1
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Hahn MW, Peña-Garcia Y, Wang RJ. The 'faulty male' hypothesis for sex-biased mutation and disease. Curr Biol 2023; 33:R1166-R1172. [PMID: 37989088 DOI: 10.1016/j.cub.2023.09.028] [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] [Indexed: 11/23/2023]
Abstract
Biological differences between males and females lead to many differences in physiology, disease, and overall health. One of the most prominent disparities is in the number of germline mutations passed to offspring: human males transmit three times as many mutations as do females. While the classic explanation for this pattern invokes differences in post-puberty germline replication between the sexes, recent whole-genome evidence in humans and other mammals has cast doubt on this mechanism. Here, we review recent work that is inconsistent with a replication-driven model of male-biased mutation, and propose an alternative, 'faulty male' hypothesis. This model proposes that males are less able to repair and/or protect DNA from damage compared to females. Importantly, we suggest that this new model for male-biased mutation may also help to explain several pronounced differences between the sexes in cancer, aging, and DNA repair. Although the detailed contributions of genetic, epigenetic, and hormonal influences of biological sex on mutation remain to be fully understood, a reconsideration of the mechanisms underlying these differences will lead to a deeper understanding of evolution and disease.
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Affiliation(s)
- Matthew W Hahn
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA.
| | - Yadira Peña-Garcia
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA
| | - Richard J Wang
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA
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2
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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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3
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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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4
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Bergeron LA, Besenbacher S, Zheng J, Li P, Bertelsen MF, Quintard B, Hoffman JI, Li Z, St Leger J, Shao C, Stiller J, Gilbert MTP, Schierup MH, Zhang G. Evolution of the germline mutation rate across vertebrates. Nature 2023; 615:285-291. [PMID: 36859541 PMCID: PMC9995274 DOI: 10.1038/s41586-023-05752-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/23/2023] [Indexed: 03/03/2023]
Abstract
The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies2. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis3. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.
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Affiliation(s)
- Lucie A Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | | | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Judy St Leger
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | | | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Centre for Evolutionary & Organismal Biology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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5
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de Manuel M, Wu FL, Przeworski M. A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers. eLife 2022; 11:e80008. [PMID: 35916372 PMCID: PMC9439683 DOI: 10.7554/elife.80008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
In humans and other mammals, germline mutations are more likely to arise in fathers than in mothers. Although this sex bias has long been attributed to DNA replication errors in spermatogenesis, recent evidence from humans points to the importance of mutagenic processes that do not depend on cell division, calling into question our understanding of this basic phenomenon. Here, we infer the ratio of paternal-to-maternal mutations, α, in 42 species of amniotes, from putatively neutral substitution rates of sex chromosomes and autosomes. Despite marked differences in gametogenesis, physiologies and environments across species, fathers consistently contribute more mutations than mothers in all the species examined, including mammals, birds, and reptiles. In mammals, α is as high as 4 and correlates with generation times; in birds and snakes, α appears more stable around 2. These observations are consistent with a simple model, in which mutations accrue at equal rates in both sexes during early development and at a higher rate in the male germline after sexual differentiation, with a conserved paternal-to-maternal ratio across species. Thus, α may reflect the relative contributions of two or more developmental phases to total germline mutations, and is expected to depend on generation time even if mutations do not track cell divisions.
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Affiliation(s)
- Marc de Manuel
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Felix L Wu
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Molly Przeworski
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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6
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Connallon T, Beasley IJ, McDonough Y, Ruzicka F. How much does the unguarded X contribute to sex differences in life span? Evol Lett 2022; 6:319-329. [PMID: 35937469 PMCID: PMC9346086 DOI: 10.1002/evl3.292] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/22/2022] [Accepted: 06/12/2022] [Indexed: 11/09/2022] Open
Abstract
Females and males often have markedly different mortality rates and life spans, but it is unclear why these forms of sexual dimorphism evolve. The unguarded X hypothesis contends that dimorphic life spans arise from sex differences in X or Z chromosome copy number (i.e., one copy in the "heterogametic" sex; two copies in the "homogametic" sex), which leads to a disproportionate expression of deleterious mutations by the heterogametic sex (e.g., mammalian males; avian females). Although data on adult sex ratios and sex-specific longevity are consistent with predictions of the unguarded X hypothesis, direct experimental evidence remains scant, and alternative explanations are difficult to rule out. Using a simple population genetic model, we show that the unguarded X effect on sex differential mortality is a function of several reasonably well-studied evolutionary parameters, including the proportion of the genome that is sex linked, the genomic deleterious mutation rate, the mean dominance of deleterious mutations, the relative rates of mutation and strengths of selection in each sex, and the average effect of mutations on survival and longevity relative to their effects on fitness. We review published estimates of these parameters, parameterize our model with them, and show that unguarded X effects are too small to explain observed sex differences in life span across species. For example, sex differences in mean life span are known to often exceed 20% (e.g., in mammals), whereas our parameterized models predict unguarded X effects of a few percent (e.g., 1-3% in Drosophila and mammals). Indeed, these predicted unguarded X effects fall below statistical thresholds of detectability in most experiments, potentially explaining why direct tests of the hypothesis have generated little support for it. Our results suggest that evolution of sexually dimorphic life spans is predominantly attributable to other mechanisms, potentially including "toxic Y" effects and sexual dimorphism for optimal investment in survival versus reproduction.
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Affiliation(s)
- Tim Connallon
- School of Biological SciencesMonash UniversityClaytonVIC3800Australia
| | - Isobel J. Beasley
- School of BioSciencesThe University of MelbourneParkvilleVIC3010Australia
- Melbourne Integrative GenomicsThe University of MelbourneParkvilleVIC3010Australia
- St. Vincent's Institute of Medical ResearchFitzroyVIC3065Australia
| | - Yasmine McDonough
- School of Biological SciencesMonash UniversityClaytonVIC3800Australia
| | - Filip Ruzicka
- School of Biological SciencesMonash UniversityClaytonVIC3800Australia
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7
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Bazzicalupo E, Lucena‐Perez M, Kleinman‐Ruiz D, Pavlov A, Trajçe A, Hoxha B, Sanaja B, Gurielidze Z, Kerdikoshvili N, Mamuchadze J, Yarovenko YA, Akkiev MI, Ratkiewicz M, Saveljev AP, Melovski D, Gavashelishvili A, Schmidt K, Godoy JA. History, demography and genetic status of Balkan and Caucasian
Lynx lynx
(Linnaeus, 1758) populations revealed by genome‐wide variation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Enrico Bazzicalupo
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
| | - Maria Lucena‐Perez
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
| | - Daniel Kleinman‐Ruiz
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
| | | | - Aleksandër Trajçe
- Protection and Preservation of Natural Environment in Albania (PPNEA) Tirana Albania
| | - Bledi Hoxha
- Protection and Preservation of Natural Environment in Albania (PPNEA) Tirana Albania
| | - Bardh Sanaja
- Environmentally Responsible Action (ERA) Peje Montenegro
| | - Zurab Gurielidze
- Program for the Ecology and Conservation of Large Mammals Institute of Ecology Ilia State University Tbilisi Georgia
| | - Niko Kerdikoshvili
- Program for the Ecology and Conservation of Large Mammals Institute of Ecology Ilia State University Tbilisi Georgia
| | | | - Yuriy A. Yarovenko
- Pre‐Caspian Institute of Biological Resources Dagestan Federal Scientific Centre of RAS Makhachkala Russian Federation
| | - Muzigit I. Akkiev
- Kabardino‐Balkarian State High‐Mountain Nature Reserve Kashkhatau Russian Federation
| | | | - Alexander P. Saveljev
- Russian Research Institute of Game Management and Fur Farming Kirov Russian Federation
| | - Dime Melovski
- Macedonian Ecological Society (MES) Skopje Macedonia
- Wildlife Sciences Georg‐August University Göttingen Germany
| | | | - Krzysztof Schmidt
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - José A. Godoy
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
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8
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Raj Kolora SR, Owens GL, Vazquez JM, Stubbs A, Chatla K, Jainese C, Seeto K, McCrea M, Sandel MW, Vianna JA, Maslenikov K, Bachtrog D, Orr JW, Love M, Sudmant PH. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science 2021; 374:842-847. [PMID: 34762458 PMCID: PMC8923369 DOI: 10.1126/science.abg5332] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some species being among the most long-lived extant vertebrates. We de novo assembled the genomes of 88 rockfish species and from these identified repeated signatures of positive selection in DNA repair pathways in long-lived taxa and 137 longevity-associated genes with direct effects on life span through insulin signaling and with pleiotropic effects through size and environmental adaptations. A genome-wide screen of structural variation reveals copy number expansions in the immune modulatory butyrophilin gene family in long-lived species. The evolution of different rockfish life histories is coupled to genetic diversity and reshapes the mutational spectrum driving segregating CpG→TpG variants in long-lived species. These analyses highlight the genetic innovations that underlie life history trait adaptations and, in turn, how they shape genomic diversity.
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Affiliation(s)
| | - Gregory L. Owens
- University of California Berkeley Department of Integrative Biology
- University of Victoria Department of Biology
| | | | - Alexander Stubbs
- University of California Berkeley Department of Integrative Biology
| | - Kamalakar Chatla
- University of California Berkeley Department of Integrative Biology
| | - Conner Jainese
- University of California Santa Barbara Marine Sciences Institute
| | - Katelin Seeto
- University of California Santa Barbara Marine Sciences Institute
| | - Merit McCrea
- University of California Santa Barbara Marine Sciences Institute
| | | | - Juliana A. Vianna
- Pontificia Universidad Católica de Chile, Departamento de Ecosistemas y Medio Ambiente
| | - Katherine Maslenikov
- University of Washington, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture
| | - Doris Bachtrog
- University of California Berkeley Department of Integrative Biology
| | - James W. Orr
- University of Washington, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture
| | - Milton Love
- University of California Santa Barbara Marine Sciences Institute
| | - Peter H. Sudmant
- University of California Berkeley Department of Integrative Biology
- University of California Berkeley Center for Computational Biology
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9
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Tollis M, Schneider-Utaka AK, Maley CC. The Evolution of Human Cancer Gene Duplications across Mammals. Mol Biol Evol 2021; 37:2875-2886. [PMID: 32421773 PMCID: PMC7530603 DOI: 10.1093/molbev/msaa125] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer is caused by genetic alterations that affect cellular fitness, and multicellular organisms have evolved mechanisms to suppress cancer such as cell cycle checkpoints and apoptosis. These pathways may be enhanced by the addition of tumor suppressor gene paralogs or deletion of oncogenes. To provide insights to the evolution of cancer suppression across the mammalian radiation, we estimated copy numbers for 548 human tumor suppressor gene and oncogene homologs in 63 mammalian genome assemblies. The naked mole rat contained the most cancer gene copies, consistent with the extremely low rates of cancer found in this species. We found a positive correlation between a species’ cancer gene copy number and its longevity, but not body size, contrary to predictions from Peto’s Paradox. Extremely long-lived mammals also contained more copies of caretaker genes in their genomes, suggesting that the maintenance of genome integrity is an essential form of cancer prevention in long-lived species. We found the strongest association between longevity and copy numbers of genes that are both germline and somatic tumor suppressor genes, suggesting that selection has acted to suppress both hereditary and sporadic cancers. We also found a strong relationship between the number of tumor suppressor genes and the number of oncogenes in mammalian genomes, suggesting that complex regulatory networks mediate the balance between cell proliferation and checks on tumor progression. This study is the first to investigate cancer gene expansions across the mammalian radiation and provides a springboard for potential human therapies based on evolutionary medicine.
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Affiliation(s)
- Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ.,Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ
| | | | - Carlo C Maley
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ
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10
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Schield DR, Perry BW, Nikolakis ZL, Mackessy SP, Castoe TA. Population Genomic Analyses Confirm Male-Biased Mutation Rates in Snakes. J Hered 2021; 112:221-227. [PMID: 33502475 DOI: 10.1093/jhered/esab005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
Male-biased mutation rates occur in a diverse array of organisms. The ratio of male-to-female mutation rate may have major ramifications for evolution across the genome, and for sex-linked genes in particular. In ZW species, the Z chromosome is carried by males two-thirds of the time, leading to the prediction that male-biased mutation rates will have a disproportionate effect on the evolution of Z-linked genes relative to autosomes and the W chromosome. Colubroid snakes (including colubrids, elapids, and viperids) have ZW sex determination, yet male-biased mutation rates have not been well studied in this group. Here we analyze a population genomic dataset from rattlesnakes to quantify genetic variation within and genetic divergence between species. We use a new method for unbiased estimation of population genetic summary statistics to compare variation between the Z chromosome and autosomes and to calculate net nucleotide differentiation between species. We find evidence for a 2.03-fold greater mutation rate in male rattlesnakes relative to females, corresponding to an average μZ/μA ratio of 1.1. Our results from snakes are quantitatively similar to birds, suggesting that male-biased mutation rates may be a common feature across vertebrate lineages with ZW sex determination.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | | | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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11
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Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations. Proc Natl Acad Sci U S A 2020; 117:20063-20069. [PMID: 32747577 DOI: 10.1073/pnas.1915664117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.
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12
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Wu FL, Strand AI, Cox LA, Ober C, Wall JD, Moorjani P, Przeworski M. A comparison of humans and baboons suggests germline mutation rates do not track cell divisions. PLoS Biol 2020; 18:e3000838. [PMID: 32804933 PMCID: PMC7467331 DOI: 10.1371/journal.pbio.3000838] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 09/02/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
In humans, most germline mutations are inherited from the father. This observation has been widely interpreted as reflecting the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3-4 generation nuclear families (totaling 29 individuals) of olive baboons (Papio anubis), who reproduce at approximately 10 years of age on average, and analyzed the data in parallel with three 3-generation human pedigrees (26 individuals). We estimated a mutation rate per generation in baboons of 0.57×10-8 per base pair, approximately half that of humans. Strikingly, however, the degree of male bias in germline mutations is approximately 4:1, similar to that of humans-indeed, a similar male bias is seen across mammals that reproduce months, years, or decades after birth. These results mirror the finding in humans that the male mutation bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle, suggesting a divergence time between apes and Old World monkeys of 65 million years, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons.
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Affiliation(s)
- Felix L. Wu
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America
| | - Alva I. Strand
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jeffrey D. Wall
- Institute for Human Genetics, Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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13
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Chintalapati M, Moorjani P. Evolution of the mutation rate across primates. Curr Opin Genet Dev 2020; 62:58-64. [PMID: 32634682 DOI: 10.1016/j.gde.2020.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/10/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
Abstract
Germline mutations are the source of all heritable variation. In the past few years, whole genome sequencing has allowed direct and comprehensive surveys of mutation patterns in humans and other species. These studies have documented substantial variation in both mutation rates and spectra across primates, the causes of which remain unclear. Here, we review what is currently known about mutation rates in primates, highlight the factors proposed to explain the variation across species, and discuss some implications of these findings on our understanding of the chronology of primate evolution and the process of mutagenesis.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States; Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States; Center for Computational Biology, University of California, Berkeley, CA, United States.
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14
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Life History Effects on Neutral Diversity Levels of Autosomes and Sex Chromosomes. Genetics 2020; 215:1133-1142. [PMID: 32554702 DOI: 10.1534/genetics.120.303119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the determinants of neutral diversity patterns on autosomes and sex chromosomes provides a bedrock for the interpretation of population genetic data; in particular, differences between the two informs our understanding of sex-specific demographic and mutation processes. While sex-specific age-structure and variation in reproductive success have long been known to affect neutral diversity, theoretical descriptions of these effects were complicated and lacking in generality, stymying attempts to relate diversity patterns of species with their life history. Here, we derive general yet simple expressions for these effects. In particular, we show that life history effects on X-to-autosome ratios of pairwise diversity levels (X:A diversity ratios) depend only on the male-to-female ratios of mutation rates, generation times, and reproductive variances. Our results reveal that changing the male-to-female ratio of generation times has opposite effects on X:A ratios of diversity and divergence. They also explain how sex-specific life histories modulate the response of X:A diversity ratios to changes in population size. More generally, they clarify that sex-specific life history-generation times in particular-should have marked effects on X:A diversity ratios in many taxa and enable further investigation of these effects.
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15
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Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Res 2020; 30:826-834. [PMID: 32461224 PMCID: PMC7370888 DOI: 10.1101/gr.255174.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Mutation is the ultimate source of all genetic novelty and the cause of heritable genetic disorders. Mutational burden has been linked to complex disease, including neurodevelopmental disorders such as schizophrenia and autism. The rate of mutation is a fundamental genomic parameter and direct estimates of this parameter have been enabled by accurate comparisons of whole-genome sequences between parents and offspring. Studies in humans have revealed that the paternal age at conception explains most of the variation in mutation rate: Each additional year of paternal age in humans leads to approximately 1.5 additional inherited mutations. Here, we present an estimate of the de novo mutation rate in the rhesus macaque (Macaca mulatta) using whole-genome sequence data from 32 individuals in four large pedigrees. We estimated an average mutation rate of 0.58 × 10−8 per base pair per generation (at an average parental age of 7.5 yr), much lower than found in direct estimates from great apes. As in humans, older macaque fathers transmit more mutations to their offspring, increasing the per generation mutation rate by 4.27 × 10−10 per base pair per year. We found that the rate of mutation accumulation after puberty is similar between macaques and humans, but that a smaller number of mutations accumulate before puberty in macaques. We additionally investigated the role of paternal age on offspring sociability, a proxy for normal neurodevelopment, by studying 203 male macaques in large social groups.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - John P Capitanio
- California National Primate Research Center, University of California-Davis, Davis, California 95616, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA.,Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
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16
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Ruan Y, Wang H, Chen B, Wen H, Wu CI. Mutations Beget More Mutations-Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation. Mol Biol Evol 2020; 37:1007-1019. [PMID: 31778175 DOI: 10.1093/molbev/msz283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haiyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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17
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Acosta A, Martínez-Pacheco ML, Díaz-Barba K, Porras N, Gutiérrez-Mariscal M, Cortez D. Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias. Genome Biol Evol 2020; 11:3054-3067. [PMID: 31605487 PMCID: PMC6823514 DOI: 10.1093/gbe/evz221] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2019] [Indexed: 12/13/2022] Open
Abstract
The age of sex chromosomes is commonly obtained by comparing the substitution rates of XY gametologs. Coupled with phylogenetic reconstructions, one can refine the origin of a sex chromosome system relative to specific speciation events. However, these approaches are insufficient to determine the presence and duration of ancestral sex chromosome systems that were lost in some species. In this study, we worked with genomic and transcriptomic data from mammals and squamates and analyzed the effect of male mutation bias on X-linked sequences in these groups. We searched for signatures indicating whether monotremes shared the same sex chromosomes with placental mammals or whether pleurodonts and acrodonts had a common ancestral sex chromosome system. Our analyses indicate that platypus did not share the XY chromosomes with placental mammals, in agreement with previous work. In contrast, analyses of agamids showed that this lineage maintained the pleurodont XY chromosomes for several million years. We performed multiple simulations using different strengths of male mutation bias to confirm the results. Overall, our work shows that variations in substitution rates due to male mutation bias could be applied to uncover signatures of ancestral sex chromosome systems.
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Affiliation(s)
| | | | | | | | | | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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18
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Koch EM, Schweizer RM, Schweizer TM, Stahler DR, Smith DW, Wayne RK, Novembre J. De Novo Mutation Rate Estimation in Wolves of Known Pedigree. Mol Biol Evol 2019; 36:2536-2547. [PMID: 31297530 PMCID: PMC6805234 DOI: 10.1093/molbev/msz159] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022] Open
Abstract
Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 × 10-9 per base pair per generation and provide conservative bounds between 2.6 × 10-9 and 7.1 × 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 × 10-9 and 3.0-4.5 × 10-9), it suggests a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000-64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates and is likely to be vital to future investigations of mutation rate evolution.
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Affiliation(s)
- Evan M Koch
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Teia M Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
- Department of Human Genetics, University of Chicago, Chicago, IL
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19
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Tollis M, Robbins J, Webb AE, Kuderna LFK, Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O’Connell MJ, Palsbøll PJ, Maley CC. Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Mol Biol Evol 2019; 36:1746-1763. [PMID: 31070747 PMCID: PMC6657726 DOI: 10.1093/molbev/msz099] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans-an observation known as Peto's Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.
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Affiliation(s)
- Marc Tollis
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | | | - Andrew E Webb
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | | | - Aleah F Caulin
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, PA
| | | | - Martine Bèrubè
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Nader Pourmand
- Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Tomas Marques-Bonet
- Instituto de Biologia Evolutiva (UPF-CSIC), PRBB, Barcelona, Spain
- CNAG‐CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Mary J O’Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Per J Palsbøll
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Carlo C Maley
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
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20
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Mello B, Schrago CG. The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis. Evol Bioinform Online 2019; 15:1176934319855988. [PMID: 31223232 PMCID: PMC6566470 DOI: 10.1177/1176934319855988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/17/2019] [Indexed: 11/16/2022] Open
Abstract
The recent surge of genomic data has prompted the investigation of substitution rate variation across the genome, as well as among lineages. Evolutionary trees inferred from distinct genomic regions may display branch lengths that differ between loci by simple proportionality constants, indicating that rate variation follows a pacemaker model, which may be attributed to lineage effects. Analyses of genes from diverse biological clades produced contrasting results, supporting either this model or alternative scenarios where multiple pacemakers exist. So far, an evaluation of the pacemaker hypothesis for all great apes has never been carried out. In this work, we tested whether the evolutionary rates of hominids conform to pacemakers, which were inferred accounting for gene tree/species tree discordance. For higher precision, substitution rates in branches were estimated with a calibration-free approach, the relative rate framework. A predominant evolutionary trend in great apes was evidenced by the recovery of a large pacemaker, encompassing most hominid genomic regions. In addition, the majority of genes followed a pace of evolution that was closely related to the strict molecular clock. However, slight rate decreases were recovered in the internal branches leading to humans, corroborating the hominoid slowdown hypothesis. Our findings suggest that in great apes, life history traits were the major drivers of substitution rate variation across the genome.
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Affiliation(s)
- Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M. Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proc Natl Acad Sci U S A 2019; 116:9491-9500. [PMID: 31019089 PMCID: PMC6511033 DOI: 10.1073/pnas.1901259116] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The textbook view that most germline mutations in mammals arise from replication errors is indirectly supported by the fact that there are both more mutations and more cell divisions in the male than in the female germline. When analyzing large de novo mutation datasets in humans, we find multiple lines of evidence that call that view into question. Notably, despite the drastic increase in the ratio of male to female germ cell divisions after the onset of spermatogenesis, even young fathers contribute three times more mutations than young mothers, and this ratio barely increases with parental age. This surprising finding points to a substantial contribution of damage-induced mutations. Indeed, C-to-G transversions and CpG transitions, which together constitute over one-fourth of all base substitution mutations, show genomic distributions and sex-specific age dependencies indicative of double-strand break repair and methylation-associated damage, respectively. Moreover, we find evidence that maternal age at conception influences the mutation rate both because of the accumulation of damage in oocytes and potentially through an influence on the number of postzygotic mutations in the embryo. These findings reveal underappreciated roles of DNA damage and maternal age in the genesis of human germline mutations.
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Affiliation(s)
- Ziyue Gao
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305;
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Guy Amster
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027;
- Department of Systems Biology, Columbia University, New York, NY 10027
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22
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Smeds L, Kojola I, Ellegren H. The evolutionary history of grey wolf Y chromosomes. Mol Ecol 2019; 28:2173-2191. [PMID: 30788868 PMCID: PMC6850511 DOI: 10.1111/mec.15054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Rovaniemi, Finland
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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23
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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24
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Xu S, Van Tran K, Neupane S, Snyman M, Huynh TV, Sung W. Single-sperm sequencing reveals the accelerated mitochondrial mutation rate in male Daphnia pulex (Crustacea, Cladocera). Proc Biol Sci 2018; 284:rspb.2017.1548. [PMID: 28931740 DOI: 10.1098/rspb.2017.1548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/16/2017] [Indexed: 01/23/2023] Open
Abstract
Mutation rate in the nuclear genome differs between sexes, with males contributing more mutations than females to their offspring. The male-biased mutation rates in the nuclear genome is most likely to be driven by a higher number of cell divisions in spermatogenesis than in oogenesis, generating more opportunities for DNA replication errors. However, it remains unknown whether male-biased mutation rates are present in mitochondrial DNA (mtDNA). Although mtDNA is maternally inherited and male mtDNA mutation typically does not contribute to genetic variation in offspring, male mtDNA mutations are critical for male reproductive health. In this study, we measured male mtDNA mutation rate using publicly available whole-genome sequences of single sperm of the freshwater microcrustacean Daphnia pulex Using a stringent mutation detection pipeline, we found that the male mtDNA mutation rate is 3.32 × 10-6 per site per generation. All the detected mutations are heteroplasmic base substitutions, with 57% of mutations converting G/C to A/T nucleotides. Consistent with the male-biased mutation in the nuclear genome, the male mtDNA mutation rate in D. pulex is approximately 20 times higher than the female rate per generation. We propose that the elevated mutation rate per generation in male mtDNA is consistent with an increased number of cell divisions during male gametogenesis.
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Affiliation(s)
- Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kenny Van Tran
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Swatantra Neupane
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Trung Viet Huynh
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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25
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Link V, Aguilar-Gómez D, Ramírez-Suástegui C, Hurst LD, Cortez D. Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals. Genome Biol Evol 2018; 9:2198-2210. [PMID: 28922870 PMCID: PMC5604096 DOI: 10.1093/gbe/evx155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/12/2022] Open
Abstract
In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12–3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates.
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Affiliation(s)
- Vivian Link
- Department of Biology, University of Fribourg, Switzerland
| | | | | | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Somerset, United Kingdom
| | - Diego Cortez
- Center for Genomic Sciences, UNAM, Cuernavaca, México
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Tollis M, Hutchins ED, Stapley J, Rupp SM, Eckalbar WL, Maayan I, Lasku E, Infante CR, Dennis SR, Robertson JA, May CM, Crusoe MR, Bermingham E, DeNardo DF, Hsieh STT, Kulathinal RJ, McMillan WO, Menke DB, Pratt SC, Rawls JA, Sanjur O, Wilson-Rawls J, Wilson Sayres MA, Fisher RE, Kusumi K. Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. Genome Biol Evol 2018; 10:489-506. [PMID: 29360978 PMCID: PMC5798147 DOI: 10.1093/gbe/evy013] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2018] [Indexed: 11/21/2022] Open
Abstract
Squamates include all lizards and snakes, and display some of the most diverse and extreme morphological adaptations among vertebrates. However, compared with birds and mammals, relatively few resources exist for comparative genomic analyses of squamates, hampering efforts to understand the molecular bases of phenotypic diversification in such a speciose clade. In particular, the ∼400 species of anole lizard represent an extensive squamate radiation. Here, we sequence and assemble the draft genomes of three anole species-Anolis frenatus, Anolis auratus, and Anolis apletophallus-for comparison with the available reference genome of Anolis carolinensis. Comparative analyses reveal a rapid background rate of molecular evolution consistent with a model of punctuated equilibrium, and strong purifying selection on functional genomic elements in anoles. We find evidence for accelerated evolution in genes involved in behavior, sensory perception, and reproduction, as well as in genes regulating limb bud development and hindlimb specification. Morphometric analyses of anole fore and hindlimbs corroborated these findings. We detect signatures of positive selection across several genes related to the development and regulation of the forebrain, hormones, and the iguanian lizard dewlap, suggesting molecular changes underlying behavioral adaptations known to reinforce species boundaries were a key component in the diversification of anole lizards.
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Affiliation(s)
- Marc Tollis
- School of Life Sciences, Arizona State University
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University
| | - Elizabeth D Hutchins
- School of Life Sciences, Arizona State University
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jessica Stapley
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | - Shawn M Rupp
- School of Life Sciences, Arizona State University
| | | | - Inbar Maayan
- School of Life Sciences, Arizona State University
| | - Eris Lasku
- School of Life Sciences, Arizona State University
| | - Carlos R Infante
- Department of Genetics, University of Georgia
- Department of Molecular and Cellular Biology, University of Arizona
| | - Stuart R Dennis
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | | | | | | | - Eldredge Bermingham
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
- Patricia and Phillip Frost Museum of Science, Miami, Florida
| | | | | | | | | | | | | | | | - Oris Sanjur
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | | | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University
- The Center for Evolution and Medicine, Arizona State University
| | - Rebecca E Fisher
- School of Life Sciences, Arizona State University
- Department of Basic Medical Sciences, University of Arizona College of Medicine–Phoenix
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
- Department of Basic Medical Sciences, University of Arizona College of Medicine–Phoenix
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27
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Inferring sex-specific demographic history from SNP data. PLoS Genet 2018; 14:e1007191. [PMID: 29385127 PMCID: PMC5809101 DOI: 10.1371/journal.pgen.1007191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/12/2018] [Accepted: 01/08/2018] [Indexed: 12/04/2022] Open
Abstract
The relative female and male contributions to demography are of great importance to better understand the history and dynamics of populations. While earlier studies relied on uniparental markers to investigate sex-specific questions, the increasing amount of sequence data now enables us to take advantage of tens to hundreds of thousands of independent loci from autosomes and the X chromosome. Here, we develop a novel method to estimate effective sex ratios or ESR (defined as the female proportion of the effective population) from allele count data for each branch of a rooted tree topology that summarizes the history of the populations of interest. Our method relies on Kimura’s time-dependent diffusion approximation for genetic drift, and is based on a hierarchical Bayesian model to integrate over the allele frequencies along the branches. We show via simulations that parameters are inferred robustly, even under scenarios that violate some of the model assumptions. Analyzing bovine SNP data, we infer a strongly female-biased ESR in both dairy and beef cattle, as expected from the underlying breeding scheme. Conversely, we observe a strongly male-biased ESR in early domestication times, consistent with an easier taming and management of cows, and/or introgression from wild auroch males, that would both cause a relative increase in male effective population size. In humans, analyzing a subsample of non-African populations, we find a male-biased ESR in Oceanians that may reflect complex marriage patterns in Aboriginal Australians. Because our approach relies on allele count data, it may be applied on a wide range of species. The history of populations and their social organization is often intricate due to breeding structures, migration patterns or population bottlenecks. Estimation of the female proportion of the effective population (sex ratio) is therefore important to better understand this underlying social structure and dynamics. This question has been mainly investigated so far by comparing genetic variation of mitochondrial DNA and the Y chromosome, two uniparentally inherited markers that reflect the demographic history of females and males, respectively. To overcome the intrinsic limitations of these genetic markers, and to take advantage of the increasing amount of sequence data, we propose a new approach that uses large numbers of independent polymorphisms from autosomes and the X chromosome to estimate sex ratios, throughout the history of populations. This method allows us to confirm a strongly female-biased sex ratio in modern dairy and beef cattle breeds. Yet, we find a strongly male-biased sex ratio during domestication times, consistent with an easier taming and management of cows, and/or introgression from wild auroch males. Analyzing human data from a sample of non-African populations, we find a male bias in Oceanians, possibly indicating complex marriage patterns among Aboriginal Australian groups.
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Rollings N, Uhrig EJ, Krohmer RW, Waye HL, Mason RT, Olsson M, Whittington CM, Friesen CR. Age-related sex differences in body condition and telomere dynamics of red-sided garter snakes. Proc Biol Sci 2018; 284:rspb.2016.2146. [PMID: 28381620 DOI: 10.1098/rspb.2016.2146] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/06/2017] [Indexed: 12/15/2022] Open
Abstract
Life-history strategies vary dramatically between the sexes, which may drive divergence in sex-specific senescence and mortality rates. Telomeres are tandem nucleotide repeats that protect the ends of chromosomes from erosion during cell division. Telomeres have been implicated in senescence and mortality because they tend to shorten with stress, growth and age. We investigated age-specific telomere length in female and male red-sided garter snakes, Thamnophis sirtalis parietalis We hypothesized that age-specific telomere length would differ between males and females given their divergent reproductive strategies. Male garter snakes emerge from hibernation with high levels of corticosterone, which facilitates energy mobilization to fuel mate-searching, courtship and mating behaviours during a two to four week aphagous breeding period at the den site. Conversely, females remain at the dens for only about 4 days and seem to invest more energy in growth and cellular maintenance, as they usually reproduce biennially. As male investment in reproduction involves a yearly bout of physiologically stressful activities, while females prioritize self-maintenance, we predicted male snakes would experience more age-specific telomere loss than females. We investigated this prediction using skeletochronology to determine the ages of individuals and qPCR to determine telomere length in a cross-sectional study. For both sexes, telomere length was positively related to body condition. Telomere length decreased with age in male garter snakes, but remained stable in female snakes. There was no correlation between telomere length and growth in either sex, suggesting that our results are a consequence of divergent selection on life histories of males and females. Different selection on the sexes may be the physiological consequence of the sexual dimorphism and mating system dynamics displayed by this species.
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Affiliation(s)
- Nicky Rollings
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building (A08), New South Wales 2006, Australia
| | - Emily J Uhrig
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Randolph W Krohmer
- Department of Biological Sciences, Saint Xavier University, Chicago, IL, USA
| | - Heather L Waye
- Division of Science and Mathematics, University of Minnesota, Morris, MN, USA
| | - Robert T Mason
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Mats Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Camilla M Whittington
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building (A08), New South Wales 2006, Australia.,Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - Christopher R Friesen
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building (A08), New South Wales 2006, Australia
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29
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Pfeifer SP. Direct estimate of the spontaneous germ line mutation rate in African green monkeys. Evolution 2017; 71:2858-2870. [PMID: 29068052 DOI: 10.1111/evo.13383] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 12/30/2022]
Abstract
Here, I provide the first direct estimate of the spontaneous mutation rate in an Old World monkey, using a seven individual, three-generation pedigree of African green monkeys. Eight de novo mutations were identified within ∼1.5 Gbp of accessible genome, corresponding to an estimated point mutation rate of 0.94 × 10-8 per site per generation, suggesting an effective population size of ∼12000 for the species. This estimation represents a significant improvement in our knowledge of the population genetics of the African green monkey, one of the most important nonhuman primate models in biomedical research. Furthermore, by comparing mutation rates in Old World monkeys with the only other direct estimates in primates to date-humans and chimpanzees-it is possible to uniquely address how mutation rates have evolved over longer time scales. While the estimated spontaneous mutation rate for African green monkeys is slightly lower than the rate of 1.2 × 10-8 per base pair per generation reported in chimpanzees, it is similar to the lower range of rates of 0.96 × 10-8 -1.28 × 10-8 per base pair per generation recently estimated from whole genome pedigrees in humans. This result suggests a long-term constraint on mutation rate that is quite different from similar evidence pertaining to recombination rate evolution in primates.
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Affiliation(s)
- Susanne P Pfeifer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,School of Life Sciences, Arizona State University (ASU), Tempe, Arizona 85281
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30
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Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet 2017; 33:266-282. [DOI: 10.1016/j.tig.2017.01.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
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31
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Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
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Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
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32
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Abstract
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
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33
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Narang P, Wilson Sayres MA. Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes. Genome Biol Evol 2016; 8:3393-3405. [PMID: 27702816 PMCID: PMC5203777 DOI: 10.1093/gbe/evw232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias.
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Affiliation(s)
- Pooja Narang
- School of Life Sciences, Arizona State University, Tempe
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe .,Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe
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34
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Harpak A, Bhaskar A, Pritchard JK. Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans. PLoS Genet 2016; 12:e1006489. [PMID: 27977673 PMCID: PMC5157949 DOI: 10.1371/journal.pgen.1006489] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/16/2016] [Indexed: 01/06/2023] Open
Abstract
The site frequency spectrum (SFS) has long been used to study demographic history and natural selection. Here, we extend this summary by examining the SFS conditional on the alleles found at the same site in other species. We refer to this extension as the "phylogenetically-conditioned SFS" or cSFS. Using recent large-sample data from the Exome Aggregation Consortium (ExAC), combined with primate genome sequences, we find that human variants that occurred independently in closely related primate lineages are at higher frequencies in humans than variants with parallel substitutions in more distant primates. We show that this effect is largely due to sites with elevated mutation rates causing significant departures from the widely-used infinite sites mutation model. Our analysis also suggests substantial variation in mutation rates even among mutations involving the same nucleotide changes. In summary, we show that variable mutation rates are key determinants of the SFS in humans.
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Affiliation(s)
- Arbel Harpak
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Anand Bhaskar
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Jonathan K. Pritchard
- Department of Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
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35
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Abstract
Our understanding of the chronology of human evolution relies on the “molecular clock” provided by the steady accumulation of substitutions on an evolutionary lineage. Recent analyses of human pedigrees have called this understanding into question by revealing unexpectedly low germline mutation rates, which imply that substitutions accrue more slowly than previously believed. Translating mutation rates estimated from pedigrees into substitution rates is not as straightforward as it may seem, however. We dissect the steps involved, emphasizing that dating evolutionary events requires not “a mutation rate” but a precise characterization of how mutations accumulate in development in males and females—knowledge that remains elusive.
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Affiliation(s)
- Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Ziyue Gao
- Howard Hughes Medical Institute & Dept. of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
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36
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Abstract
Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years, and the human and gorilla divergence time is 15.1 million years.
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37
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Webster TH, Wilson Sayres MA. Genomic signatures of sex-biased demography: progress and prospects. Curr Opin Genet Dev 2016; 41:62-71. [PMID: 27599147 DOI: 10.1016/j.gde.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023]
Abstract
Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
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38
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Abstract
Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities in our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our long-standing model of spermatogenesis. I consider possible explanations for these discrepancies, including evolutionary changes in life-history parameters such as generation time and the age of puberty, a possible contribution from undetected post-zygotic mutations early in embryo development, and changes in cellular mutation processes at different stages of the germline. I suggest a revised model of stem-cell state transitions during spermatogenesis, in which 'dark' gonial stem cells play a more active role than hitherto envisaged, with a long cycle time undetected in experimental observations. More generally, I argue that the mutation rate and its evolution depend intimately on the structure of the germline in humans and other primates.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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39
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Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PCM, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. Genome Res 2016; 26:530-40. [PMID: 26934921 PMCID: PMC4817776 DOI: 10.1101/gr.199448.115] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/21/2016] [Indexed: 01/25/2023]
Abstract
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
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Affiliation(s)
- Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Samarth Rangavittal
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Monika Cechova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Rebeca Campos Sanchez
- Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard W Fescemyer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Danling Ye
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Patricia C M O'Brien
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Rayan Chikhi
- University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France; Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | | | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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40
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Mendes FK, Hahn MW. Gene Tree Discordance Causes Apparent Substitution Rate Variation. Syst Biol 2016; 65:711-21. [DOI: 10.1093/sysbio/syw018] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/23/2016] [Indexed: 01/01/2023] Open
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Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C, Jobling MA. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res 2016; 26:427-39. [PMID: 26883546 PMCID: PMC4817767 DOI: 10.1101/gr.198754.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/30/2022]
Abstract
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Mariano Rocchi
- Department of Biology, University of Bari, 70124 Bari, Italy
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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42
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Amster G, Sella G. Life history effects on the molecular clock of autosomes and sex chromosomes. Proc Natl Acad Sci U S A 2016; 113:1588-93. [PMID: 26811451 PMCID: PMC4760823 DOI: 10.1073/pnas.1515798113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
One of the foundational results in molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic "molecular clock." We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in hominids (great apes), considering a model that approximates features of the mutational process in mammals, birds, and some other vertebrates. As we show, this model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among hominine lineages (i.e., humans, chimpanzees, and gorillas). The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant hominoids (apes), given sex-specific life histories. In so doing, it largely bridges the gap reported between estimates of split times based on fossil and molecular evidence, in particular suggesting that the human-chimpanzee split may have occurred as recently as 6.6 Mya. The model also implies that the "generation time effect" should be stronger in short-lived species, explaining why the generation time has a major influence on yearly substitution rates in mammals but only a subtle one in human pedigrees.
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Affiliation(s)
- Guy Amster
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, NY 10027
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43
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Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B, Stratton MR, Hurles ME. Timing, rates and spectra of human germline mutation. Nat Genet 2016; 48:126-133. [PMID: 26656846 PMCID: PMC4731925 DOI: 10.1038/ng.3469] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 11/20/2015] [Indexed: 12/15/2022]
Abstract
Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. The mutation rate increased with paternal age in all families, but the number of additional mutations per year differed by more than twofold between families. Meta-analysis of 6,570 mutations showed that germline methylation influences mutation rates. In contrast to somatic mutations, we found remarkable consistency in germline mutation spectra between the sexes and at different paternal ages. In parental germ line, 3.8% of mutations were mosaic, resulting in 1.3% of mutations being shared by siblings. The number of these shared mutations varied significantly between families. Our data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells but is reduced substantially during post-pubertal spermatogenesis. These findings have important consequences for the recurrence risks of disorders caused by de novo mutations.
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Affiliation(s)
- Raheleh Rahbari
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Arthur Wuster
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Department of Human Genetics and Department of Bioinformatics and Computational Biology, Genentech Inc, 1 DNA Way, CA 94080 South San Francisco, USA
| | - Sarah J Lindsay
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Saeed Al Turki
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Anna Dominiczak
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew Morris
- Medical Research Institute, University of Dundee, Dundee, United Kingdom
| | - David Porteous
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Blair Smith
- Medical Research Institute, University of Dundee, Dundee, United Kingdom
| | | | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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44
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Huang H, Rabosky DL. Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection. BMC Evol Biol 2015; 15:199. [PMID: 26377432 PMCID: PMC4574164 DOI: 10.1186/s12862-015-0480-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/08/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sexual dichromatism is the tendency for sexes to differ in color pattern and represents a striking form of within-species morphological variation. Conspicuous intersexual differences in avian plumage are generally thought to result from Darwinian sexual selection, to the extent that dichromatism is often treated as a surrogate for the intensity of sexual selection in phylogenetic comparative studies. Intense sexual selection is predicted to leave a footprint on genetic evolution by reducing the relative genetic diversity on sex chromosome to that on the autosomes. RESULTS In this study, we test the association between plumage dichromatism and sex-linked genetic diversity using eight species pairs with contrasting levels of dichromatism. We estimated Z-linked and autosomal genetic diversity for these non-model avian species using restriction-site associated (RAD) loci that covered ~3 % of the genome. We find that monochromatic birds consistently have reduced sex-linked genomic variation relative to phylogenetically-paired dichromatic species and this pattern is robust to mutational biases. CONCLUSIONS Our results are consistent with several interpretations. If present-day sexual selection is stronger in dichromatic birds, our results suggest that its impact on sex-linked genomic variation is offset by other processes that lead to proportionately lower Z-linked variation in monochromatic species. We discuss possible factors that may contribute to this discrepancy between phenotypes and genomic variation. Conversely, it is possible that present-day sexual selection -- as measured by the variance in male reproductive success -- is stronger in the set of monochromatic taxa we have examined, potentially reflecting the importance of song, behavior and other non-plumage associated traits as targets of sexual selection. This counterintuitive finding suggests that the relationship between genomic variation and sexual selection is complex and highlights the need for a more comprehensive survey of genomic variation in avian taxa that vary markedly in social and genetic mating systems.
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Affiliation(s)
- Huateng Huang
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, 48109, USA.
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45
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Weber CC, Nabholz B, Romiguier J, Ellegren H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol 2015; 15:542. [PMID: 25607475 PMCID: PMC4264323 DOI: 10.1186/s13059-014-0542-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/13/2014] [Indexed: 02/02/2023] Open
Abstract
Background The ratio of the rates of non-synonymous and synonymous substitution (dN/dS) is commonly used to estimate selection in coding sequences. It is often suggested that, all else being equal, dN/dS should be lower in populations with large effective size (Ne) due to increased efficacy of purifying selection. As Ne is difficult to measure directly, life history traits such as body mass, which is typically negatively associated with population size, have commonly been used as proxies in empirical tests of this hypothesis. However, evidence of whether the expected positive correlation between body mass and dN/dS is consistently observed is conflicting. Results Employing whole genome sequence data from 48 avian species, we assess the relationship between rates of molecular evolution and life history in birds. We find a negative correlation between dN/dS and body mass, contrary to nearly neutral expectation. This raises the question whether the correlation might be a method artefact. We therefore in turn consider non-stationary base composition, divergence time and saturation as possible explanations, but find no clear patterns. However, in striking contrast to dN/dS, the ratio of radical to conservative amino acid substitutions (Kr/Kc) correlates positively with body mass. Conclusions Our results in principle accord with the notion that non-synonymous substitutions causing radical amino acid changes are more efficiently removed by selection in large populations, consistent with nearly neutral theory. These findings have implications for the use of dN/dS and suggest that caution is warranted when drawing conclusions about lineage-specific modes of protein evolution using this metric. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0542-8) contains supplementary material, which is available to authorized users.
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46
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Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet 2015; 16:213-23. [PMID: 25732611 PMCID: PMC4500049 DOI: 10.1038/nrg3890] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The variation in local rates of mutations can affect both the evolution of genes and their function in normal and cancer cells. Deciphering the molecular determinants of this variation will be aided by the elucidation of distinct types of mutations, as they differ in regional preferences and in associations with genomic features. Chromatin organization contributes to regional variation in mutation rates, but its contribution differs among mutation types. In both germline and somatic mutations, base substitutions are more abundant in regions of closed chromatin, perhaps reflecting error accumulation late in replication. By contrast, a distinctive mutational state with very high levels of insertions and deletions (indels) and substitutions is enriched in regions of open chromatin. These associations indicate an intricate interplay between the nucleotide sequence of DNA and its dynamic packaging into chromatin, and have important implications for current biomedical research. This Review focuses on recent studies showing associations between chromatin state and mutation rates, including pairwise and multivariate investigations of germline and somatic (particularly cancer) mutations.
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Affiliation(s)
- Kateryna D Makova
- Department of Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA
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47
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Wang Z, Zhang J, Yang W, An N, Zhang P, Zhang G, Zhou Q. Temporal genomic evolution of bird sex chromosomes. BMC Evol Biol 2014; 14:250. [PMID: 25527260 PMCID: PMC4272511 DOI: 10.1186/s12862-014-0250-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias ('male-driven evolution' effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. CONCLUSIONS In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.
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Affiliation(s)
- Zongji Wang
- />School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 China
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jilin Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Wei Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Na An
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pei Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Qi Zhou
- />Department of Integrative Biology, University of California, Berkeley, CA94720 USA
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48
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Mendez FL, Veeramah KR, Thomas MG, Karafet TM, Hammer MF. Reply to 'The 'extremely ancient' chromosome that isn't' by Elhaik et al. Eur J Hum Genet 2014; 23:564-7. [PMID: 25315660 DOI: 10.1038/ejhg.2014.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Fernando L Mendez
- 1] ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA [2] Department of Genetics, Stanford University, Stanford, CA, USA
| | - Krishna R Veeramah
- 1] ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA [2] Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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49
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Ségurel L, Wyman MJ, Przeworski M. Determinants of Mutation Rate Variation in the Human Germline. Annu Rev Genomics Hum Genet 2014; 15:47-70. [DOI: 10.1146/annurev-genom-031714-125740] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laure Ségurel
- Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle–Centre National de la Recherche Scientifique–Université Paris 7 Diderot, Paris 75231, France;
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, NY 10027;
| | - Molly Przeworski
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637;
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50
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Larger mammalian body size leads to lower retroviral activity. PLoS Pathog 2014; 10:e1004214. [PMID: 25033295 PMCID: PMC4102558 DOI: 10.1371/journal.ppat.1004214] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/15/2014] [Indexed: 02/07/2023] Open
Abstract
Retroviruses have been infecting mammals for at least 100 million years, leaving descendants in host genomes known as endogenous retroviruses (ERVs). The abundance of ERVs is partly determined by their mode of replication, but it has also been suggested that host life history traits could enhance or suppress their activity. We show that larger bodied species have lower levels of ERV activity by reconstructing the rate of ERV integration across 38 mammalian species. Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. Furthermore, 68% of the variance in the mean age of ERVs per genome can also be explained by body size. These results indicate that body size limits the number of recently replicating ERVs due to their detrimental effects on their host. To comprehend the possible mechanistic links between body size and ERV integration we built a mathematical model, which shows that ERV abundance is favored by lower body size and higher horizontal transmission rates. We argue that because retroviral integration is tumorigenic, the negative correlation between body size and ERV numbers results from the necessity to reduce the risk of cancer, under the assumption that this risk scales positively with body size. Our model also fits the empirical observation that the lifetime risk of cancer is relatively invariant among mammals regardless of their body size, known as Peto's paradox, and indicates that larger bodied mammals may have evolved mechanisms to limit ERV activity. Retroviruses have been invading mammalian genomes for over 100 million years, leaving traces known as endogenous retroviruses (ERVs). Early genome sequencing studies revealed a marked difference in the activity of retroviruses among species, with humans largely containing inactive lineages of ERVs, while the mouse contains numerous lineages of active ERVs. We explore the hypothesis that life history traits determine the activity of ERVs in mammalian genomes, and show that larger mammals have fewer ERV copies over recent evolutionary time (the last 10 million years) compared to smaller mammals. This association is determined by body size independently of any confounding variables. We build a mathematical model that shows that ERV abundance in genomes decreases with larger body size and increases with horizontal transmission. Retroviral integration can cause cancer, and our analysis suggests that larger bodied animals control ERV replication in order to postpone cancer until a post-reproductive age. This is in line with a long-standing observation that cancer rates do not fluctuate among mammals of different body size, a phenomenon known as Peto's paradox, and opens up the possibility that larger animals have evolved mechanisms to limit ERV activity.
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