1
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Wang Y, McNeil P, Abdulazeez R, Pascual M, Johnston SE, Keightley PD, Obbard DJ. Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans. Genome Res 2023; 33:587-598. [PMID: 37037625 PMCID: PMC10234296 DOI: 10.1101/gr.277383.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
The rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses to ongoing selection, and levels of genetic load. However, even for key evolutionary model species such as Drosophila melanogaster and Drosophila simulans, few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, or populations. Knowledge of this variation is fundamental for parameterizing models of genome evolution. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogaster and a European population of D. simulans Across 89 flies, we observe 58 single-nucleotide mutations, 286 crossovers, and 89 transposable element (TE) insertions. Compared to the European D. melanogaster, we find the West African population has a lower mutation rate (1.67 × 10-9 site-1 gen-1 vs. 4.86 × 10-9 site-1 gen-1) and a lower transposition rate (8.99 × 10-5 copy-1 gen-1 vs. 23.36 × 10-5 copy-1 gen-1), but a higher recombination rate (3.44 cM/Mb vs. 2.06 cM/Mb). The European D. simulans population has a similar mutation rate to European D. melanogaster, but a significantly higher recombination rate and a lower, but not significantly different, transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species. Our study quantifies the variation in rates of mutation, recombination, and transposition among different populations and sexes, and our direct estimates of these parameters in D. melanogaster and D. simulans will benefit future studies in population and evolutionary genetics.
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Affiliation(s)
- Yiguan Wang
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
| | - Paul McNeil
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | | | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística and IRBio, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Susan E Johnston
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Peter D Keightley
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
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2
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Ke L, Shen J, Feng J, Chen J, Shen S, Li S, Kuang M, Liang L, Lu C, Li D, He Q, Peng B, Hua Y. Somatic Mutation Profiles Revealed by Next Generation Sequencing (NGS) in 39 Chinese Hepatocellular Carcinoma Patients. Front Mol Biosci 2022; 8:800679. [PMID: 35118119 PMCID: PMC8804344 DOI: 10.3389/fmolb.2021.800679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
The features and significance of somatic mutation profiles in hepatocellular carcinoma (HCC) have not been completely elucidated to date. In this study, 39 tumor specimens from HCC patients were collected for gene variation analysis by next-generation sequencing (NGS), and a correlation analysis between mutated genes and clinical characteristics was also conducted. The results were compared with genome data from cBioPortal database. Our study found that T > G/A > C transversions (Tv) and C > T/G > A transitions (Ti) were dominant. The sequence variations of TP53, MUC16, MUC12, MUC4 and others, and the copy number variations (CNVs) of FGF3, TERT, and SOX2 were found to be more frequent in our cohort than in cBioPortal datasets, and they were highly enriched in pathways in cancer and participated in complex biological regulatory processes. The TP53 mutation was the key mutation (76.9%, 30/39), and the most common amino acid alteration and mutation types were p.R249S (23.5%) and missense mutation (82.3%) in the TP53 variation. Furthermore, TP53 had more co-mutations with MUC17, NBPF10, and AHNAK2. However, there were no significant differences in clinical characteristics between HCC patients with mutant TP53 and wild-type TP53, and the overall survival rate between treatment via precision medication guided by NGS and that via empirical medication (logrank p = 0.181). Therefore, the role of NGS in the guidance of personalized targeted therapy, solely based on NGS, may be limited. Multi-center, large sample, prospective studies are needed to further verify these results.
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Affiliation(s)
- Lixin Ke
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianming Shen
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jikun Feng
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jialin Chen
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shunli Shen
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaoqiang Li
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ming Kuang
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lijian Liang
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cuncun Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dongming Li
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
| | - Qiang He
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
| | - Baogang Peng
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
| | - Yunpeng Hua
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
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3
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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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4
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Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes. Proc Natl Acad Sci U S A 2019; 116:17916-17924. [PMID: 31427530 PMCID: PMC6731651 DOI: 10.1073/pnas.1900714116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The sources of human germline mutations are poorly understood. Part of the difficulty is that mutations occur very rarely, and so direct pedigree-based approaches remain limited in the numbers that they can examine. To address this problem, we consider the spectrum of low-frequency variants in a dataset (Genome Aggregation Database, gnomAD) of 13,860 human X chromosomes and autosomes. X-autosome differences are reflective of germline sex differences and have been used extensively to learn about male versus female mutational processes; what is less appreciated is that they also reflect chromosome-level biochemical features that differ between the X and autosomes. We tease these components apart by comparing the mutation spectrum in multiple genomic compartments on the autosomes and between the X and autosomes. In so doing, we are able to ascribe specific mutation patterns to replication timing and recombination and to identify differences in the types of mutations that accrue in males and females. In particular, we identify C > G as a mutagenic signature of male meiotic double-strand breaks on the X, which may result from late repair. Our results show how biochemical processes of damage and repair in the germline interact with sex-specific life history traits to shape mutation patterns on both the X chromosome and autosomes.
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5
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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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6
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Cioppi F, Casamonti E, Krausz C. Age-Dependent De Novo Mutations During Spermatogenesis and Their Consequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:29-46. [DOI: 10.1007/978-3-030-21664-1_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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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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8
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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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9
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Gao Z, Wyman MJ, Sella G, Przeworski M. Interpreting the Dependence of Mutation Rates on Age and Time. PLoS Biol 2016; 14:e1002355. [PMID: 26761240 PMCID: PMC4711947 DOI: 10.1371/journal.pbio.1002355] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/11/2015] [Indexed: 01/06/2023] Open
Abstract
Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell divisions, providing a framework for understanding how mutation rates depend on sex, age, and cell division rate. We show that the accrual of mutations should track cell divisions not only when mutations are replicative in origin but also when they are non-replicative and repaired efficiently. One implication is that observations from diverse fields that to date have been interpreted as pointing to a replicative origin of most mutations could instead reflect the accumulation of mutations arising from endogenous reactions or exogenous mutagens. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, unless life history traits co-vary, the phylogenetic “molecular clock” should not be expected to run steadily across species. Modeling how the source of mutations relates to their rate of accumulation with age, sex, and number of cell divisions helps to explain perplexing observations about germline and somatic mutations. We relate how mutations arise to how they accumulate in different sexes, with age and with cell division. This model provides a single framework within which to interpret emerging results from evolutionary biology, human genetics, and cancer genetics. We show that the accrual of mutations should track cell divisions not only when mutations originate during DNA replication but also when they arise through non-replicative mechanisms and are repaired efficiently. This realization means that previous observations of correlations between mutation and cell division rates actually provide little support to the commonly held belief that most germline and somatic mutations arise from replication errors. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, without covariation in life history traits, the phylogenetic “molecular clock” should not be expected to run at constant rates across species.
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Affiliation(s)
- Ziyue Gao
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (ZG); (MP)
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - 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: (ZG); (MP)
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10
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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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11
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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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12
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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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13
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Venn O, Turner I, Mathieson I, de Groot N, Bontrop R, McVean G. Nonhuman genetics. Strong male bias drives germline mutation in chimpanzees. Science 2014; 344:1272-5. [PMID: 24926018 PMCID: PMC4746749 DOI: 10.1126/science.344.6189.1272] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Germline mutation determines rates of molecular evolution, genetic diversity, and fitness load. In humans, the average point mutation rate is 1.2 × 10(-8) per base pair per generation, with every additional year of father's age contributing two mutations across the genome and males contributing three to four times as many mutations as females. To assess whether such patterns are shared with our closest living relatives, we sequenced the genomes of a nine-member pedigree of Western chimpanzees, Pan troglodytes verus. Our results indicate a mutation rate of 1.2 × 10(-8) per base pair per generation, but a male contribution seven to eight times that of females and a paternal age effect of three mutations per year of father's age. Thus, mutation rates and patterns differ between closely related species.
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Affiliation(s)
- Oliver Venn
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Isaac Turner
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Iain Mathieson
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Natasja de Groot
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.
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14
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Wei W, Ning LW, Ye YN, Li SJ, Zhou HQ, Huang J, Guo FB. SMAL: A Resource of Spontaneous Mutation Accumulation Lines. Mol Biol Evol 2014; 31:1302-8. [DOI: 10.1093/molbev/msu073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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15
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The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. Eur J Hum Genet 2014; 22:1111-6. [PMID: 24448544 DOI: 10.1038/ejhg.2013.303] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/21/2013] [Accepted: 11/27/2013] [Indexed: 12/29/2022] Open
Abstract
Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338,000 years ago (95% CI=237,000-581,000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100,000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208,300 (95% CI=163,900-260,200) years ago.
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16
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Grégoire MC, Massonneau J, Simard O, Gouraud A, Brazeau MA, Arguin M, Leduc F, Boissonneault G. Male-driven de novo mutations in haploid germ cells. Mol Hum Reprod 2013; 19:495-9. [PMID: 23515669 DOI: 10.1093/molehr/gat022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
At the sequence level, genetic diversity is provided by de novo transmittable mutations that may act as a substrate for natural selection. The gametogenesis process itself is considered more likely to induce endogenous mutations and a clear male bias has been demonstrated from recent next-generation sequencing analyses. As new experimental evidence accumulates, the post-meiotic events of the male gametogenesis (spermiogenesis) appear as an ideal context to induce de novo genetic polymorphism transmittable to the next generation. It may prove to be a major component of the observed male mutation bias. As spermatids undergo chromatin remodeling, transient endogenous DNA double-stranded breaks are produced and trigger a DNA damage response. In these haploid cells, one would expect that the non-templated, DNA end-joining repair processes may generate a repertoire of sequence alterations in every sperm cell potentially transmittable to the next generation. This may therefore represent a novel physiological mechanism contributing to genetic diversity and evolution.
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Affiliation(s)
- Marie-Chantal Grégoire
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada J1E4K8
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17
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Follow-up study of 22 Chinese children with Alexander disease and analysis of parental origin of de novo GFAP mutations. J Hum Genet 2013; 58:183-8. [DOI: 10.1038/jhg.2012.152] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Research proceedings on primate comparative genomics. Zool Res 2013; 33:108-18. [DOI: 10.3724/sp.j.1141.2012.01108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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19
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Katsura Y, Satta Y. No evidence for a second evolutionary stratum during the early evolution of mammalian sex chromosomes. PLoS One 2012; 7:e45488. [PMID: 23094017 PMCID: PMC3477149 DOI: 10.1371/journal.pone.0045488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 08/20/2012] [Indexed: 11/19/2022] Open
Abstract
Mammalian sex chromosomes originated from a pair of autosomes, and homologous genes on the sex chromosomes (gametologs) differentiated through recombination arrest between the chromosomes. It was hypothesized that this differentiation in eutherians took place in a stepwise fashion and left a footprint on the X chromosome termed "evolutionary strata." The evolutionary stratum hypothesis claims that strata 1 and 2 (which correspond to the first two steps of chromosomal differentiation) were generated in the stem lineage of Theria or before the divergence between eutherians and marsupials. However, this prediction relied solely on the molecular clock hypothesis between pairs of human gametologs, and molecular evolution of marsupial sex chromosomal genes has not yet been investigated. In this study, we analyzed the following 7 pairs of marsupial gametologs, together with their eutherian orthologs that reside in stratum 1 or 2: SOX3/SRY, RBMX/Y, RPS4X/Y, HSFX/Y, XKRX/Y, SMCX/Y (KDM5C/D, JARID1C/D), and UBE1X/Y (UBA1/UBA1Y). Phylogenetic analyses and estimated divergence time of these gametologs reveal that they all differentiated at the same time in the therian ancestor. We have also provided strong evidence for gene conversion that occurred in the 3' region of the eutherian stratum 2 genes (SMCX/Y and UBE1X/Y). The results of the present study show that (1) there is no compelling evidence for the second stratum in the stem lineage of Theria; (2) gene conversion, which may have occurred between SMCX/Y and UBE1X/Y in the eutherian lineage, potentially accounts for their apparently lower degree of overall divergence.
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Affiliation(s)
| | - Yoko Satta
- Department of Evolutionary Study of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
- * E-mail:
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20
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Lartillot N. Interaction between selection and biased gene conversion in mammalian protein-coding sequence evolution revealed by a phylogenetic covariance analysis. Mol Biol Evol 2012; 30:356-68. [PMID: 23024185 DOI: 10.1093/molbev/mss231] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
According to the nearly-neutral model, variation in long-term effective population size among species should result in correlated variation in the ratio of nonsynonymous over synonymous substitution rates (dN/dS). Previous empirical investigations in mammals have been consistent with this prediction, suggesting an important role for nearly-neutral effects on protein-coding sequence evolution. GC-biased gene conversion (gBGC), on the other hand, is increasingly recognized as a major evolutionary force shaping genome nucleotide composition. When sufficiently strong compared with random drift, gBGC may significantly interfere with a nearly-neutral regime and impact dN/dS in a complex manner. Here, we investigate the phylogenetic correlations between dN/dS, the equilibrium GC composition (GC*), and several life-history and karyotypic traits in placental mammals. We show that the equilibrium GC composition decreases with body mass and increases with the number of chromosomes, suggesting a modulation of the strength of biased gene conversion due to changes in effective population size and genome-wide recombination rate. The variation in dN/dS is complex and only partially fits the prediction of the nearly-neutral theory. However, specifically restricting estimation of the dN/dS ratio on GC-conservative transversions, which are immune from gBGC, results in correlations that are more compatible with a nearly-neutral interpretation. Our investigation indicates the presence of complex interactions between selection and biased gene conversion and suggests that further mechanistic development is warranted, to tease out mutation, selection, drift, and conversion.
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Affiliation(s)
- Nicolas Lartillot
- Centre Robert-Cedergren pour la Bioinformatique, Département de Biochimie, Université de Montréal, Québec, Canada.
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21
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Choi SK, Yoon SR, Calabrese P, Arnheim N. Positive selection for new disease mutations in the human germline: evidence from the heritable cancer syndrome multiple endocrine neoplasia type 2B. PLoS Genet 2012; 8:e1002420. [PMID: 22359510 PMCID: PMC3280958 DOI: 10.1371/journal.pgen.1002420] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/19/2011] [Indexed: 01/15/2023] Open
Abstract
Multiple endocrine neoplasia type 2B (MEN2B) is a highly aggressive thyroid cancer syndrome. Since almost all sporadic cases are caused by the same nucleotide substitution in the RET proto-oncogene, the calculated disease incidence is 100-200 times greater than would be expected based on the genome average mutation frequency. In order to determine whether this increased incidence is due to an elevated mutation rate at this position (true mutation hot spot) or a selective advantage conferred on mutated spermatogonial stem cells, we studied the spatial distribution of the mutation in 14 human testes. In donors aged 36-68, mutations were clustered with small regions of each testis having mutation frequencies several orders of magnitude greater than the rest of the testis. In donors aged 19-23 mutations were almost non-existent, demonstrating that clusters in middle-aged donors grew during adulthood. Computational analysis showed that germline selection is the only plausible explanation. Testes of men aged 75-80 were heterogeneous with some like middle-aged and others like younger testes. Incorporating data on age-dependent death of spermatogonial stem cells explains the results from all age groups. Germline selection also explains MEN2B's male mutation bias and paternal age effect. Our discovery focuses attention on MEN2B as a model for understanding the genetic and biochemical basis of germline selection. Since RET function in mouse spermatogonial stem cells has been extensively studied, we are able to suggest that the MEN2B mutation provides a selective advantage by altering the PI3K/AKT and SFK signaling pathways. Mutations that are preferred in the germline but reduce the fitness of offspring increase the population's mutational load. Our approach is useful for studying other disease mutations with similar characteristics and could uncover additional germline selection pathways or identify true mutation hot spots.
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Affiliation(s)
- Soo-Kyung Choi
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Song-Ro Yoon
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Peter Calabrese
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
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22
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Paternal age effect mutations and selfish spermatogonial selection: causes and consequences for human disease. Am J Hum Genet 2012; 90:175-200. [PMID: 22325359 DOI: 10.1016/j.ajhg.2011.12.017] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/05/2011] [Accepted: 12/26/2011] [Indexed: 12/25/2022] Open
Abstract
Advanced paternal age has been associated with an increased risk for spontaneous congenital disorders and common complex diseases (such as some cancers, schizophrenia, and autism), but the mechanisms that mediate this effect have been poorly understood. A small group of disorders, including Apert syndrome (caused by FGFR2 mutations), achondroplasia, and thanatophoric dysplasia (FGFR3), and Costello syndrome (HRAS), which we collectively term "paternal age effect" (PAE) disorders, provides a good model to study the biological and molecular basis of this phenomenon. Recent evidence from direct quantification of PAE mutations in sperm and testes suggests that the common factor in the paternal age effect lies in the dysregulation of spermatogonial cell behavior, an effect mediated molecularly through the growth factor receptor-RAS signal transduction pathway. The data show that PAE mutations, although arising rarely, are positively selected and expand clonally in normal testes through a process akin to oncogenesis. This clonal expansion, which is likely to take place in the testes of all men, leads to the relative enrichment of mutant sperm over time-explaining the observed paternal age effect associated with these disorders-and in rare cases to the formation of testicular tumors. As regulation of RAS and other mediators of cellular proliferation and survival is important in many different biological contexts, for example during tumorigenesis, organ homeostasis and neurogenesis, the consequences of selfish mutations that hijack this process within the testis are likely to extend far beyond congenital skeletal disorders to include complex diseases, such as neurocognitive disorders and cancer predisposition.
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23
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Keightley PD. Rates and fitness consequences of new mutations in humans. Genetics 2012; 190:295-304. [PMID: 22345605 PMCID: PMC3276617 DOI: 10.1534/genetics.111.134668] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/13/2011] [Indexed: 12/13/2022] Open
Abstract
The human mutation rate per nucleotide site per generation (μ) can be estimated from data on mutation rates at loci causing Mendelian genetic disease, by comparing putatively neutrally evolving nucleotide sequences between humans and chimpanzees and by comparing the genome sequences of relatives. Direct estimates from genome sequencing of relatives suggest that μ is about 1.1 × 10(-8), which is about twofold lower than estimates based on the human-chimp divergence. This implies that an average of ~70 new mutations arise in the human diploid genome per generation. Most of these mutations are paternal in origin, but the male:female mutation rate ratio is currently uncertain and might vary even among individuals within a population. On the basis of a method proposed by Kondrashov and Crow, the genome-wide deleterious mutation rate (U) can be estimated from the product of the number of nucleotide sites in the genome, μ, and the mean selective constraint per site. Although the presence of many weakly selected mutations in human noncoding DNA makes this approach somewhat problematic, estimates are U ≈ 2.2 for the whole diploid genome per generation and 0.35 for mutations that change an amino acid of a protein-coding gene. A genome-wide deleterious mutation rate of 2.2 seems higher than humans could tolerate if natural selection is "hard," but could be tolerated if selection acts on relative fitness differences between individuals or if there is synergistic epistasis. I argue that in the foreseeable future, an accumulation of new deleterious mutations is unlikely to lead to a detectable decline in fitness of human populations.
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Affiliation(s)
- Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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24
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Zhang J, Bao X, Cao G, Jiang S, Zhu X, Lu H, Jia L, Pan H, Fehr S, Davis M, Leonard H, Ravine D, Wu X. What does the nature of the MECP2 mutation tell us about parental origin and recurrence risk in Rett syndrome? Clin Genet 2012; 82:526-33. [PMID: 22182064 DOI: 10.1111/j.1399-0004.2011.01838.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MECP2 mutations occurring in the severe neurological disorder Rett syndrome are predominantly de novo, with rare familial cases. The aims of this study were to provide a precise estimate of the parental origin of MECP2 mutations using a large Chinese sample and to assess whether parental origin varied by mutation type. The parental origin was paternal in 84/88 [95.5%, (95% confidence interval 88.77-98.75)] of sporadic Chinese cases. However, in a pooled sample including data from the literature the spectrum of mutations occurring on maternally and paternally derived chromosomes differed significantly. The excess we found of 'single base pair gains or losses' on maternally derived MECP2 gene alleles suggests that this mutational category is associated with an elevated risk of gonadal mosaicism, which has implications for genetic counseling.
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Affiliation(s)
- J Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, PR China
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25
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Abstract
In many species the mutation rate is higher in males than in females, a phenomenon denoted as male mutation bias. This is often observed in animals where males produce many more sperm than females produce eggs, and is thought to result from differences in the number of replication-associated mutations accumulated in each sex. Thus, studies of male mutation bias have the capacity to reveal information about the replication-dependent or replication-independent nature of different mutations. The availability of whole genome sequences for many species, as well as for multiple individuals within a species, has opened the door to studying factors, both sequence-specific and those acting on the genome globally, that affect differences in mutation rates between males and females. Here, we assess the advantages that genomic sequences provide for studies of male mutation bias and general mutation mechanisms, discuss major challenges left unresolved, and speculate about the direction of future studies.
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Affiliation(s)
- Melissa A. Wilson Sayres
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, USA
| | - Kateryna D. Makova
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, USA
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26
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Abstract
A major weakness of most genome-wide association studies has been their inability to fully explain the heritable component of complex disease. Nearly all such studies consider the two parental alleles to be functionally equivalent. However, the existence of imprinted genes demonstrates that this assumption can be wrong. In this review, we describe a wide variety of different mechanisms that underlie many other parent of origin and trans-generational effects that are known to operate in both humans and model organisms, suggesting that these phenomena are perhaps not uncommon in the genome. We propose that the consideration of alternative models of inheritance will improve our understanding of the heritability and causes of human traits and could have significant impacts on the study of complex disorders.
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Affiliation(s)
- A Guilmatre
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
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27
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Abstract
It has been known for many years that the mutation rate varies across the genome. However, only with the advent of large genomic data sets is the full extent of this variation becoming apparent. The mutation rate varies over many different scales, from adjacent sites to whole chromosomes, with the strongest variation seen at the smallest scales. Some of these patterns have clear mechanistic bases, but much of the rate variation remains unexplained, and some of it is deeply perplexing. Variation in the mutation rate has important implications in evolutionary biology and underexplored implications for our understanding of hereditary disease and cancer.
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28
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Reproductive benefit of oxidative damage: an oxidative stress "malevolence"? OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2011; 2011:760978. [PMID: 21969876 PMCID: PMC3182373 DOI: 10.1155/2011/760978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 06/09/2011] [Accepted: 07/28/2011] [Indexed: 12/23/2022]
Abstract
High levels of reactive oxygen species (ROS) compared to antioxidant defenses are considered to play a major role in diverse chronic age-related diseases and aging. Here we present an attempt to synthesize information about proximate oxidative processes in aging (relevant to free radical or oxidative damage hypotheses of aging) with an evolutionary scenario (credited here to Dawkins hypotheses) involving tradeoffs between the costs and benefits of oxidative stress to reproducing organisms. Oxidative stress may be considered a biological imperfection; therefore, the Dawkins' theory of imperfect adaptation of beings to environment was applied to the role of oxidative stress in processes like famine and infectious diseases and their consequences at the molecular level such as mutations and cell signaling. Arguments are presented that oxidative damage is not necessarily an evolutionary mistake but may be beneficial for reproduction; this may prevail over its harmfulness to health and longevity in evolution. Thus, Dawkins' principle of biological “malevolence” may be an additional biological paradigm for explaining the consequences of oxidative stress.
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29
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Misawa K. A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes. BMC Genomics 2011; 12:397. [PMID: 21819607 PMCID: PMC3169530 DOI: 10.1186/1471-2164-12-397] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 08/06/2011] [Indexed: 11/16/2022] Open
Abstract
Background Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human genome are negatively correlated to the local GC content and to the densities of functional elements. This study aimed at understanding the effect of genomic features, namely, GC content, gene density, and frequency of CpG islands, on the rates of codon substitution in human chromosomes. Results Codon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions in humans were estimated by comparing the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by using macaque genes as the outgroup. Since the genomic features are depending on each other, partial regression coefficients of these features were obtained. Conclusion The substitution rates of codons depend on gene densities of the chromosomes. Transcription-associated mutation is one such pressure. On the basis of these results, a model of codon substitutions that incorporates the effect of genomic features on codon substitution in human chromosomes was developed.
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Affiliation(s)
- Kazuharu Misawa
- Research Program for Computational Science, Research and Development Group for Next-Generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan.
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30
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Mugal CF, Ellegren H. Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol 2011; 12:R58. [PMID: 21696599 PMCID: PMC3218846 DOI: 10.1186/gb-2011-12-6-r58] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 05/04/2011] [Accepted: 06/22/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A major goal in the study of molecular evolution is to unravel the mechanisms that induce variation in the germ line mutation rate and in the genome-wide mutation profile. The rate of germ line mutation is considerably higher for cytosines at CpG sites than for any other nucleotide in the human genome, an increase commonly attributed to cytosine methylation at CpG sites. The CpG mutation rate, however, is not uniform across the genome and, as methylation levels have recently been shown to vary throughout the genome, it has been hypothesized that methylation status may govern variation in the rate of CpG mutation. RESULTS Here, we use genome-wide methylation data from human sperm cells to investigate the impact of DNA methylation on the CpG substitution rate in introns of human genes. We find that there is a significant correlation between the extent of methylation and the substitution rate at CpG sites. Further, we show that the CpG substitution rate is positively correlated with non-CpG divergence, suggesting susceptibility to factors responsible for the general mutation rate in the genome, and negatively correlated with GC content. We only observe a minor contribution of gene expression level, while recombination rate appears to have no significant effect. CONCLUSIONS Our study provides the first direct empirical support for the hypothesis that variation in the level of germ line methylation contributes to substitution rate variation at CpG sites. Moreover, we show that other genomic features also impact on CpG substitution rate variation.
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Affiliation(s)
- Carina F Mugal
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
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31
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Wilson Sayres MA, Venditti C, Pagel M, Makova KD. Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes. Evolution 2011; 65:2800-15. [PMID: 21967423 DOI: 10.1111/j.1558-5646.2011.01337.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Life-history traits vary substantially across species, and have been demonstrated to affect substitution rates. We compute genome-wide, branch-specific estimates of male mutation bias (the ratio of male-to-female mutation rates) across 32 mammalian genomes and study how these vary with life-history traits (generation time, metabolic rate, and sperm competition). We also investigate the influence of life-history traits on substitution rates at unconstrained sites across a wide phylogenetic range. We observe that increased generation time is the strongest predictor of variation in both substitution rates (for which it is a negative predictor) and male mutation bias (for which it is a positive predictor). Although less significant, we also observe that estimates of metabolic rate, reflecting replication-independent DNA damage and repair mechanisms, correlate negatively with autosomal substitution rates, and positively with male mutation bias. Finally, in contrast to expectations, we find no significant correlation between sperm competition and either autosomal substitution rates or male mutation bias. Our results support the important but frequently opposite effects of some, but not all, life-history traits on substitution rates.
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Affiliation(s)
- Melissa A Wilson Sayres
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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32
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Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Cassals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau G, Daly M, Stone EA, Hurles ME, Awadalla P. Variation in genome-wide mutation rates within and between human families. Nat Genet 2011; 43:712-4. [PMID: 21666693 PMCID: PMC3322360 DOI: 10.1038/ng.862] [Citation(s) in RCA: 390] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 05/19/2011] [Indexed: 11/09/2022]
Abstract
J.B.S. Haldane proposed in 1947 that the male germline may be more mutagenic than the female germline. Diverse studies have supported Haldane's contention of a higher average mutation rate in the male germline in a variety of mammals, including humans. Here we present, to our knowledge, the first direct comparative analysis of male and female germline mutation rates from the complete genome sequences of two parent-offspring trios. Through extensive validation, we identified 49 and 35 germline de novo mutations (DNMs) in two trio offspring, as well as 1,586 non-germline DNMs arising either somatically or in the cell lines from which the DNA was derived. Most strikingly, in one family, we observed that 92% of germline DNMs were from the paternal germline, whereas, in contrast, in the other family, 64% of DNMs were from the maternal germline. These observations suggest considerable variation in mutation rates within and between families.
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Affiliation(s)
| | - Jonathan E.M. Keebler
- Ste Justine Hospital Research Centre, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal H3T 1C5, Canada
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA
| | - Mark A. DePristo
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Five Cambridge Center, Cambridge, Massachusetts 02142, USA
| | | | - Yujun Zhang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Ferran Cassals
- Ste Justine Hospital Research Centre, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal H3T 1C5, Canada
| | - Youssef Idaghdour
- Ste Justine Hospital Research Centre, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal H3T 1C5, Canada
| | - Chris L. Hartl
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Five Cambridge Center, Cambridge, Massachusetts 02142, USA
| | | | - Kiran V. Garimella
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Five Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Martine Zilversmit
- Ste Justine Hospital Research Centre, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal H3T 1C5, Canada
| | - Reed Cartwright
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Guy Rouleau
- Ste Justine Hospital Research Centre, Department of Medicine, Faculty of Medicine, University of Montreal, Montreal H3T 1C5, Canada
| | - Mark Daly
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Five Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Eric A. Stone
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
| | | | - Philip Awadalla
- Ste Justine Hospital Research Centre, Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal H3T 1C5, Canada
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33
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Ananda G, Chiaromonte F, Makova KD. A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biol 2011; 12:R27. [PMID: 21426544 PMCID: PMC3129677 DOI: 10.1186/gb-2011-12-3-r27] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/21/2011] [Accepted: 03/22/2011] [Indexed: 01/03/2023] Open
Abstract
Background While the abundance of available sequenced genomes has led to many studies of regional heterogeneity in mutation rates, the co-variation among rates of different mutation types remains largely unexplored, hindering a deeper understanding of mutagenesis and genome dynamics. Here, utilizing primate and rodent genomic alignments, we apply two multivariate analysis techniques (principal components and canonical correlations) to investigate the structure of rate co-variation for four mutation types and simultaneously explore the associations with multiple genomic features at different genomic scales and phylogenetic distances. Results We observe a consistent, largely linear co-variation among rates of nucleotide substitutions, small insertions and small deletions, with some non-linear associations detected among these rates on chromosome X and near autosomal telomeres. This co-variation appears to be shaped by a common set of genomic features, some previously investigated and some novel to this study (nuclear lamina binding sites, methylated non-CpG sites and nucleosome-free regions). Strong non-linear relationships are also detected among genomic features near the centromeres of large chromosomes. Microsatellite mutability co-varies with other mutation rates at finer scales, but not at 1 Mb, and shows varying degrees of association with genomic features at different scales. Conclusions Our results allow us to speculate about the role of different molecular mechanisms, such as replication, recombination, repair and local chromatin environment, in mutagenesis. The software tools developed for our analyses are available through Galaxy, an open-source genomics portal, to facilitate the use of multivariate techniques in future large-scale genomics studies.
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Affiliation(s)
- Guruprasad Ananda
- Center for Medical Genomics, Penn State University, University Park, PA 16802, USA
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34
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Misawa K, Kikuno RF. Relationship between amino acid composition and gene expression in the mouse genome. BMC Res Notes 2011; 4:20. [PMID: 21272306 PMCID: PMC3038927 DOI: 10.1186/1756-0500-4-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Codon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. In many organisms, natural selection is considered to be a cause of codon bias because codon usage in highly expressed genes is biased toward optimal codons. Methods have previously been developed to predict the expression level of genes from their nucleotide sequences, which is based on the observation that synonymous codon usage shows an overall bias toward a few codons called major codons. However, the relationship between codon bias and gene expression level, as proposed by the translation-selection model, is less evident in mammals. FINDINGS We investigated the correlations between the expression levels of 1,182 mouse genes and amino acid composition, as well as between gene expression and codon preference. We found that a weak but significant correlation exists between gene expression levels and amino acid composition in mouse. In total, less than 10% of variation of expression levels is explained by amino acid components. We found the effect of codon preference on gene expression was weaker than the effect of amino acid composition, because no significant correlations were observed with respect to codon preference. CONCLUSION These results suggest that it is difficult to predict expression level from amino acid components or from codon bias in mouse.
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Affiliation(s)
- Kazuharu Misawa
- Research Program for Computational Science, Research and Development Group for Next-Generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, RIKEN, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.
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Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments. J Mol Evol 2010; 71:192-201. [PMID: 20700734 DOI: 10.1007/s00239-010-9377-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 07/26/2010] [Indexed: 01/21/2023]
Abstract
I have studied mutation patterns around very short microsatellites, focusing mainly on sequences carrying only two repeat units. By using human-chimpanzee-orangutan alignments, inferences can be made about both the relative rates of mutations and which bases have mutated. I find remarkable non-randomness, with mutation rate depending on a base's position relative to the microsatellite, the identity of the base itself and the motif in the microsatellite. Comparing the patterns around AC2 with those around other four-base combinations reveals that AC2 does not stand out as being special in the sense that non-repetitive tetramers also generate strong mutation biases. However, comparing AC2 and AC3 with AC4 reveals a step change in both the rate and nature of mutations occurring, suggesting a transition state, AC4 exhibiting an alternating high-low mutation rate pattern consistent with the sequence patterning seen around longer microsatellites. Surprisingly, most changes in repeat number occur through base substitutions rather than slippage, and the relative probability of gaining versus losing a repeat in this way varies greatly with repeat number. Slippage mutations reveal rather similar patterns of mutability compared with point mutations, being rare at two repeats where most cause the loss of a repeat, with both mutation rate and the proportion of expansion mutations increasing up to 6-8 repeats. Inferences about longer repeat tracts are hampered by uncertainties about the proportion of multi-species alignments that fail due to multi-repeat mutations and other rearrangements.
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Leclercq S, Rivals E, Jarne P. DNA slippage occurs at microsatellite loci without minimal threshold length in humans: a comparative genomic approach. Genome Biol Evol 2010; 2:325-35. [PMID: 20624737 PMCID: PMC2997547 DOI: 10.1093/gbe/evq023] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The dynamics of microsatellite, or short tandem repeats (STRs), is well documented for long, polymorphic loci, but much less is known for shorter ones. For example, the issue of a minimum threshold length for DNA slippage remains contentious. Model-fitting methods have generally concluded that slippage only occurs over a threshold length of about eight nucleotides, in contradiction with some direct observations of tandem duplications at shorter repeated sites. Using a comparative analysis of the human and chimpanzee genomes, we examined the mutation patterns at microsatellite loci with lengths as short as one period plus one nucleotide. We found that the rates of tandem insertions and deletions at microsatellite loci strongly deviated from background rates in other parts of the human genome and followed an exponential increase with STR size. More importantly, we detected no lower threshold length for slippage. The rate of tandem duplications at unrepeated sites was higher than expected from random insertions, providing evidence for genome-wide action of indel slippage (an alternative mechanism generating tandem repeats). The rate of point mutations adjacent to STRs did not differ from that estimated elsewhere in the genome, except around dinucleotide loci. Our results suggest that the emergence of STR depends on DNA slippage, indel slippage, and point mutations. We also found that the dynamics of tandem insertions and deletions differed in both rates and size at which these mutations take place. We discuss these results in both evolutionary and mechanistic terms.
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Affiliation(s)
- Sébastien Leclercq
- Centre d'Ecologie Fonctionnelle et d'Evolution, UMR 5175 CNRS, 1919 route de Mende, 34095 Montpellier cedex 5, France.
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Abstract
The accumulation of base substitutions (mutations) not subject to natural selection is the neutral mutation rate. Because this rate reflects the in vivo processes involved in maintaining the integrity of genetic information, the factors that affect the neutral mutation rate are of considerable interest. Mammals exhibit two dramatically different neutral mutation rates: the CpG mutation rate, wherein the C of most CpGs (i.e., methyl-CpG) mutate at 10-50 times that of C in any other context or of any other base. The latter mutations constitute the non-CpG rate. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs. Here, we determined the neutral non-CpG mutation rate as a function of CpG content by comparing sequence divergence of thousands of pairs of neutrally evolving chimpanzee and human orthologs that differ primarily in CpG content. Both the mutation rate and the mutational spectrum (transition/transversion ratio) of non-CpG residues change in parallel as sigmoidal (logistic) functions of CpG content. As different mechanisms generate transitions and transversions, these results indicate that both mutation rate and mutational processes are contingent on the local CpG content. We consider several possible mechanisms that might explain how CpG exerts these effects.
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Affiliation(s)
- Jean-Claude Walser
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
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Labuda D, Lefebvre JF, Nadeau P, Roy-Gagnon MH. Female-to-male breeding ratio in modern humans-an analysis based on historical recombinations. Am J Hum Genet 2010; 86:353-63. [PMID: 20188344 DOI: 10.1016/j.ajhg.2010.01.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 01/18/2010] [Accepted: 01/22/2010] [Indexed: 12/22/2022] Open
Abstract
Was the past genetic contribution of women and men to the current human population equal? Was polygyny (excess of breeding women) present among hominid lineages? We addressed these questions by measuring the ratio of population recombination rates between the X chromosome and the autosomes, rho(X)/rho(A). The X chromosome recombines only in female meiosis, whereas autosomes undergo crossovers in both sexes; thus, rho(X)/rho(A) reflects the female-to-male breeding ratio, beta. We estimated beta from rho(X)/rho(A) inferred from genomic diversity data and calibrated with recombination rates derived from pedigree data. For the HapMap populations, we obtained beta of 1.4 in the Yoruba from West Africa, 1.3 in Europeans, and 1.1 in East Asian samples. These values are consistent with a high prevalence of monogamy and limited polygyny in human populations. More mutations occur during male meiosis as compared to female meiosis at the rate ratio referred to as alpha. We show that at alpha not equal 1, the divergence rates and genetic diversities of the X chromosome relative to the autosomes are complex functions of both alpha and beta, making their independent estimation difficult. Because our estimator of beta does not require any knowledge of the mutation rates, our approach should allow us to dissociate the effects of alpha and beta on the genetic diversity and divergence rate ratios of the sex chromosomes to the autosomes.
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Affiliation(s)
- Damian Labuda
- Research Center, Hôpital Sainte-Justine, Université de Montréal, 3175 Cote Sainte-Catherine, Montreal, QC, Canada H3T 1C5.
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Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d'Aubenton-Carafa Y, Arneodo A, Hyrien O, Thermes C. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res 2010; 20:447-57. [PMID: 20103589 DOI: 10.1101/gr.098947.109] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. Here, we study the role of replication in the neutral substitution pattern. We obtained a high-resolution replication timing profile of the whole human genome by massively parallel sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates increase monotonously with replication timing even after controlling for local or regional nucleotide composition, crossover rate, distance to telomeres, and chromatin compaction. The increase in non-CpG substitution rates might result from several mechanisms including the increase in mutation-prone activities or the decrease in efficiency of DNA repair during the S phase. In contrast, the rate of C --> T transitions in CpG dinucleotides increases in later-replicating regions due to increasing DNA methylation level that reflects a negative correlation between timing and gene expression. Similar results are observed in the mouse, which indicates that replication timing is a main factor affecting nucleotide substitution dynamics at non-CpG sites and constitutes a major neutral process driving mammalian genome evolution.
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Affiliation(s)
- Chun-Long Chen
- Centre de Génétique Moléculaire, Allée de la Terrasse, 91198 Gif-sur-Yvette, France
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Activating mutations in FGFR3 and HRAS reveal a shared genetic origin for congenital disorders and testicular tumors. Nat Genet 2009; 41:1247-52. [PMID: 19855393 PMCID: PMC2817493 DOI: 10.1038/ng.470] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/21/2009] [Indexed: 12/19/2022]
Abstract
Genes mutated in congenital malformation syndromes are frequently implicated in oncogenesis, but the causative germline and somatic mutations occur in separate cells at different times of an organism's life. Here we unify these processes to a single cellular event for mutations arising in male germ cells that show a paternal age effect. Screening of 30 spermatocytic seminomas for oncogenic mutations in 17 genes identified 2 mutations in FGFR3 (both 1948A>G, encoding K650E, which causes thanatophoric dysplasia in the germline) and 5 mutations in HRAS. Massively parallel sequencing of sperm DNA showed that levels of the FGFR3 mutation increase with paternal age and that the mutation spectrum at the Lys650 codon is similar to that observed in bladder cancer. Most spermatocytic seminomas show increased immunoreactivity for FGFR3 and/or HRAS. We propose that paternal age-effect mutations activate a common 'selfish' pathway supporting proliferation in the testis, leading to diverse phenotypes in the next generation including fetal lethality, congenital syndromes and cancer predisposition.
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Abstract
Sex chromosomes have evolved multiple times in many taxa. The recent explosion in the availability of whole genome sequences from a variety of organisms makes it possible to investigate sex chromosome evolution within and across genomes. Comparative genomic studies have shown that quite distant species may share fundamental properties of sex chromosome evolution, while very similar species can evolve unique sex chromosome systems. Furthermore, within-species genomic analyses can illuminate chromosome-wide sequence and expression polymorphisms. Here, we explore recent advances in the study of vertebrate sex chromosomes achieved using genomic analyses.
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Affiliation(s)
- Melissa A Wilson
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Presgraves DC, Yi SV. Doubts about complex speciation between humans and chimpanzees. Trends Ecol Evol 2009; 24:533-40. [PMID: 19664844 PMCID: PMC2743777 DOI: 10.1016/j.tree.2009.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 04/10/2009] [Accepted: 04/20/2009] [Indexed: 01/15/2023]
Abstract
Two patterns from large-scale DNA sequence data have been put forward as evidence that speciation between humans and chimpanzees was complex, involving hybridization and strong selection. First, divergence between humans and chimpanzees varies considerably across the autosomes. Second, divergence between humans and chimpanzees (but not gorillas) is markedly lower on the X chromosome. Here, we describe how simple speciation and neutral molecular evolution explain both patterns. In particular, the wide range in autosomal divergence is consistent with stochastic variation in coalescence times in the ancestral population; and the lower human-chimpanzee divergence on the X chromosome is consistent with species differences in the strength of male-biased mutation caused by differences in mating system. We also highlight two further patterns of divergence that are problematic for the complex speciation model. Our conclusions raise doubts about complex speciation between humans and chimpanzees.
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Affiliation(s)
- Daven C Presgraves
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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43
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Understanding what determines the frequency and pattern of human germline mutations. Nat Rev Genet 2009; 10:478-88. [PMID: 19488047 DOI: 10.1038/nrg2529] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Surprising findings about human germline mutation have come from applying new technologies to detect rare mutations in germline DNA, from analysing DNA sequence divergence between humans and closely related species, and from investigating human polymorphic variation. In this Review we discuss how these approaches affect our current understanding of the roles of sex, age, mutation hot spots, germline selection and genomic factors in determining human nucleotide substitution mutation patterns and frequencies. To enhance our understanding of mutation and disease, more extensive molecular data on the human germ line with regard to mutation origin, DNA repair, epigenetic status and the effect of newly arisen mutations on gamete development are needed.
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Pink CJ, Swaminathan SK, Dunham I, Rogers J, Ward A, Hurst LD. Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates. Genome Biol Evol 2009; 1:13-22. [PMID: 20333173 PMCID: PMC2817397 DOI: 10.1093/gbe/evp001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2009] [Indexed: 12/12/2022] Open
Abstract
Since Haldane first noticed an excess of paternally derived mutations, it has been considered that most mutations derive from errors during germ line replication. Miyata et al. (1987) proposed that differences in the rate of neutral evolution on X, Y, and autosome can be employed to measure the extent of this male bias. This commonly applied method assumes replication to be the sole source of between-chromosome variation in substitution rates. We propose a simple test of this assumption: If true, estimates of the male bias should be independent of which two chromosomal classes are compared. Prior evidence from rodents suggested that this might not be true, but conclusions were limited by a lack of rat Y-linked sequence. We therefore sequenced two rat Y-linked bacterial artificial chromosomes and determined evolutionary rate by comparison with mouse. For estimation of rates we consider both introns and synonymous rates. Surprisingly, for both data sets the prediction of congruent estimates of alpha is strongly rejected. Indeed, some comparisons suggest a female bias with autosomes evolving faster than Y-linked sequence. We conclude that the method of Miyata et al. (1987) has the potential to provide incorrect estimates. Correcting the method requires understanding of the other causes of substitution that might differ between chromosomal classes. One possible cause is recombination-associated substitution bias for which we find some evidence. We note that if, as some suggest, this association is dominantly owing to male recombination, the high estimates of alpha seen in birds is to be expected as Z chromosomes recombine in males.
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Affiliation(s)
- Catherine J Pink
- Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
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45
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Abstract
Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (N(eX)) is equal to three-quarters of the autosomal population size (N(eA)). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that N(eX)/N(eA) is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when N(eX)/N(eA) > (3)/(4). We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution.
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Affiliation(s)
- Beatriz Vicoso
- Institute of Evolutionary Biology, School of Biological Science, University of Edinburgh, United Kingdom
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46
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Velando A, Torres R, Alonso-Alvarez C. Avoiding bad genes: oxidatively damaged DNA in germ line and mate choice. Bioessays 2008; 30:1212-9. [DOI: 10.1002/bies.20838] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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47
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Gaffney DJ, Keightley PD. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. BMC Evol Biol 2008; 8:265. [PMID: 18826599 PMCID: PMC2576242 DOI: 10.1186/1471-2148-8-265] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 09/30/2008] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. RESULTS Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. CONCLUSION Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.
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Affiliation(s)
- Daniel J Gaffney
- McGill University and Genome Québec Innovation Centre, 740 ave Dr Penfield Rm 7208, Montréal (Québec), H3A 1A4, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
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Burgess R, Yang Z. Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors. Mol Biol Evol 2008; 25:1979-94. [DOI: 10.1093/molbev/msn148] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Walser JC, Ponger L, Furano AV. CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res 2008; 18:1403-14. [PMID: 18550801 DOI: 10.1101/gr.076455.108] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The neutral mutation rate is equal to the base substitution rate when the latter is not affected by natural selection. Differences between these rates may reveal that factors such as natural selection, linkage, or a mutator locus are affecting a given sequence. We examined the neutral base substitution rate by measuring the sequence divergence of approximately 30,000 pairs of inactive orthologous L1 retrotransposon sequences interspersed throughout the human and chimpanzee genomes. In contrast to other studies, we related ortholog divergence to the time (age) that the L1 sequences resided in the genome prior to the chimpanzee and human speciation. As expected, the younger orthologs contained more hypermutable CpGs than the older ones because of their conversion to TpGs (and CpAs). Consequently, the younger orthologs accumulated more CpG mutations than the older ones during the approximately 5 million years since the human and chimpanzee lineages separated. But during this same time, the younger orthologs also accumulated more non-CpG mutations than the older ones. In fact, non-CpG and CpG mutations showed an almost perfect (R2 = 0.98) correlation for approximately 97% of the ortholog pairs. The correlation is independent of G + C content, recombination rate, and chromosomal location. Therefore, it likely reflects an intrinsic effect of CpGs, or mutations thereof, on non-CpG DNA rather than the joint manifestation of the chromosomal environment. The CpG effect is not uniform for all regions of non-CpG DNA. Therefore, the mutation rate of non-CpG DNA is contingent to varying extents on local CpG content. Aside from their implications for mutational mechanisms, these results indicate that a precise determination of a uniform genome-wide neutral mutation rate may not be attainable.
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Affiliation(s)
- Jean-Claude Walser
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
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Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol 2008; 9:R76. [PMID: 18447906 PMCID: PMC2643947 DOI: 10.1186/gb-2008-9-4-r76] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 04/04/2008] [Accepted: 04/30/2008] [Indexed: 11/10/2022] Open
Abstract
The evolutionary distance between human and macaque is particularly attractive for investigating neutral substitution rates, which were calculated as a function of a number of genomic parameters. Background The evolutionary distance between human and macaque is particularly attractive for investigating local variation in neutral substitution rates, because substitutions can be inferred more reliably than in comparisons with rodents and are less influenced by the effects of current and ancient diversity than in comparisons with closer primates. Here we investigate the human-macaque neutral substitution rate as a function of a number of genomic parameters. Results Using regression analyses we find that male mutation bias, male (but not female) recombination rate, distance to telomeres and substitution rates computed from orthologous regions in mouse-rat and dog-cow comparisons are prominent predictors of the neutral rate. Additionally, we demonstrate that the previously observed biphasic relationship between neutral rate and GC content can be accounted for by properly combining rates at CpG and non-CpG sites. Finally, we find the neutral rate to be negatively correlated with the densities of several classes of computationally predicted functional elements, and less so with the densities of certain classes of experimentally verified functional elements. Conclusion Our results suggest that while female recombination may be mainly responsible for driving evolution in GC content, male recombination may be mutagenic, and that other mutagenic mechanisms acting near telomeres, and mechanisms whose effects are shared across mammalian genomes, play significant roles. We also have evidence that the nonlinear increase in rates at high GC levels may be largely due to hyper-mutability of CpG dinucleotides. Finally, our results suggest that the performance of conservation-based prediction methods can be improved by accounting for neutral rates.
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Affiliation(s)
- Svitlana Tyekucheva
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
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