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Kerdoncuff E, Skov L, Patterson N, Zhao W, Lueng YY, Schellenberg GD, Smith JA, Dey S, Ganna A, Dey AB, Kardia SL, Lee J, Moorjani P. 50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580575. [PMID: 38405782 PMCID: PMC10888882 DOI: 10.1101/2024.02.15.580575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.
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Affiliation(s)
- Elise Kerdoncuff
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuk Yee Lueng
- Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Gerard D. Schellenberg
- Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Jennifer A. Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - AB Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jinkook Lee
- Department of Economics, and Center for Economic & Social Research, University of Southern California, Los Angeles, California, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
- Center for Computational Biology, University of California, Berkeley, United States of America
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2
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van der Valk T, Jensen A, Caillaud D, Guschanski K. Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas. BMC Ecol Evol 2024; 24:14. [PMID: 38273244 PMCID: PMC10811819 DOI: 10.1186/s12862-023-02195-x] [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: 06/30/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000-180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer's gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer's gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.
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Affiliation(s)
- Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- SciLifeLab, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Damien Caillaud
- Department of Anthropology, University of CA - Davis, Davis, California, USA
| | - Katerina Guschanski
- SciLifeLab, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Quilodrán CS, Rio J, Tsoupas A, Currat M. Past human expansions shaped the spatial pattern of Neanderthal ancestry. SCIENCE ADVANCES 2023; 9:eadg9817. [PMID: 37851812 PMCID: PMC10584333 DOI: 10.1126/sciadv.adg9817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.
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Affiliation(s)
| | - Jérémy Rio
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Alexandros Tsoupas
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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4
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Beichman AC, Robinson J, Lin M, Moreno-Estrada A, Nigenda-Morales S, Harris K. Evolution of the Mutation Spectrum Across a Mammalian Phylogeny. Mol Biol Evol 2023; 40:msad213. [PMID: 37770035 PMCID: PMC10566577 DOI: 10.1093/molbev/msad213] [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: 06/01/2023] [Revised: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023] Open
Abstract
Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
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Affiliation(s)
- Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Meixi Lin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Advanced Genomics Unit (UGA-LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Sergio Nigenda-Morales
- Department of Biological Sciences, California State University, San Marcos, San Marcos, CA, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Ragsdale AP, Thornton KR. Multiple Sources of Uncertainty Confound Inference of Historical Human Generation Times. Mol Biol Evol 2023; 40:msad160. [PMID: 37450583 PMCID: PMC10404577 DOI: 10.1093/molbev/msad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Wang et al. (2023) recently proposed an approach to infer the history of human generation intervals from changes in mutation profiles over time. As the relative proportions of different mutation types depend on the ages of parents, binning variants by the time they arose allows for the inference of changes in average paternal and maternal generation intervals. Applying this approach to published allele age estimates, Wang et al. (2023) inferred long-lasting sex differences in average generation times and surprisingly found that ancestral generation times of West African populations remained substantially higher than those of Eurasian populations extending tens of thousands of generations into the past. Here, we argue that the results and interpretations in Wang et al. (2023) are primarily driven by noise and biases in input data and a lack of validation using independent approaches for estimating allele ages. With the recent development of methods to reconstruct genome-wide gene genealogies, coalescence times, and allele ages, we caution that downstream analyses may be strongly influenced by uncharacterized biases in their output.
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Affiliation(s)
- Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin R Thornton
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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6
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Beichman AC, Robinson J, Lin M, Moreno-Estrada A, Nigenda-Morales S, Harris K. "Evolution of the mutation spectrum across a mammalian phylogeny". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543114. [PMID: 37398383 PMCID: PMC10312511 DOI: 10.1101/2023.05.31.543114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Little is known about how the spectrum and etiology of germline mutagenesis might vary among mammalian species. To shed light on this mystery, we quantify variation in mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k -mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clocklike mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these clocklike signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the mutation spectrum's phylogenetic signal when fit to non-context-dependent mutation spectrum data in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
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Affiliation(s)
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Meixi Lin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Advanced Genomics Unit (UGA-LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Sergio Nigenda-Morales
- Department of Biological Sciences, California State University, San Marcos, San Marcos CA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle WA
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7
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Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023; 40:msad085. [PMID: 37039557 PMCID: PMC10124870 DOI: 10.1093/molbev/msad085] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/07/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
| | | | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA
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8
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Gao Z, Zhang Y, Cramer N, Przeworski M, Moorjani P. Limited role of generation time changes in driving the evolution of the mutation spectrum in humans. eLife 2023; 12:e81188. [PMID: 36779395 PMCID: PMC10014080 DOI: 10.7554/elife.81188] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023] Open
Abstract
Recent studies have suggested that the human germline mutation rate and spectrum evolve rapidly. Variation in generation time has been linked to these changes, though its contribution remains unclear. We develop a framework to characterize temporal changes in polymorphisms within and between populations, while controlling for the effects of natural selection and biased gene conversion. Application to the 1000 Genomes Project dataset reveals multiple independent changes that arose after the split of continental groups, including a previously reported, transient elevation in TCC>TTC mutations in Europeans and novel signals of divergence in C>Gand T>A mutation rates among population samples. We also find a significant difference between groups sampled in and outside of Africa in old T>C polymorphisms that predate the out-of-Africa migration. This surprising signal is driven by TpG>CpG mutations and stems in part from mis-polarized CpG transitions, which are more likely to undergo recurrent mutations. Finally, by relating the mutation spectrum of polymorphisms to parental age effects on de novo mutations, we show that plausible changes in the generation time cannot explain the patterns observed for different mutation types jointly. Thus, other factors - genetic modifiers or environmental exposures - must have had a non-negligible impact on the human mutation landscape.
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Affiliation(s)
- Ziyue Gao
- Department of Genetics, University of Pennsylvania, Perelman School of MedicinePhiladelphiaUnited States
| | - Yulin Zhang
- Center for Computational Biology, University of California, BerkeleyBerkeleyUnited States
| | - Nathan Cramer
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
| | - Priya Moorjani
- Center for Computational Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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9
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Kreier F. Dads older than mums since dawn of humanity, study suggests. Nature 2023:10.1038/d41586-023-00076-3. [PMID: 36639449 DOI: 10.1038/d41586-023-00076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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10
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Wang RJ, Al-Saffar SI, Rogers J, Hahn MW. Human generation times across the past 250,000 years. SCIENCE ADVANCES 2023; 9:eabm7047. [PMID: 36608127 PMCID: PMC9821931 DOI: 10.1126/sciadv.abm7047] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The generation times of our recent ancestors can tell us about both the biology and social organization of prehistoric humans, placing human evolution on an absolute time scale. We present a method for predicting historical male and female generation times based on changes in the mutation spectrum. Our analyses of whole-genome data reveal an average generation time of 26.9 years across the past 250,000 years, with fathers consistently older (30.7 years) than mothers (23.2 years). Shifts in sex-averaged generation times have been driven primarily by changes to the age of paternity, although we report a substantial increase in female generation times in the recent past. We also find a large difference in generation times among populations, reaching back to a time when all humans occupied Africa.
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Affiliation(s)
- Richard J. Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Corresponding author.
| | - Samer I. Al-Saffar
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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11
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Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 mutational spectrum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.19.517207. [PMID: 36451887 PMCID: PMC9709787 DOI: 10.1101/2022.11.19.517207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single nucleotide mutations at four-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly two-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al (2022). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors-although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution, and suggests that human SARS-CoV-2 may be trending towards a mutation spectrum more similar to that of other animal sarbecoviruses.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Annabel C Beichman
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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12
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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13
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Castro e Silva MA, Ferraz T, Couto-Silva CM, Lemes RB, Nunes K, Comas D, Hünemeier T. Population Histories and Genomic Diversity of South American Natives. Mol Biol Evol 2022; 39:msab339. [PMID: 34875092 PMCID: PMC8789086 DOI: 10.1093/molbev/msab339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.
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Affiliation(s)
- Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Ferraz
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Cainã M Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Renan B Lemes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - David Comas
- Departament de Ciències, Institut de Biologia Evolutiva, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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