleoepigenetic research, tracing DNA methylation changes throughout human history, using data from thousands of ancient samples.
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Affiliation(s)
- Arielle Barouch
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yoav Mathov
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Benjamin Yakir
- Department of Statistics and Data Science, The Hebrew University of Jerusalem, Jerusalem 9190500, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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7
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Piszczek L, Kaczanowska J, Haubensak W. Towards correlative archaeology of the human mind. Biol Chem 2024; 405:5-12. [PMID: 37819768 PMCID: PMC10687516 DOI: 10.1515/hsz-2023-0199] [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: 05/01/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
Retracing human cognitive origins started out at the systems level with the top-down interpretation of archaeological records spanning from man-made artifacts to endocasts of ancient skulls. With emerging evolutionary genetics and organoid technologies, it is now possible to deconstruct evolutionary processes on a molecular/cellular level from the bottom-up by functionally testing archaic alleles in experimental models. The current challenge is to complement these approaches with novel strategies that allow a holistic reconstruction of evolutionary patterns across human cognitive domains. We argue that computational neuroarcheology can provide such a critical mesoscale framework at the brain network-level, linking molecular/cellular (bottom-up) to systems (top-down) level data for the correlative archeology of the human mind.
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Affiliation(s)
- Lukasz Piszczek
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
| | | | - Wulf Haubensak
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, A-1030Vienna, Austria
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8
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Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
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Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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9
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Anastasiadou K, Silva M, Booth T, Speidel L, Audsley T, Barrington C, Buckberry J, Fernandes D, Ford B, Gibson M, Gilardet A, Glocke I, Keefe K, Kelly M, Masters M, McCabe J, McIntyre L, Ponce P, Rowland S, Ruiz Ventura J, Swali P, Tait F, Walker D, Webb H, Williams M, Witkin A, Holst M, Loe L, Armit I, Schulting R, Skoglund P. Detection of chromosomal aneuploidy in ancient genomes. Commun Biol 2024; 7:14. [PMID: 38212558 PMCID: PMC10784527 DOI: 10.1038/s42003-023-05642-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.
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Affiliation(s)
- Kyriaki Anastasiadou
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
| | - Marina Silva
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Booth
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Leo Speidel
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
- Genetics Institute, University College London, London, United Kingdom
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Jo Buckberry
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | | | - Ben Ford
- Oxford Archaeology, Oxford, United Kingdom
| | | | - Alexandre Gilardet
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Isabelle Glocke
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Katie Keefe
- York Osteoarchaeology, York, United Kingdom
- On-Site Archaeology, York, United Kingdom
| | - Monica Kelly
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mackenzie Masters
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Jesse McCabe
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Paola Ponce
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | | | - Jordi Ruiz Ventura
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Pooja Swali
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frankie Tait
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Helen Webb
- Oxford Archaeology, Oxford, United Kingdom
| | - Mia Williams
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Malin Holst
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Louise Loe
- Oxford Archaeology, Oxford, United Kingdom
| | - Ian Armit
- Department of Archaeology, University of York, York, United Kingdom
| | - Rick Schulting
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Pontus Skoglund
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
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10
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Yang S, Sun X, Jin L, Zhang M. Inferring language dispersal patterns with velocity field estimation. Nat Commun 2024; 15:190. [PMID: 38167834 PMCID: PMC10761963 DOI: 10.1038/s41467-023-44430-5] [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: 06/05/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Reconstructing the spatial evolution of languages can deepen our understanding of the demic diffusion and cultural spread. However, the phylogeographic approach that is frequently used to infer language dispersal patterns has limitations, primarily because the phylogenetic tree cannot fully explain the language evolution induced by the horizontal contact among languages, such as borrowing and areal diffusion. Here, we introduce the language velocity field estimation, which does not rely on the phylogenetic tree, to infer language dispersal trajectories and centre. Its effectiveness and robustness are verified through both simulated and empirical validations. Using language velocity field estimation, we infer the dispersal patterns of four agricultural language families and groups, encompassing approximately 700 language samples. Our results show that the dispersal trajectories of these languages are primarily compatible with population movement routes inferred from ancient DNA and archaeological materials, and their dispersal centres are geographically proximate to ancient homelands of agricultural or Neolithic cultures. Our findings highlight that the agricultural languages dispersed alongside the demic diffusions and cultural spreads during the past 10,000 years. We expect that language velocity field estimation could aid the spatial analysis of language evolution and further branch out into the studies of demographic and cultural dynamics.
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Affiliation(s)
- Sizhe Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaoru Sun
- Human Phenome Institute, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Human Phenome Institute, Fudan University, Shanghai, 200438, China.
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, 200433, China.
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, 200433, China.
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11
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Gao Z. Unveiling recent and ongoing adaptive selection in human populations. PLoS Biol 2024; 22:e3002469. [PMID: 38236800 PMCID: PMC10796035 DOI: 10.1371/journal.pbio.3002469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
Genome-wide scans for signals of selection have become a routine part of the analysis of population genomic variation datasets and have resulted in compelling evidence of selection during recent human evolution. This Essay spotlights methodological innovations that have enabled the detection of selection over very recent timescales, even in contemporary human populations. By harnessing large-scale genomic and phenotypic datasets, these new methods use different strategies to uncover connections between genotype, phenotype, and fitness. This Essay outlines the rationale and key findings of each strategy, discusses challenges in interpretation, and describes opportunities to improve detection and understanding of ongoing selection in human populations.
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Affiliation(s)
- Ziyue Gao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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12
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Di Santo LN, Quilodrán CS, Currat M. Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses. Mol Biol Evol 2023; 40:msad252. [PMID: 37992125 PMCID: PMC10715198 DOI: 10.1093/molbev/msad252] [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: 04/18/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.
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Affiliation(s)
- Lionel N Di Santo
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
| | | | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva CH-1205
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13
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand CM, Rinker DC, Siemann JK, McMahon DG, Capra JA. Archaic Introgression Shaped Human Circadian Traits. Genome Biol Evol 2023; 15:evad203. [PMID: 38095367 PMCID: PMC10719892 DOI: 10.1093/gbe/evad203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology and whether archaic introgression adaptively contributed to human chronotypes remain unknown. Here, we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, and RORC) and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among expression quantitative trait loci for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, SanFrancisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, SanFrancisco, California, USA
| | - David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Justin K Siemann
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Douglas G McMahon
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, SanFrancisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, SanFrancisco, California, USA
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14
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Guevara E, Gopalan S, Massey DJ, Adegboyega M, Zhou W, Solis A, Anaya AD, Churchill SE, Feldblum J, Lawler RR. Getting it right: Teaching undergraduate biology to undermine racial essentialism. Biol Methods Protoc 2023; 8:bpad032. [PMID: 38023347 PMCID: PMC10674104 DOI: 10.1093/biomethods/bpad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students' racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students' racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and the misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographical distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students' endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.
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Affiliation(s)
- Elaine Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Dashiell J Massey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Mayowa Adegboyega
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Wen Zhou
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
- Department of Evolutionary Anthropology, Duke Kunshan University, Kunshan, Jiangsu 215316, China
| | - Alma Solis
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Alisha D Anaya
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Steven E Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Joseph Feldblum
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, United States
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15
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Miga KH, Eichler EE. Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes. Am J Hum Genet 2023; 110:1832-1840. [PMID: 37922882 PMCID: PMC10645551 DOI: 10.1016/j.ajhg.2023.09.011] [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: 06/28/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
Advances in long-read sequencing and assembly now mean that individual labs can generate phased genomes that are more accurate and more contiguous than the original human reference genome. With declining costs and increasing democratization of technology, we suggest that complete genome assemblies, where both parental haplotypes are phased telomere to telomere, will become standard in human genetics. Soon, even in clinical settings where rigorous sample-handling standards must be met, affected individuals could have reference-grade genomes fully sequenced and assembled in just a few hours given advances in technology, computational processing, and annotation. Complete genetic variant discovery will transform how we map, catalog, and associate variation with human disease and fundamentally change our understanding of the genetic diversity of all humans.
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Affiliation(s)
- Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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16
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Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023; 23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
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Affiliation(s)
- Roberta Davidson
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew P Williams
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Biology Department, The Pennsylvania State University, Pennsylvania, USA
| | - Xavier Roca-Rada
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kalina Kassadjikova
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
| | - Raymond Tobler
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
- UCSC Genomics Institute, University of California, California, USA
| | - Bastien Llamas
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
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17
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Sun X, Liu YC, Tiunov MP, Gimranov DO, Zhuang Y, Han Y, Driscoll CA, Pang Y, Li C, Pan Y, Velasco MS, Gopalakrishnan S, Yang RZ, Li BG, Jin K, Xu X, Uphyrkina O, Huang Y, Wu XH, Gilbert MTP, O'Brien SJ, Yamaguchi N, Luo SJ. Ancient DNA reveals genetic admixture in China during tiger evolution. Nat Ecol Evol 2023; 7:1914-1929. [PMID: 37652999 DOI: 10.1038/s41559-023-02185-8] [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: 09/14/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.
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Affiliation(s)
- Xin Sun
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Dmitry O Gimranov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Ural Federal University, Yekaterinburg, Russia
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Han
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Carlos A Driscoll
- Section of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, MD, USA
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yan Pan
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Marcela Sandoval Velasco
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui-Zheng Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kun Jin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, China
| | - Xiao-Hong Wu
- School of Archaeology and Museology, Peking University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia.
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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18
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023; 40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [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: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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Affiliation(s)
- Md Ruhul Amin
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mahmudul Hasan
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Sandipan Paul Arnab
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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19
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Tretmanis JM, Jay F, Avila-Árcos MC, Huerta-Sanchez E. Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560049. [PMID: 37808674 PMCID: PMC10557694 DOI: 10.1101/2023.09.28.560049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.
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Affiliation(s)
| | - Flora Jay
- Interdisciplinary Laboratory of Numerical Sciences, Université Paris-Saclay
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20
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand C, Rinker D, Siemann J, McMahon D, Capra JA. Archaic Introgression Shaped Human Circadian Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527061. [PMID: 36778254 PMCID: PMC9915721 DOI: 10.1101/2023.02.03.527061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Introduction When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown. Results Here we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. Conclusions These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | | | - Colin Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University
| | - Justin Siemann
- Department of Biological Sciences, Vanderbilt University
| | | | - John A. Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
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21
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes. PLoS Genet 2023; 19:e1010931. [PMID: 37676865 PMCID: PMC10508636 DOI: 10.1371/journal.pgen.1010931] [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: 01/22/2023] [Revised: 09/19/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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22
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Gospodarska E, Ghosh Dastidar R, Carlberg C. Intervention Approaches in Studying the Response to Vitamin D 3 Supplementation. Nutrients 2023; 15:3382. [PMID: 37571318 PMCID: PMC10420637 DOI: 10.3390/nu15153382] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Vitamin D intervention studies are designed to evaluate the impact of the micronutrient vitamin D3 on health and disease. The appropriate design of studies is essential for their quality, successful execution, and interpretation. Randomized controlled trials (RCTs) are considered the "gold standard" for intervention studies. However, the most recent large-scale (up to 25,000 participants), long-term RCTs involving vitamin D3 did not provide any statistically significant primary results. This may be because they are designed similarly to RCTs of a therapeutic drug but not of a nutritional compound and that only a limited set of parameters per individual were determined. We propose an alternative concept using the segregation of study participants into different groups of responsiveness to vitamin D3 supplementation and in parallel measuring a larger set of genome-wide parameters over multiple time points. This is in accordance with recently developed mechanistic modeling approaches that do not require a large number of study participants, as in the case of statistical modeling of the results of a RCT. Our experience is based on the vitamin D intervention trials VitDmet, VitDbol, and VitDHiD, which allowed us to distinguish the study participants into high, mid, and low vitamin D responders. In particular, investigating the vulnerable group of low vitamin D responders will provide future studies with more conclusive results both on the clinical and molecular benefits of vitamin D3 supplementation. In conclusion, our approach suggests a paradigm shift towards detailed investigations of transcriptome and epigenome-wide parameters of a limited set of individuals, who, due to a longitudinal design, can act as their own controls.
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Affiliation(s)
- Emilia Gospodarska
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, PL-10-748 Olsztyn, Poland; (E.G.); (R.G.D.)
| | - Ranjini Ghosh Dastidar
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, PL-10-748 Olsztyn, Poland; (E.G.); (R.G.D.)
| | - Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, PL-10-748 Olsztyn, Poland; (E.G.); (R.G.D.)
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
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23
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Tobler R, Souilmi Y, Huber CD, Bean N, Turney CSM, Grey ST, Cooper A. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proc Natl Acad Sci U S A 2023; 120:e2213061120. [PMID: 37220274 PMCID: PMC10235988 DOI: 10.1073/pnas.2213061120] [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: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 05/25/2023] Open
Abstract
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
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Affiliation(s)
- Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Environment Institute, The University of Adelaide, Adelaide, SA5005, Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Nigel Bean
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA5005, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Chris S. M. Turney
- Division of Research, University of Technology Sydney, Ultimo, NSW2007, Australia
| | - Shane T. Grey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW2052, Australia
- Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW2010, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Blue Sky Genetics, Ashton, SA5137, Australia
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dos Santos ALC, Sullasi HSL, Gokcumen O, Lindo J, DeGiorgio M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:703-714. [PMID: 39081397 PMCID: PMC11288623 DOI: 10.1002/ajpa.24673] [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] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/15/2022] [Indexed: 08/02/2024]
Abstract
Objectives Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. Materials and Methods The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP. Results We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. Discussion Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
- Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
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Affiliation(s)
- Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, Centre National de la Recherche Scientifique (CNRS) UMR, 2000, Paris, France
| | - Jeremy Choin
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, Centre National de la Recherche Scientifique (CNRS) UMR, 2000, Paris, France. .,Chair of Human Genomics and Evolution, Collège de France, Paris, France.
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26
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Carlberg C. Nutrigenomics in the context of evolution. Redox Biol 2023; 62:102656. [PMID: 36933390 PMCID: PMC10036735 DOI: 10.1016/j.redox.2023.102656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.
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Affiliation(s)
- Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Juliana Tuwima 10, PL-10748, Olsztyn, Poland; School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211, Kuopio, Finland.
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27
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Kerner G, Neehus AL, Philippot Q, Bohlen J, Rinchai D, Kerrouche N, Puel A, Zhang SY, Boisson-Dupuis S, Abel L, Casanova JL, Patin E, Laval G, Quintana-Murci L. Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe. CELL GENOMICS 2023; 3:100248. [PMID: 36819665 PMCID: PMC9932995 DOI: 10.1016/j.xgen.2022.100248] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/24/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.
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Affiliation(s)
- Gaspard Kerner
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nacim Kerrouche
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, New York, NY 10065, USA
- Department of Pediatrics, Necker Hospital for Sick Children, 75015 Paris, France
| | - Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Guillaume Laval
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
- Collège de France, Chair of Human Genomics and Evolution, 75005 Paris, France
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525077. [PMID: 36711923 PMCID: PMC9882349 DOI: 10.1101/2023.01.22.525077] [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: 01/24/2023]
Abstract
f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Current advances in primate genomics: novel approaches for understanding evolution and disease. Nat Rev Genet 2023; 24:314-331. [PMID: 36599936 DOI: 10.1038/s41576-022-00554-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.
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30
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Söylev A, Çokoglu SS, Koptekin D, Alkan C, Somel M. CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PLoS Comput Biol 2022; 18:e1010788. [PMID: 36516232 PMCID: PMC9873172 DOI: 10.1371/journal.pcbi.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/24/2023] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.
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Affiliation(s)
- Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- * E-mail: (AS); (MS)
| | | | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biology, Middle East Technical University, Ankara, Turkey
- * E-mail: (AS); (MS)
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31
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Caliebe A, Tekola‐Ayele F, Darst BF, Wang X, Song YE, Gui J, Sebro RA, Balding DJ, Saad M, Dubé M. Including diverse and admixed populations in genetic epidemiology research. Genet Epidemiol 2022; 46:347-371. [PMID: 35842778 PMCID: PMC9452464 DOI: 10.1002/gepi.22492] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
The inclusion of ancestrally diverse participants in genetic studies can lead to new discoveries and is important to ensure equitable health care benefit from research advances. Here, members of the Ethical, Legal, Social, Implications (ELSI) committee of the International Genetic Epidemiology Society (IGES) offer perspectives on methods and analysis tools for the conduct of inclusive genetic epidemiology research, with a focus on admixed and ancestrally diverse populations in support of reproducible research practices. We emphasize the importance of distinguishing socially defined population categorizations from genetic ancestry in the design, analysis, reporting, and interpretation of genetic epidemiology research findings. Finally, we discuss the current state of genomic resources used in genetic association studies, functional interpretation, and clinical and public health translation of genomic findings with respect to diverse populations.
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Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and StatisticsKiel University and University Hospital Schleswig‐HolsteinKielGermany
| | - Fasil Tekola‐Ayele
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMarylandUSA
| | - Burcu F. Darst
- Center for Genetic EpidemiologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Xuexia Wang
- Department of MathematicsUniversity of North TexasDentonTexasUSA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth CollegeOne Medical Center Dr.LebanonNew HampshireUSA
| | | | - David J. Balding
- Melbourne Integrative Genomics, Schools of BioSciences and of Mathematics & StatisticsUniversity of MelbourneMelbourneAustralia
| | - Mohamad Saad
- Qatar Computing Research InstituteHamad Bin Khalifa UniversityDohaQatar
- Neuroscience Research Center, Faculty of Medical SciencesLebanese UniversityBeirutLebanon
| | - Marie‐Pierre Dubé
- Department of Medicine, and Social and Preventive MedicineUniversité de MontréalMontréalQuébecCanada
- Beaulieu‐Saucier Pharmacogenomcis CentreMontreal Heart InstituteMontrealCanada
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Vitamin D in the Context of Evolution. Nutrients 2022; 14:nu14153018. [PMID: 35893872 PMCID: PMC9332464 DOI: 10.3390/nu14153018] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 12/12/2022] Open
Abstract
For at least 1.2 billion years, eukaryotes have been able to synthesize sterols and, therefore, can produce vitamin D when exposed to UV-B. Vitamin D endocrinology was established some 550 million years ago in animals, when the high-affinity nuclear receptor VDR (vitamin D receptor), transport proteins and enzymes for vitamin D metabolism evolved. This enabled vitamin D to regulate, via its target genes, physiological process, the first of which were detoxification and energy metabolism. In this way, vitamin D was enabled to modulate the energy-consuming processes of the innate immune system in its fight against microbes. In the evolving adaptive immune system, vitamin D started to act as a negative regulator of growth, which prevents overboarding reactions of T cells in the context of autoimmune diseases. When, some 400 million years ago, species left the ocean and were exposed to gravitation, vitamin D endocrinology took over the additional role as a major regulator of calcium homeostasis, being important for a stable skeleton. Homo sapiens evolved approximately 300,000 years ago in East Africa and had adapted vitamin D endocrinology to the intensive exposure of the equatorial sun. However, when some 75,000 years ago, when anatomically modern humans started to populate all continents, they also reached regions with seasonally low or no UV-B, i.e., and under these conditions vitamin D became a vitamin.
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Tournebize R, Chu G, Moorjani P. Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals. PLoS Genet 2022; 18:e1010243. [PMID: 35737729 PMCID: PMC9223333 DOI: 10.1371/journal.pgen.1010243] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
Founder events play a critical role in shaping genetic diversity, fitness and disease risk in a population. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods require large sample sizes or phased genomes. Thus, we developed ASCEND that measures the correlation in allele sharing between pairs of individuals across the genome to infer the age and strength of founder events. We show that ASCEND can reliably estimate the parameters of founder events under a range of demographic scenarios. We then apply ASCEND to two species with contrasting evolutionary histories: ~460 worldwide human populations and ~40 modern dog breeds. In humans, we find that over half of the analyzed populations have evidence for recent founder events, associated with geographic isolation, modes of sustenance, or cultural practices such as endogamy. Notably, island populations have lower population sizes than continental groups and most hunter-gatherer, nomadic and indigenous groups have evidence of recent founder events. Many present-day groups––including Native Americans, Oceanians and South Asians––have experienced more extreme founder events than Ashkenazi Jews who have high rates of recessive diseases due their known history of founder events. Using ancient genomes, we show that the strength of founder events differs markedly across geographic regions and time––with three major founder events related to the peopling of Americas and a trend in decreasing strength of founder events in Europe following the Neolithic transition and steppe migrations. In dogs, we estimate extreme founder events in most breeds that occurred in the last 25 generations, concordant with the establishment of many dog breeds during the Victorian times. Our analysis highlights a widespread history of founder events in humans and dogs and elucidates some of the demographic and cultural practices related to these events. A founder event occurs when small numbers of ancestral individuals give rise to a large fraction of the population. Founder events reduce genetic variation and increase the risk of recessive diseases. Despite their importance in evolutionary and disease studies, we still only have a limited comprehension of their prevalence and properties in humans and other species, as most existing methods require large sample sizes or phased genomes. Here, we present a flexible method, ASCEND, to infer the timing and the strength of founder events that is suitable for sparse datasets with few samples or limited coverage. ASCEND provides reliable estimates across a wide range of demographic scenarios. By applying it to data from two species (humans and dogs), we document a widespread history of recent founder events in both species and provide insights about the demographic processes related to these events. Our analysis helps to identify groups with strong founder events that should be prioritized for future studies as they offer a unique opportunity for biological discovery and reducing disease burden through mapping of recessive disease-causing genes and pathways, as previously shown in studies of Ashkenazi Jews and Finns.
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Affiliation(s)
- Rémi Tournebize
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RT); (PM)
| | - Gillian Chu
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, California, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RT); (PM)
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Choin J, Quintana-Murci L. Paleogenomics: The demographic past of prehistoric Europeans. Curr Biol 2022; 32:R535-R538. [PMID: 35671731 DOI: 10.1016/j.cub.2022.04.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ancient DNA provides answers to long-standing debates about past human history. New work using demographic modeling on ancient genomes documents the nature and timing of the demographic processes - population size changes, divergences and admixture - that took place in prehistoric Europe.
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Affiliation(s)
- Jeremy Choin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Unit of Human Evolutionary Genetics, F-75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, F-75005 Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Unit of Human Evolutionary Genetics, F-75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, F-75005 Paris, France.
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35
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Fleskes RE, Bader AC, Tsosie KS, Wagner JK, Claw KG, Garrison NA. Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives. Annu Rev Genomics Hum Genet 2022; 23:627-652. [PMID: 35537469 DOI: 10.1146/annurev-genom-120621-090239] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities, such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Raquel E Fleskes
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA;
| | - Alyssa C Bader
- Department of Anthropology, University of Colorado Boulder, Boulder, Colorado, USA; .,Sealaska Heritage Institute, Juneau, Alaska, USA
| | - Krystal S Tsosie
- Native BioData Consortium, Eagle Butte, South Dakota, USA; .,College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer K Wagner
- School of Engineering Design, Technology, and Professional Programs; Institute for Computational and Data Sciences; and Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Katrina G Claw
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, Institute for Precision Health, and Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, California, USA;
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36
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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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37
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Török T, Maár K, Varga IG, Juhász Z. A new linear combination method of haplogroup distribution central vectors to model population admixtures. Mol Genet Genomics 2022; 297:889-901. [PMID: 35411488 PMCID: PMC9130205 DOI: 10.1007/s00438-022-01888-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/19/2022] [Indexed: 11/26/2022]
Abstract
We introduce a novel population genetic approach suitable to model the origin and relationships of populations, using new computation methods analyzing Hg frequency distributions. Hgs were selected into groups which show correlated frequencies in subsets of populations, based on the assumption that correlations were established in ancient separation, migration and admixture processes. Populations are defined with this universal Hg database, then using unsupervised artificial intelligence, central vectors (CVs) are determined from local condensations of the Hg-distribution vectors in the multidimensional point system. Populations are clustered according to their proximity to CVs. We show that CVs can be regarded as approximations of ancient populations and real populations can be modeled as weighted linear combinations of the CVs using a new linear combination algorithm based on a gradient search for the weights. The efficacy of the method is demonstrated by comparing Copper Age populations of the Carpathian Basin to Middle Age ones and modern Hungarians. Our analysis reveals significant population continuity since the Middle Ages, and the presence of a substrate component since the Copper Age.
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Affiliation(s)
- Tibor Török
- Department of Genetics, University of Szeged, Szeged, Hungary
- Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary
| | - Kitti Maár
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - István Gergely Varga
- Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Zoltán Juhász
- Institute of Technical Physics and Materials Science, Centre for Energy Research, Budapest, Hungary.
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38
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Biddanda A, Steinrücken M, Novembre J. Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples. Genetics 2022; 221:6549526. [PMID: 35294015 PMCID: PMC9245597 DOI: 10.1093/genetics/iyac038] [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: 01/10/2022] [Accepted: 02/06/2022] [Indexed: 11/13/2022] Open
Abstract
Archaeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the non-random association of genetic variants at different loci (i.e., linkage disequilibrium, LD). This may be in part because basic properties of LD in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: 1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; 2) The product of the LD coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and 3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.
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Affiliation(s)
- Arjun Biddanda
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthias Steinrücken
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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39
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Lee M, Lindo J, Rilling JK. Exploring gene-culture coevolution in humans by inferring neuroendophenotypes: A case study of the oxytocin receptor gene and cultural tightness. GENES, BRAIN, AND BEHAVIOR 2022; 21:e12783. [PMID: 35044077 PMCID: PMC8917075 DOI: 10.1111/gbb.12783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 01/17/2023]
Abstract
The gene-culture coevolution (GCC) framework has gained increasing prominence in the social and biological sciences. While most studies on human GCC concern the evolution of low-level physiological traits, attempts have also been made to apply GCC to complex human traits, including social behavior and cognition. One major methodological challenge in this endeavor is to reconstruct a specific biological pathway between the implicated genes and their distal phenotypes. Here, we introduce a novel approach that combines data on population genetics and expression quantitative trait loci to infer the specific intermediate phenotypes of genes in the brain. We suggest that such "neuroendophenotypes" will provide more detailed mechanistic insights into the GCC process. We present a case study where we explored a GCC dynamics between the oxytocin receptor gene (OXTR) and cultural tightness-looseness. By combining data from the 1000 Genomes project and the Gene-Tissue-Expression project (GTEx), we estimated and compared OXTR expression in 10 brain regions across five human superpopulations. We found that OXTR expression in the anterior cingulate cortex (ACC) was highly variable across populations, and this variation correlated with cultural tightness and socio-ecological threats worldwide. The mediation models also suggested possible GCC dynamics where the increased OXTR expression in the ACC mediates or emerges from the tight culture and higher socio-ecological threats. Formal selection scans further confirmed that OXTR alleles linked to enhanced receptor expression in the ACC underwent positive selection in East Asian countries with tighter social norms. We discuss the implications of our method in human GCC research.
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Affiliation(s)
- Minwoo Lee
- Department of Anthropology, Emory UniversityAtlantaGeorgiaUSA
| | - John Lindo
- Department of Anthropology, Emory UniversityAtlantaGeorgiaUSA
| | - James K. Rilling
- Department of Anthropology, Emory UniversityAtlantaGeorgiaUSA,Department of Psychiatry and Behavioral Science, Emory UniversityAtlantaGeorgiaUSA,Center for Behavioral Neuroscience, Emory UniversityAtlantaGeorgiaUSA,Yerkes National Primate Research Center, Emory UniversityAtlantaGeorgiaUSA,Center for Translational Social Neuroscience, Emory UniversityAtlantaGeorgiaUSA
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40
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Vitamin D and Pigmented Skin. Nutrients 2022; 14:nu14020325. [PMID: 35057504 PMCID: PMC8781604 DOI: 10.3390/nu14020325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 01/27/2023] Open
Abstract
The default supply of vitamin D3 to humans is its endogenous production in UV-B-exposed skin [...].
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41
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Pathak AK, Sukhavasi K, Marnetto D, Chaubey G, Pandey AK. Human population genomics approach in food metabolism. FUTURE FOODS 2022. [DOI: 10.1016/b978-0-323-91001-9.00033-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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42
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Mathieson I, Terhorst J. Direct detection of natural selection in Bronze Age Britain. Genome Res 2022; 32:2057-2067. [PMID: 36316157 PMCID: PMC9808619 DOI: 10.1101/gr.276862.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/29/2022] [Indexed: 11/04/2022]
Abstract
We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, Michigan 48109, USA
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43
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Laval G, Patin E, Boutillier P, Quintana-Murci L. Sporadic occurrence of recent selective sweeps from standing variation in humans as revealed by an approximate Bayesian computation approach. Genetics 2021; 219:6377789. [PMID: 34849862 DOI: 10.1093/genetics/iyab161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
During their dispersals over the last 100,000 years, modern humans have been exposed to a large variety of environments, resulting in genetic adaptation. While genome-wide scans for the footprints of positive Darwinian selection have increased knowledge of genes and functions potentially involved in human local adaptation, they have globally produced evidence of a limited contribution of selective sweeps in humans. Conversely, studies based on machine learning algorithms suggest that recent sweeps from standing variation are widespread in humans, an observation that has been recently questioned. Here, we sought to formally quantify the number of recent selective sweeps in humans, by leveraging approximate Bayesian computation and whole-genome sequence data. Our computer simulations revealed suitable ABC estimations, regardless of the frequency of the selected alleles at the onset of selection and the completion of sweeps. Under a model of recent selection from standing variation, we inferred that an average of 68 (from 56 to 79) and 140 (from 94 to 198) sweeps occurred over the last 100,000 years of human history, in African and Eurasian populations, respectively. The former estimation is compatible with human adaptation rates estimated since divergence with chimps, and reveals numbers of sweeps per generation per site in the range of values estimated in Drosophila. Our results confirm the rarity of selective sweeps in humans and show a low contribution of sweeps from standing variation to recent human adaptation.
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Affiliation(s)
- Guillaume Laval
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Pierre Boutillier
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France.,Human Genomics and Evolution, Collège de France, 75005 Paris, France
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44
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Colbran LL, Johnson MR, Mathieson I, Capra JA. Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment. Genome Biol Evol 2021; 13:evab237. [PMID: 34718543 PMCID: PMC8576593 DOI: 10.1093/gbe/evab237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2021] [Indexed: 12/16/2022] Open
Abstract
As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple noncoding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, for example, at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2,999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.
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Affiliation(s)
- Laura L Colbran
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA
| | - Maya R Johnson
- School for Science and Math at Vanderbilt, Vanderbilt University, USA
- Department of Computer Science, Bryn Mawr College, Pennsylvania, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA
- Department of Biological Sciences, Vanderbilt University, USA
- Department of Biomedical Informatics, Vanderbilt University, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
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45
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Cox SL, Moots HM, Stock JT, Shbat A, Bitarello BD, Nicklisch N, Alt KW, Haak W, Rosenstock E, Ruff CB, Mathieson I. Predicting skeletal stature using ancient
DNA. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2021. [PMCID: PMC9298243 DOI: 10.1002/ajpa.24426] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samantha L. Cox
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Physical Anthropology Section, Penn Museum University of Pennsylvania Philadelphia Pennsylvania USA
| | - Hannah M. Moots
- Department of Anthropology Stanford University Stanford California USA
| | - Jay T. Stock
- Department of Anthropology Western University London Ontario Canada
- Department of Archaeology Max Planck Institute for the Science of Human History Jena Germany
| | - Andrej Shbat
- Institute of Anatomy, First Faculty of Medicine Charles University Prague Czech Republic
| | - Bárbara D. Bitarello
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Kurt W. Alt
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Wolfgang Haak
- Department of Archaeogenetics Max Planck Institute for the Science of Human History Jena Germany
| | - Eva Rosenstock
- Bonn Center for ArchaeoSciences Institut für Archäologie und Kulturanthropologie, Universität Bonn Bonn Germany
| | - Christopher B. Ruff
- Center for Functional Anatomy and Evolution Johns Hopkins University School of Medicine Baltimore Maryland USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
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46
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Truelsen D, Freire-Aradas A, Nazari M, Aliferi A, Ballard D, Phillips C, Morling N, Pereira V, Børsting C. Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the Illumina MiSeq. Sci Rep 2021; 11:21040. [PMID: 34702940 PMCID: PMC8548529 DOI: 10.1038/s41598-021-99933-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/29/2021] [Indexed: 11/08/2022] Open
Abstract
Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.
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Affiliation(s)
- D Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Nazari
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - A Aliferi
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - V Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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47
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Liu Y, Mao X, Krause J, Fu Q. Insights into human history from the first decade of ancient human genomics. Science 2021; 373:1479-1484. [PMID: 34554811 DOI: 10.1126/science.abi8202] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
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48
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Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat Commun 2021; 12:5425. [PMID: 34521843 PMCID: PMC8440622 DOI: 10.1038/s41467-021-25289-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.
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49
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Ferreira JC, Alshamali F, Montinaro F, Cavadas B, Torroni A, Pereira L, Raveane A, Fernandes V. Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. Genome Biol Evol 2021; 13:6364187. [PMID: 34480555 PMCID: PMC8435661 DOI: 10.1093/gbe/evab194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.
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Affiliation(s)
- Joana C Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy.,Laboratory of Haematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Veronica Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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Herd P, Mills MC, Dowd JB. Reconstructing Sociogenomics Research: Dismantling Biological Race and Genetic Essentialism Narratives. JOURNAL OF HEALTH AND SOCIAL BEHAVIOR 2021; 62:419-435. [PMID: 34100668 DOI: 10.1177/00221465211018682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We detail the implications of sociogenomics for social determinants research. We focus on education and race because of how early twentieth-century scientific eugenic thinking facilitated a range of racist and eugenic policies, most of which helped justify and pattern racial and educational morbidity and mortality disparities that remain today, and are central to sociological research. Consequently, we detail the implications of sociogenomics research by unpacking key controversies and opportunities in sociogenomics as they pertain to the understanding of racial and educational inequalities. We clarify why race is not a valid biological or genetic construct, the ways that environments powerfully shape genetic influence, and risks linked to this field of research. We argue that sociologists can usefully engage in genetics research, a domain dominated by psychologists and behaviorists who, given their focus on individuals, have mostly not examined the role of history and social structure in shaping genetic influence.
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