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Librado P. Reconstructing generation intervals over time. Nat Rev Genet 2024:10.1038/s41576-024-00766-2. [PMID: 39103589 DOI: 10.1038/s41576-024-00766-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Affiliation(s)
- Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
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2
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Beichman AC, Zhu L, Harris K. The Evolutionary Interplay of Somatic and Germline Mutation Rates. Annu Rev Biomed Data Sci 2024; 7:83-105. [PMID: 38669515 DOI: 10.1146/annurev-biodatasci-102523-104225] [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] [Indexed: 04/28/2024]
Abstract
Novel sequencing technologies are making it increasingly possible to measure the mutation rates of somatic cell lineages. Accurate germline mutation rate measurement technologies have also been available for a decade, making it possible to assess how this fundamental evolutionary parameter varies across the tree of life. Here, we review some classical theories about germline and somatic mutation rate evolution that were formulated using principles of population genetics and the biology of aging and cancer. We find that somatic mutation rate measurements, while still limited in phylogenetic diversity, seem consistent with the theory that selection to preserve the soma is proportional to life span. However, germline and somatic theories make conflicting predictions regarding which species should have the most accurate DNA repair. Resolving this conflict will require carefully measuring how mutation rates scale with time and cell division and achieving a better understanding of mutation rate pleiotropy among cell types.
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Affiliation(s)
- Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA;
| | - Luke Zhu
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Kelley Harris
- Computational Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA;
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3
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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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4
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Lynch M, Ali F, Lin T, Wang Y, Ni J, Long H. The divergence of mutation rates and spectra across the Tree of Life. EMBO Rep 2023; 24:e57561. [PMID: 37615267 PMCID: PMC10561183 DOI: 10.15252/embr.202357561] [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: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Farhan Ali
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
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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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6
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Moorjani P, Hellenthal G. Methods for Assessing Population Relationships and History Using Genomic Data. Annu Rev Genomics Hum Genet 2023; 24:305-332. [PMID: 37220313 PMCID: PMC11040641 DOI: 10.1146/annurev-genom-111422-025117] [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] [Indexed: 05/25/2023]
Abstract
Genetic data contain a record of our evolutionary history. The availability of large-scale datasets of human populations from various geographic areas and timescales, coupled with advances in the computational methods to analyze these data, has transformed our ability to use genetic data to learn about our evolutionary past. Here, we review some of the widely used statistical methods to explore and characterize population relationships and history using genomic data. We describe the intuition behind commonly used approaches, their interpretation, and important limitations. For illustration, we apply some of these techniques to genome-wide autosomal data from 929 individuals representing 53 worldwide populations that are part of the Human Genome Diversity Project. Finally, we discuss the new frontiers in genomic methods to learn about population history. In sum, this review highlights the power (and limitations) of DNA to infer features of human evolutionary history, complementing the knowledge gleaned from other disciplines, such as archaeology, anthropology, and linguistics.
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Affiliation(s)
- Priya Moorjani
- Department of Molecular and Cell Biology and Center for Computational Biology, University of California, Berkeley, California, USA;
| | - Garrett Hellenthal
- UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom;
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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: 2] [Impact Index Per Article: 2.0] [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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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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