1
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Beichman AC, Zhu L, Harris K. The Evolutionary Interplay of Somatic and Germline Mutation Rates. Annu Rev Biomed Data Sci 2024; 7:83-105. [PMID: 38669515 DOI: 10.1146/annurev-biodatasci-102523-104225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Novel sequencing technologies are making it increasingly possible to measure the mutation rates of somatic cell lineages. Accurate germline mutation rate measurement technologies have also been available for a decade, making it possible to assess how this fundamental evolutionary parameter varies across the tree of life. Here, we review some classical theories about germline and somatic mutation rate evolution that were formulated using principles of population genetics and the biology of aging and cancer. We find that somatic mutation rate measurements, while still limited in phylogenetic diversity, seem consistent with the theory that selection to preserve the soma is proportional to life span. However, germline and somatic theories make conflicting predictions regarding which species should have the most accurate DNA repair. Resolving this conflict will require carefully measuring how mutation rates scale with time and cell division and achieving a better understanding of mutation rate pleiotropy among cell types.
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Affiliation(s)
- Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA;
| | - Luke Zhu
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Kelley Harris
- Computational Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA;
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2
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Hull KL, Greenwood MP, Lloyd M, Brink-Hull M, Bester-van der Merwe AE, Rhode C. Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38963286 DOI: 10.1111/imb.12940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.
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Affiliation(s)
- Kelvin L Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Melissa Lloyd
- Research and Development Department, Insect Technology Group Holdings UK Ltd., Guildford, UK
| | - Marissa Brink-Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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3
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Baur J, Koppik M, Savković U, Đorđević M, Stojkovic B, Berger D. Coevolution of longevity and female germline maintenance. Proc Biol Sci 2024; 291:20240532. [PMID: 38864321 PMCID: PMC11338575 DOI: 10.1098/rspb.2024.0532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 06/13/2024] Open
Abstract
An often-overlooked aspect of life-history optimization is the allocation of resources to protect the germline and secure safe transmission of genetic information. While failure to do so renders significant fitness consequences in future generations, germline maintenance comes with substantial costs. Thus, germline allocation should trade off with other life-history decisions and be optimized in accordance with an organism's reproductive schedule. Here, we tested this hypothesis by studying germline maintenance in lines of seed beetle, selected for early (E) or late (L) reproduction for 350 and 240 generations, respectively. Female animals provide maintenance and screening of male gametes in their reproductive tract and oocytes. Here, we reveal the ability of young and aged E- and L-females to provide this form of germline maintenance by mating them to males with ejaculates with artificially elevated levels of protein and DNA damage. We find that germline maintenance in E-females peaks at young age and then declines, while the opposite is true for L-females, in accordance with the age of reproduction in the respective regime. These findings identify the central role of allocation to secure germline integrity in life-history evolution and highlight how females can play a crucial role in mitigating the effects of male germline decisions on mutation rate and offspring quality.
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Affiliation(s)
- Julian Baur
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mareike Koppik
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Animal Ecology, Department of Zoology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Uroš Savković
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade11000, Serbia
| | - Mirko Đorđević
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade11000, Serbia
| | - Biljana Stojkovic
- Institute of Zoology, Chair of Genetics and Evolution, Faculty of Biology, Studentski trg 16, 11000 Belgrade, Serbia
| | - David Berger
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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4
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Wielgoss S, Van Dyken JD, Velicer GJ. Mutation Rate and Effective Population Size of the Model Cooperative Bacterium Myxococcus xanthus. Genome Biol Evol 2024; 16:evae066. [PMID: 38526062 PMCID: PMC11069108 DOI: 10.1093/gbe/evae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here, we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation accumulation experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life cycle-such as group-size reduction during fruiting-body development-or its highly structured spatial distribution have significantly influenced how these parameters have evolved.
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Affiliation(s)
- Sébastien Wielgoss
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - James David Van Dyken
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Gregory J Velicer
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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5
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Calabrese EJ, Selby PB. Background radiation and cancer risks: A major intellectual confrontation within the domain of radiation genetics with multiple converging biological disciplines. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2023; 20:621-632. [PMID: 37642576 DOI: 10.1080/15459624.2023.2252032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
This paper assesses the judgments of leading radiation geneticists and cancer risk assessment scientists from the mid-1950s to mid-1970s that background radiation has a significant effect on human genetic disease and cancer incidence. This assumption was adopted by the National Academy of Sciences (NAS) Biological Effects of Atomic Radiation (BEAR) I Genetics Panel for genetic diseases and subsequently applied to cancer risk assessment by other leading individuals/advisory groups (e.g., International Commission on Radiation Protection-ICRP). These recommendations assumed that a sizeable proportion of human mutations originated from background radiation due to cumulative exposure over prolonged reproductive periods and the linear nature of the dose-response. This paper shows that the assumption that background radiation is a significant cause of spontaneous mutation, genetic diseases, and cancer incidence is not supported by experimental and epidemiological findings, and discredits erroneous risk assessments that improperly influenced the recommendations of national and international advisory committees, risk assessment policies, and beliefs worldwide.
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Affiliation(s)
- Edward J Calabrese
- Department of Environmental Health Sciences, Morrill I, N344, University of Massachusetts, Amherst, MA, USA
| | - Paul B Selby
- Retired from Oak Ridge National Laboratory, Oak Ridge, TN, USA
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6
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Lynch M, Ali F, Lin T, Wang Y, Ni J, Long H. The divergence of mutation rates and spectra across the Tree of Life. EMBO Rep 2023; 24:e57561. [PMID: 37615267 PMCID: PMC10561183 DOI: 10.15252/embr.202357561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Farhan Ali
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
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7
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Wang Y, Obbard DJ. Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis. Evol Lett 2023; 7:216-226. [PMID: 37475753 PMCID: PMC10355183 DOI: 10.1093/evlett/qrad027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
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Affiliation(s)
- Yiguan Wang
- Corresponding author: Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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8
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Treaster S, Deelen J, Daane JM, Murabito J, Karasik D, Harris MP. Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation. SCIENCE ADVANCES 2023; 9:eadd2743. [PMID: 36630509 PMCID: PMC9833670 DOI: 10.1126/sciadv.add2743] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/09/2022] [Indexed: 05/16/2023]
Abstract
Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years. Multiple shifts in rockfish longevity have occurred independently and in a short evolutionary time frame, thus empowering convergence analyses. Our analyses reveal a common network of genes under convergent evolution, encompassing established aging regulators such as insulin signaling, yet also identify flavonoid (aryl-hydrocarbon) metabolism as a pathway modulating longevity. The selective pressures on these pathways indicate the ancestral state of rockfishes was long lived and that the changes in short-lived lineages are adaptive. These pathways were also used to explore genome-wide association studies of human longevity, identifying the aryl-hydrocarbon metabolism pathway to be significantly associated with human survival to the 99th percentile. This evolutionary intersection defines and cross-validates a previously unappreciated genetic architecture that associates with the evolution of longevity across vertebrates.
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Affiliation(s)
- Stephen Treaster
- Department of Orthopaedic Surgery, Boston Children’s Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joris Deelen
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Köln, Germany
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jacob M. Daane
- Department of Biology and Biochemistry, University of Houston, Houston TX, USA
| | - Joanne Murabito
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Marcus Institute for Aging Research, Hebrew Senior Life, Boston, MA, USA
| | - Matthew P. Harris
- Department of Orthopaedic Surgery, Boston Children’s Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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9
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Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges. Nat Commun 2022; 13:4752. [PMID: 35963846 PMCID: PMC9376063 DOI: 10.1038/s41467-022-32353-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 07/26/2022] [Indexed: 11/15/2022] Open
Abstract
Ecological and demographic factors can significantly shape the evolution of microbial populations both directly and indirectly, as when changes in the effective population size affect the efficiency of natural selection on the mutation rate. However, it remains unclear how rapidly the mutation-rate responds evolutionarily to the entanglement of ecological and population-genetic factors over time. Here, we directly assess the mutation rate and spectrum of Escherichia coli clones isolated from populations evolving in response to 1000 days of different transfer volumes and resource-replenishment intervals. The evolution of mutation rates proceeded rapidly in response to demographic and/or environmental changes, with substantial bidirectional shifts observed as early as 59 generations. These results highlight the remarkable rapidity by which mutation rates are shaped in asexual lineages in response to environmental and population-genetic forces, and are broadly consistent with the drift-barrier hypothesis for the evolution of mutation rates, while also highlighting situations in which mutator genotypes may be promoted by positive selection. How rapidly the mutation rate responds evolutionarily to ecological and population-genetic factors over time is unclear. Here, the authors show that the evolution of mutation rates in E. coli proceeds rapidly in response to these factors with substantial bidirectional shifts.
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10
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Milligan WR, Amster G, Sella G. The impact of genetic modifiers on variation in germline mutation rates within and among human populations. Genetics 2022; 221:iyac087. [PMID: 35666194 PMCID: PMC9339295 DOI: 10.1093/genetics/iyac087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Mutation rates and spectra differ among human populations. Here, we examine whether this variation could be explained by evolution at mutation modifiers. To this end, we consider genetic modifier sites at which mutations, "mutator alleles," increase genome-wide mutation rates and model their evolution under purifying selection due to the additional deleterious mutations that they cause, genetic drift, and demographic processes. We solve the model analytically for a constant population size and characterize how evolution at modifier sites impacts variation in mutation rates within and among populations. We then use simulations to study the effects of modifier sites under a plausible demographic model for Africans and Europeans. When comparing populations that evolve independently, weakly selected modifier sites (2Nes≈1), which evolve slowly, contribute the most to variation in mutation rates. In contrast, when populations recently split from a common ancestral population, strongly selected modifier sites (2Nes≫1), which evolve rapidly, contribute the most to variation between them. Moreover, a modest number of modifier sites (e.g. 10 per mutation type in the standard classification into 96 types) subject to moderate to strong selection (2Nes>1) could account for the variation in mutation rates observed among human populations. If such modifier sites indeed underlie differences among populations, they should also cause variation in mutation rates within populations and their effects should be detectable in pedigree studies.
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Affiliation(s)
- William R Milligan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Guy Amster
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Flatiron Health Inc., New York, NY 10013, USA
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
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11
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Demeter M, Derényi I, Szöllősi GJ. Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization. Nat Commun 2022; 13:1666. [PMID: 35351889 PMCID: PMC8964737 DOI: 10.1038/s41467-022-29004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/23/2022] [Indexed: 11/09/2022] Open
Abstract
Species-specific differences control cancer risk across orders of magnitude variation in body size and lifespan, e.g., by varying the copy numbers of tumor suppressor genes. It is unclear, however, how different tissues within an organism can control somatic evolution despite being subject to markedly different constraints, but sharing the same genome. Hierarchical differentiation, characteristic of self-renewing tissues, can restrain somatic evolution both by limiting divisional load, thereby reducing mutation accumulation, and by increasing cells' commitment to differentiation, which can "wash out" mutants. Here, we explore the organization of hierarchical tissues that have evolved to limit their lifetime incidence of cancer. Estimating the likelihood of cancer in the presence of mutations that enhance self-proliferation, we demonstrate that a trade-off exists between mutation accumulation and the strength of washing out. Our results explain differences in the organization of widely different hierarchical tissues, such as colon and blood.
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Affiliation(s)
- Márton Demeter
- Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- ELTE-MTA "Lendület" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Imre Derényi
- Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
- ELTE-MTA Statistical and Biological Physics Research Group, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
| | - Gergely J Szöllősi
- Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
- ELTE-MTA "Lendület" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
- Institute of Evolution, Centre for Ecological Research, Konkoly-Thege M. u 29-33, Budapest, Hungary.
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12
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Gilbert KJ, Zdraljevic S, Cook DE, Cutter AD, Andersen EC, Baer CF. The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation. Genetics 2022; 220:iyab166. [PMID: 34791202 PMCID: PMC8733438 DOI: 10.1093/genetics/iyab166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
The distribution of fitness effects (DFE) for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the DFE from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, genome structure, and nonrandom mating. Although inference methods aim to control for population size changes, the influence of nonrandom mating remains incompletely understood, despite being a common feature of many species. We report the DFE estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection on linked sites can conspire to compromise estimates of the DFE from extant polymorphisms with existing methods. These factors together tend to bias inferences toward weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the DFE are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.
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Affiliation(s)
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- University of Florida Genetics Institute, Gainesville, FL 32611, USA
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13
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Klein B, Holmér L, Smith KM, Johnson MM, Swain A, Stolp L, Teufel AI, Kleppe AS. A computational exploration of resilience and evolvability of protein-protein interaction networks. Commun Biol 2021; 4:1352. [PMID: 34857859 PMCID: PMC8639913 DOI: 10.1038/s42003-021-02867-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/03/2021] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions can lead to biological changes in an organism. Recent network-based approaches have shown that a phenotype's PPI network's resilience to environmental perturbations is related to its placement in the tree of life; though we still do not know how or why certain intra-cellular factors can bring about this resilience. Here, we explore the influence of gene expression and network properties on PPI networks' resilience. We use publicly available data of PPIs for E. coli, S. cerevisiae, and H. sapiens, where we compute changes in network resilience as new nodes (proteins) are added to the networks under three node addition mechanisms-random, degree-based, and gene-expression-based attachments. By calculating the resilience of the resulting networks, we estimate the effectiveness of these node addition mechanisms. We demonstrate that adding nodes with gene-expression-based preferential attachment (as opposed to random or degree-based) preserves and can increase the original resilience of PPI network in all three species, regardless of gene expression distribution or network structure. These findings introduce a general notion of prospective resilience, which highlights the key role of network structures in understanding the evolvability of phenotypic traits.
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Affiliation(s)
- Brennan Klein
- Network Science Institute, Northeastern University, Boston, MA, USA. .,Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA, USA.
| | - Ludvig Holmér
- grid.419684.60000 0001 1214 1861Center for Data Analytics, Stockholm School of Economics, Stockholm, Sweden
| | - Keith M. Smith
- grid.12361.370000 0001 0727 0669Department of Physics and Mathematics, Nottingham Trent University, Nottingham, UK
| | - Mackenzie M. Johnson
- grid.89336.370000 0004 1936 9924Department of Integrative Biology, University of Texas at Austin, Austin, TX USA
| | - Anshuman Swain
- grid.164295.d0000 0001 0941 7177Department of Biology, University of Maryland, College Park, MD USA
| | - Laura Stolp
- grid.7177.60000000084992262Graduate School of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Ashley I. Teufel
- grid.89336.370000 0004 1936 9924Department of Integrative Biology, University of Texas at Austin, Austin, TX USA ,grid.209665.e0000 0001 1941 1940Santa Fe Institute, Santa Fe, NM USA ,grid.469272.c0000 0001 0180 5693Texas A&M University, San Antonio, San Antonio, TX USA
| | - April S. Kleppe
- grid.5949.10000 0001 2172 9288Institute for Evolution and Biodiversity, University of Münster, Münster, Germany ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine (MOMA), Aarhus University, Aarhus, Denmark
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14
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Ho WC, Behringer MG, Miller SF, Gonzales J, Nguyen A, Allahwerdy M, Boyer GF, Lynch M. Evolutionary Dynamics of Asexual Hypermutators Adapting to a Novel Environment. Genome Biol Evol 2021; 13:evab257. [PMID: 34864972 PMCID: PMC8643662 DOI: 10.1093/gbe/evab257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2021] [Indexed: 12/24/2022] Open
Abstract
How microbes adapt to a novel environment is a central question in evolutionary biology. Although adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects strong genetic linkage. Despite these linkage effects, the evolved population exhibits parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results are generally inconsistent with a hypothesized positive relationship between the mutation rate and the adaptive speed of evolution, and provide insight into how clonal adaptation occurs in novel environments.
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Affiliation(s)
- Wei-Chin Ho
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Megan G Behringer
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Samuel F Miller
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jadon Gonzales
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Amber Nguyen
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Meriem Allahwerdy
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Gwyneth F Boyer
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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15
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The rate and molecular spectrum of mutation are selectively maintained in yeast. Nat Commun 2021; 12:4044. [PMID: 34193872 PMCID: PMC8245649 DOI: 10.1038/s41467-021-24364-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
What determines the rate (μ) and molecular spectrum of mutation is a fundamental question. The prevailing hypothesis asserts that natural selection against deleterious mutations has pushed μ to the minimum achievable in the presence of genetic drift, or the drift barrier. Here we show that, contrasting this hypothesis, μ substantially exceeds the drift barrier in diverse organisms. Random mutation accumulation (MA) in yeast frequently reduces μ, and deleting the newly discovered mutator gene PSP2 nearly halves μ. These results, along with a comparison between the MA and natural yeast strains, demonstrate that μ is maintained above the drift barrier by stabilizing selection. Similar comparisons show that the mutation spectrum such as the universal AT mutational bias is not intrinsic but has been selectively preserved. These findings blur the separation of mutation from selection as distinct evolutionary forces but open the door to alleviating mutagenesis in various organisms by genome editing. How natural selection shapes the rate and molecular spectrum of mutations is debated. Yeast mutation accumulation experiments identify a gene promoting mutagenesis and show stabilizing selection maintaining the mutation rate above the drift barrier. Selection also preserves the mutation spectrum.
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16
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Goldberg ME, Harris K. Mutational signatures of replication timing and epigenetic modification persist through the global divergence of mutation spectra across the great ape phylogeny. Genome Biol Evol 2021; 14:6275268. [PMID: 33983415 PMCID: PMC8743035 DOI: 10.1093/gbe/evab104] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 11/17/2022] Open
Abstract
Great ape clades exhibit variation in the relative mutation rates of different three-base-pair genomic motifs, with closely related species having more similar mutation spectra than distantly related species. This pattern cannot be explained by classical demographic or selective forces, but imply that DNA replication fidelity has been perturbed in different ways on each branch of the great ape phylogeny. Here, we use whole-genome variation from 88 great apes to investigate whether these species’ mutation spectra are broadly differentiated across the entire genome, or whether mutation spectrum differences are driven by DNA compartments that have particular functional features or chromatin states. We perform principal component analysis (PCA) and mutational signature deconvolution on mutation spectra ascertained from compartments defined by features including replication timing and ancient repeat content, finding evidence for consistent species-specific mutational signatures that do not depend on which functional compartments the spectra are ascertained from. At the same time, we find that many compartments have their own characteristic mutational signatures that appear stable across the great ape phylogeny. For example, in a mutation spectrum PCA compartmentalized by replication timing, the second principal component explaining 21.2% of variation separates all species’ late-replicating regions from their early-replicating regions. Our results suggest that great ape mutation spectrum evolution is not driven by epigenetic changes that modify mutation rates in specific genomic regions, but instead by trans-acting mutational modifiers that affect mutagenesis across the whole genome fairly uniformly.
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Affiliation(s)
- Michael E Goldberg
- University of Washington Department of Genome Sciences, 3720 15th Ave NE, Seattle WA 98105, United States of America
| | - Kelley Harris
- University of Washington Department of Genome Sciences, 3720 15th Ave NE, Seattle WA 98105, United States of America.,Fred Hutchinson Cancer Center Computational Biology Division, 1100 Fairview Ave N, Seattle, WA 98109, United States of America
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17
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Norambuena HV, Els P, Victoriano PF, Knowles L. Genome‐wide DNA and phenotypic information supports recent colonization of South American grasslands by Correndera Pipit (Aves, Motacillidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Paul Els
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA USA
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Pedro F. Victoriano
- Departamento de Zoología Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile
| | - Lacey Knowles
- Department of Ecology and Evolutionary Biology Museum of Zoology University of Michigan Ann Arbor MI USA
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18
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Jensen JD, Stikeleather RA, Kowalik TF, Lynch M. Imposed mutational meltdown as an antiviral strategy. Evolution 2020; 74:2549-2559. [PMID: 33047822 PMCID: PMC7993354 DOI: 10.1111/evo.14107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/30/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022]
Abstract
Following widespread infections of the most recent coronavirus known to infect humans, SARS‐CoV‐2, attention has turned to potential therapeutic options. With no drug or vaccine yet approved, one focal point of research is to evaluate the potential value of repurposing existing antiviral treatments, with the logical strategy being to identify at least a short‐term intervention to prevent within‐patient progression, while long‐term vaccine strategies unfold. Here, we offer an evolutionary/population‐genetic perspective on one approach that may overwhelm the capacity for pathogen defense (i.e., adaptation) – induced mutational meltdown – providing an overview of key concepts, review of previous theoretical and experimental work of relevance, and guidance for future research. Applied with appropriate care, including target specificity, induced mutational meltdown may provide a general, rapidly implemented approach for the within‐patient eradication of a wide range of pathogens or other undesirable microorganisms.
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Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, 85281
| | - Ryan A Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, 01655
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
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19
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Ruan Y, Wang H, Chen B, Wen H, Wu CI. Mutations Beget More Mutations-Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation. Mol Biol Evol 2020; 37:1007-1019. [PMID: 31778175 DOI: 10.1093/molbev/msz283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haiyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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20
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A Theoretical Framework for Evolutionary Cell Biology. J Mol Biol 2020; 432:1861-1879. [PMID: 32087200 DOI: 10.1016/j.jmb.2020.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 11/24/2022]
Abstract
One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologies at the structural and functional levels, the potential for rapid progress is great. The primary challenge for theory development is the establishment of a quantitative framework that transcends species boundaries. Two approaches to the problem are presented here: establishing the long-term steady-state distribution of mean phenotypes under specific regimes of mutation, selection, and drift and evaluating the energetic costs of cellular structures and functions. Although not meant to be the final word, these theoretical platforms harbor potential for generating insight into a diversity of unsolved problems, ranging from genome structure to cellular architecture to aspects of motility in organisms across the Tree of Life.
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21
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Kleppe AS, Bornberg-Bauer E. Robustness by intrinsically disordered C-termini and translational readthrough. Nucleic Acids Res 2019; 46:10184-10194. [PMID: 30247639 PMCID: PMC6365619 DOI: 10.1093/nar/gky778] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
During protein synthesis genetic instructions are passed from DNA via mRNA to the ribosome to assemble a protein chain. Occasionally, stop codons in the mRNA are bypassed and translation continues into the untranslated region (3′-UTR). This process, called translational readthrough (TR), yields a protein chain that becomes longer than would be predicted from the DNA sequence alone. Protein sequences vary in propensity for translational errors, which may yield evolutionary constraints by limiting evolutionary paths. Here we investigated TR in Saccharomyces cerevisiae by analysing ribosome profiling data. We clustered proteins as either prone or non-prone to TR, and conducted comparative analyses. We find that a relatively high frequency (5%) of genes undergo TR, including ribosomal subunit proteins. Our main finding is that proteins undergoing TR are highly expressed and have a higher proportion of intrinsically disordered C-termini. We suggest that highly expressed proteins may compensate for the deleterious effects of TR by having intrinsically disordered C-termini, which may provide conformational flexibility but without distorting native function. Moreover, we discuss whether minimizing deleterious effects of TR is also enabling exploration of the phenotypic landscape of protein isoforms.
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Affiliation(s)
- April Snofrid Kleppe
- Institute of Biodiversity and Evolution, University of Münster, Hüfferstr. 1, 48151 Münster, Germany
| | - Erich Bornberg-Bauer
- Institute of Biodiversity and Evolution, University of Münster, Hüfferstr. 1, 48151 Münster, Germany
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22
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Saxena AS, Salomon MP, Matsuba C, Yeh SD, Baer CF. Evolution of the Mutational Process under Relaxed Selection in Caenorhabditis elegans. Mol Biol Evol 2019; 36:239-251. [PMID: 30445510 DOI: 10.1093/molbev/msy213] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are an ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. "First-order MA" (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of "second-order MA" (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness; the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 kb GC content. However, probability of mutation is sufficiently predicted by the three-nucleotide motif alone. Approximately 90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the "drift barrier" model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.
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Affiliation(s)
| | - Matthew P Salomon
- Department of Biology, University of Florida, Gainesville, FL
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | - Chikako Matsuba
- Department of Biology, University of Florida, Gainesville, FL
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | - Shu-Dan Yeh
- Department of Biology, University of Florida, Gainesville, FL
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute
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23
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Abstract
Mutation provides the ultimate source of all new alleles in populations, including variants that cause disease and fuel adaptation. Recent whole genome sequencing studies have uncovered variation in the mutation rate among individuals and differences in the relative frequency of specific nucleotide changes (the mutation spectrum) between populations. Although parental age is a major driver of differences in overall mutation rate among individuals, the causes of variation in the mutation spectrum remain less well understood. Here, I use high-quality whole genome sequences from 29 inbred laboratory mouse strains to explore the root causes of strain variation in the mutation spectrum. My analysis leverages the unique, mosaic patterns of genetic relatedness among inbred mouse strains to identify strain private variants residing on haplotypes shared between multiple strains due to their recent descent from a common ancestor. I show that these strain-private alleles are strongly enriched for recent de novo mutations and lack signals of widespread purifying selection, suggesting their faithful recapitulation of the spontaneous mutation landscape in single strains. The spectrum of strain-private variants varies significantly among inbred mouse strains reared under standardized laboratory conditions. This variation is not solely explained by strain differences in age at reproduction, raising the possibility that segregating genetic differences affect the constellation of new mutations that arise in a given strain. Collectively, these findings imply the action of remarkably precise nucleotide-specific genetic mechanisms for tuning the de novo mutation landscape in mammals and underscore the genetic complexity of mutation rate control.
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24
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Featherston J, Arakaki Y, Hanschen ER, Ferris PJ, Michod RE, Olson BJSC, Nozaki H, Durand PM. The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage. Mol Biol Evol 2019; 35:855-870. [PMID: 29294063 DOI: 10.1093/molbev/msx332] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage-the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes. Using conservative estimates of gene family expansions a minimal set of expanded gene families was identified that associate with the origin of multicellularity. These families are rich in genes related to developmental processes. A subset of these families is lineage specific, which suggests that at a genomic level the evolution of multicellularity also includes lineage-specific molecular developments. Multiple points of evidence associate modifications to the ubiquitin proteasomal pathway (UPP) with the beginning of coloniality. Genes undergoing positive or accelerating selection in the multicellular volvocines were found to be enriched in components of the UPP and gene families gained at the origin of multicellularity include components of the UPP. A defining feature of colonial/multicellular life cycles is the genetic control of cell number. The genomic data presented here, which includes diversification of cell cycle genes and modifications to the UPP, align the genetic components with the evolution of this trait.
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Affiliation(s)
- Jonathan Featherston
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa.,Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
| | - Yoko Arakaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Hongo, Japan
| | - Erik R Hanschen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Patrick J Ferris
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | | | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Hongo, Japan
| | - Pierre M Durand
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
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25
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Raynes Y, Sniegowski PD, Weinreich DM. Migration promotes mutator alleles in subdivided populations. Evolution 2019; 73:600-608. [PMID: 30632605 PMCID: PMC6680344 DOI: 10.1111/evo.13681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/18/2018] [Accepted: 01/01/2019] [Indexed: 11/29/2022]
Abstract
Mutator alleles that elevate the genomic mutation rate may invade nonrecombining populations by hitchhiking with beneficial mutations. Mutators have been repeatedly observed to take over adapting laboratory populations and have been found at high frequencies in both microbial pathogen and cancer populations in nature. Recently, we have shown that mutators are only favored by selection in sufficiently large populations and transition to being disfavored as population size decreases. This population size-dependent sign inversion in selective effect suggests that population structure may also be an important determinant of mutation rate evolution. Although large populations may favor mutators, subdividing such populations into sufficiently small subpopulations (demes) might effectively inhibit them. On the other hand, migration between small demes that otherwise inhibit hitchhiking may promote mutator fixation in the whole metapopulation. Here, we use stochastic, agent-based simulations and evolution experiments with the yeast Saccharomyces cerevisiae to show that mutators can, indeed, be favored by selection in subdivided metapopulations composed of small demes connected by sufficient migration. In fact, we show that population structure plays a previously unsuspected role in promoting mutator success in subdivided metapopulations when migration is rare.
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Affiliation(s)
- Yevgeniy Raynes
- Department of Ecology and Evolutionary Biology, Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, 02906
| | - Paul D Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, 02906
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26
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Pandey V, Zhang M, You M, Zhang W, Chen R, Zhang W, Ma L, Wu ZS, Zhu T, Xu XQ, Lobie PE. Expression of two non-mutated genetic elements is sufficient to stimulate oncogenic transformation of human mammary epithelial cells. Cell Death Dis 2018; 9:1147. [PMID: 30451834 PMCID: PMC6242831 DOI: 10.1038/s41419-018-1177-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022]
Abstract
Trefoil factor 3 (TFF3) expression is positively associated with advanced clinicopathological features of mammary carcinoma (MC). Herein, we provide evidence for a functional role of TFF3 in oncogenic transformation of immortalized, but otherwise normal human mammary epithelial cells (HMECs), namely, HMEC-hTERT, MCF10A, and MCF12A. Forced expression of TFF3 in immortalized-HMECs enhanced cell proliferation, cell survival, anchorage-independent growth, produced highly disorganised three-dimensional (3D) acinar structures and generated tumours in immunocompromised mice. Forced expression of TFF3 in immortalized-HMECs stimulated STAT3 activity that was required for TFF3-stimulated cell proliferation, survival, and anchorage-independent growth. TFF3 specifically utilised STAT3 activity to govern a transcriptional program, which was required for TFF3-stimulated oncogenic transformation of immortalized-HMECs, including transcriptional upregulation of CCND1 and BCL2. siRNA-mediated depletion or functional inhibition of STAT3 significantly inhibited the TFF3-stimulated transcription of CCND1 and BCL2 and oncogenicity in immortalized-HMECs. Furthermore, DOX-inducible expression of TFF3 in HMEC-hTERT cells also permitted anchorage-independent growth and produced disorganized acinar structures in 3D Matrigel culture. Removal of DOX-induced expression of TFF3 in HMEC-hTERT cells, previously grown with DOX, resulted in efficient normalisation of the disorganized acinar architecture and attenuated cell viability in Matrigel culture. Cumulatively, these findings suggest that TFF3 is a potent oncogene and its increased expression along with hTERT in HMECs is sufficient to produce oncogenic transformation.
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Affiliation(s)
- Vijay Pandey
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong, PR China
| | - Min Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Mingliang You
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Weijie Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rumei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wei Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Tianhe District, Guangzhou, Guangdong, PR China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Lan Ma
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong, PR China
| | - Zheng-Sheng Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, PR China
| | - Tao Zhu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Xiu Qin Xu
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Fujian, PR China.
| | - Peter E Lobie
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong, PR China. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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27
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Danneels B, Pinto-Carbó M, Carlier A. Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes. Genome Biol Evol 2018; 10:1792-1802. [PMID: 29982456 PMCID: PMC6054270 DOI: 10.1093/gbe/evy140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Pseudogenes are a paradigm of neutral evolution and their study has the potential to reveal intrinsic mutational biases. However, this potential is mitigated by the fact that pseudogenes are quickly purged from bacterial genomes. Here, we assembled a large set of pseudogenes from genomes experiencing reductive evolution as well as functional references for which we could establish reliable phylogenetic relationships. Using this unique dataset, we identified 857 independent insertion and deletion mutations and discover a pervasive bias towards deletions, but not insertions, with sizes multiples of 3 nt. We further show that selective constraints for the preservation of gene frame are unlikely to account for the observed mutational bias and propose that a mechanistic bias in alternative end-joining repair, a recombination-independent double strand break DNA repair mechanism, is responsible for the accumulation of 3n deletions.
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Affiliation(s)
- Bram Danneels
- Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Marta Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zurich, Switzerland
| | - Aurelien Carlier
- Department of Biochemistry and Microbiology, Ghent University, Belgium
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28
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Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. Reproductive Longevity Predicts Mutation Rates in Primates. Curr Biol 2018; 28:3193-3197.e5. [PMID: 30270182 DOI: 10.1016/j.cub.2018.08.050] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10-8 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.
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Affiliation(s)
- Gregg W C Thomas
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
| | - Richard J Wang
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Arthi Puri
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Lawrence E Williams
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christian R Abee
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, 201 Dowman Drive, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University, 201 Dowman Drive, Atlanta, GA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
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29
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Mutation, Eugenics, and the Boundaries of Science. Genetics 2017; 204:825-827. [PMID: 27729497 DOI: 10.1534/genetics.116.194621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/08/2016] [Indexed: 11/18/2022] Open
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Mutation Rate Evolution in Partially Selfing and Partially Asexual Organisms. Genetics 2017; 207:1561-1575. [PMID: 28971958 DOI: 10.1534/genetics.117.300346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
Different factors can influence the evolution of the mutation rate of a species: costs associated with DNA replication fidelity, indirect selection caused by the mutations produced (that should generally favor lower mutation rates, given that most mutations affecting fitness are deleterious), and genetic drift, which may render selection acting on weak mutators inefficient. In this paper, we use a two-locus model to compute the strength of indirect selection acting on a modifier locus that affects the mutation rate toward a deleterious allele at a second, linked, locus, in a population undergoing partial selfing or partial clonality. The results show that uniparental reproduction increases the effect of indirect selection for lower mutation rates. Extrapolating to the case of a whole genome with many deleterious alleles, and introducing a direct cost to DNA replication fidelity, the results can be used to compute the evolutionarily stable mutation rate, U In the absence of mutational bias toward higher U, the analytical prediction fits well with individual-based, multilocus simulation results. When such a bias is added into the simulations, however, genetic drift may lead to the maintenance of higher mutation rates, and this effect may be amplified in highly selfing or highly clonal populations due to their reduced effective population size.
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31
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Lynch M, Ackerman MS, Gout JF, Long H, Sung W, Thomas WK, Foster PL. Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet 2017; 17:704-714. [PMID: 27739533 DOI: 10.1038/nrg.2016.104] [Citation(s) in RCA: 438] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Matthew S Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Hongan Long
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
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32
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Peterson LE, Kovyrshina T. Progression inference for somatic mutations in cancer. Heliyon 2017; 3:e00277. [PMID: 28492066 PMCID: PMC5415494 DOI: 10.1016/j.heliyon.2017.e00277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 01/05/2023] Open
Abstract
Computational methods were employed to determine progression inference of genomic alterations in commonly occurring cancers. Using cross-sectional TCGA data, we computed evolutionary trajectories involving selectivity relationships among pairs of gene-specific genomic alterations such as somatic mutations, deletions, amplifications, downregulation, and upregulation among the top 20 driver genes associated with each cancer. Results indicate that the majority of hierarchies involved TP53, PIK3CA, ERBB2, APC, KRAS, EGFR, IDH1, VHL, etc. Research into the order and accumulation of genomic alterations among cancer driver genes will ever-increase as the costs of nextgen sequencing subside, and personalized/precision medicine incorporates whole-genome scans into the diagnosis and treatment of cancer.
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Affiliation(s)
- Leif E. Peterson
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Dept. of Biostatistics, School of Public Health, University of Texas – Health Science Center, Houston, TX 77030, USA
- Dept. of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Dept. of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Tatiana Kovyrshina
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Mathematics and Statistics, University of Houston – Downtown, Houston, TX 77002, USA
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Abstract
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
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Abstract
We propose a modification of the Crow-Kimura and Eigen models of biological molecular evolution to include a mutator gene that causes both an increase in the mutation rate and a change in the fitness landscape. This mutator effect relates to a wide range of biomedical problems. There are three possible phases: mutator phase, mixed phase and non-selective phase. We calculate the phase structure, the mean fitness and the fraction of the mutator allele in the population, which can be applied to describe cancer development and RNA viruses. We find that depending on the genome length, either the normal or the mutator allele dominates in the mixed phase. We analytically solve the model for a general fitness function. We conclude that the random fitness landscape is an appropriate choice for describing the observed mutator phenomenon in the case of a small fraction of mutators. It is shown that the increase in the mutation rates in the regular and the mutator parts of the genome should be set independently; only some combinations of these increases can push the complex biomedical system to the non-selective phase, potentially related to the eradication of tumors.
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35
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The Fitness Effects of Spontaneous Mutations Nearly Unseen by Selection in a Bacterium with Multiple Chromosomes. Genetics 2016; 204:1225-1238. [PMID: 27672096 DOI: 10.1534/genetics.116.193060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022] Open
Abstract
Mutation accumulation (MA) experiments employ the strategy of minimizing the population size of evolving lineages to greatly reduce effects of selection on newly arising mutations. Thus, most mutations fix within MA lines independently of their fitness effects. This approach, more recently combined with genome sequencing, has detailed the rates, spectra, and biases of different mutational processes. However, a quantitative understanding of the fitness effects of mutations virtually unseen by selection has remained an untapped opportunity. Here, we analyzed the fitness of 43 sequenced MA lines of the multi-chromosome bacterium Burkholderia cenocepacia that had each undergone 5554 generations of MA and accumulated an average of 6.73 spontaneous mutations. Most lineages exhibited either neutral or deleterious fitness in three different environments in comparison with their common ancestor. The only mutational class that was significantly overrepresented in lineages with reduced fitness was the loss of the plasmid, though nonsense mutations, missense mutations, and coding insertion-deletions were also overrepresented in MA lineages whose fitness had significantly declined. Although the overall distribution of fitness effects was similar between the three environments, the magnitude and even the sign of the fitness of a number of lineages changed with the environment, demonstrating that the fitness of some genotypes was environmentally dependent. These results present an unprecedented picture of the fitness effects of spontaneous mutations in a bacterium with multiple chromosomes and provide greater quantitative support for the theory that the vast majority of spontaneous mutations are neutral or deleterious.
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36
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Evolution of Mutation Rates in Rapidly Adapting Asexual Populations. Genetics 2016; 204:1249-1266. [PMID: 27646140 DOI: 10.1534/genetics.116.193565] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/13/2016] [Indexed: 11/18/2022] Open
Abstract
Mutator and antimutator alleles often arise and spread in both natural microbial populations and laboratory evolution experiments. The evolutionary dynamics of these mutation rate modifiers are determined by indirect selection on linked beneficial and deleterious mutations. These indirect selection pressures have been the focus of much earlier theoretical and empirical work, but we still have a limited analytical understanding of how the interplay between hitchhiking and deleterious load influences the fates of modifier alleles. Our understanding is particularly limited when clonal interference is common, which is the regime of primary interest in laboratory microbial evolution experiments. Here, we calculate the fixation probability of a mutator or antimutator allele in a rapidly adapting asexual population, and we show how this quantity depends on the population size, the beneficial and deleterious mutation rates, and the strength of a typical driver mutation. In the absence of deleterious mutations, we find that clonal interference enhances the fixation probability of mutators, even as they provide a diminishing benefit to the overall rate of adaptation. When deleterious mutations are included, natural selection pushes the population toward a stable mutation rate that can be suboptimal for the adaptation of the population as a whole. The approach to this stable mutation rate is not necessarily monotonic: even in the absence of epistasis, selection can favor mutator and antimutator alleles that "overshoot" the stable mutation rate by substantial amounts.
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37
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Abstract
Mutations are the ultimate source of variation used for evolutionary adaptation, while also being predominantly deleterious and a source of genetic disorders. Understanding the rate of insertion-deletion mutations (indels) is essential to understanding evolutionary processes, especially in coding regions, where such mutations can disrupt production of essential proteins. Using direct estimates of indel rates from 14 phylogenetically diverse eukaryotic and bacterial species, along with measures of standing variation in such species, we obtain results that imply an inverse relationship of mutation rate and effective population size. These results, which corroborate earlier observations on the base-substitution mutation rate, appear most compatible with the hypothesis that natural selection reduces mutation rates per effective genome to the point at which the power of random genetic drift (approximated by the inverse of effective population size) becomes overwhelming. Given the substantial differences in DNA metabolism pathways that give rise to these two types of mutations, this consistency of results raises the possibility that refinement of other molecular and cellular traits may be inversely related to species-specific levels of random genetic drift.
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38
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Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum. PLoS Biol 2016; 14:e1002419. [PMID: 27015430 PMCID: PMC4807879 DOI: 10.1371/journal.pbio.1002419] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
Abstract
Mutations affect individual health, population persistence, adaptation, diversification, and genome evolution. There is evidence that the mutation rate varies among genotypes, but the causes of this variation are poorly understood. Here, we link differences in genetic quality with variation in spontaneous mutation in a Drosophila mutation accumulation experiment. We find that chromosomes maintained in low-quality genetic backgrounds experience a higher rate of indel mutation and a lower rate of gene conversion in a manner consistent with condition-based differences in the mechanisms used to repair DNA double strand breaks. These aspects of the mutational spectrum were also associated with body mass, suggesting that the effect of genetic quality on DNA repair was mediated by overall condition, and providing a mechanistic explanation for the differences in mutational fitness decline among these genotypes. The rate and spectrum of substitutions was unaffected by genetic quality, but we find variation in the probability of substitutions and indels with respect to several aspects of local sequence context, particularly GC content, with implications for models of molecular evolution and genome scans for signs of selection. Our finding that the chances of mutation depend on genetic context and overall condition has important implications for how sequences evolve, the risk of extinction, and human health.
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39
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Keith N, Tucker AE, Jackson CE, Sung W, Lucas Lledó JI, Schrider DR, Schaack S, Dudycha JL, Ackerman M, Younge AJ, Shaw JR, Lynch M. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Res 2016; 26:60-9. [PMID: 26518480 PMCID: PMC4691751 DOI: 10.1101/gr.191338.115] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023]
Abstract
Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.
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Affiliation(s)
- Nathan Keith
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | - Abraham E Tucker
- Biology Department, Southern Arkansas University, Magnolia, Arkansas 71753, USA
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Daniel R Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sarah Schaack
- Biology Department, Reed College, Portland, Oregon 97202, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Andrew J Younge
- School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA; School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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40
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Hussain S. A new conceptual framework for investigating complex genetic disease. Front Genet 2015; 6:327. [PMID: 26583033 PMCID: PMC4631989 DOI: 10.3389/fgene.2015.00327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/21/2015] [Indexed: 01/17/2023] Open
Abstract
Some common diseases are known to have an inherited component, however, their population- and familial-incidence patterns do not conform to any known monogenic Mendelian pattern of inheritance and instead they are currently much better explained if an underlying polygenic architecture is posited. Studies that have attempted to identify the causative genetic factors have been designed on this polygenic framework, but so far the yield has been largely unsatisfactory. Based on accumulating recent observations concerning the roles of somatic mosaicism in disease, in this article a second framework which posits a single gene-two hit model which can be modulated by a mutator/anti-mutator genetic background is suggested. I discuss whether such a model can be considered a viable alternative based on current knowledge, its advantages over the current polygenic framework, and describe practical routes via which the new framework can be investigated.
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Affiliation(s)
- Shobbir Hussain
- Department of Biology and Biochemistry, University of BathBath, UK
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41
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Richter I, Fidler AE. Tunicate pregnane X receptor (PXR) orthologs: Transcript characterization and natural variation. Mar Genomics 2015; 23:99-108. [DOI: 10.1016/j.margen.2015.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 12/12/2022]
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42
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Santiago E. Probability and time to fixation of an evolving sequence. Theor Popul Biol 2015; 104:78-85. [DOI: 10.1016/j.tpb.2015.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/03/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
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43
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Abstract
Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology.
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44
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Corbett-Detig RB, Hartl DL, Sackton TB. Natural selection constrains neutral diversity across a wide range of species. PLoS Biol 2015; 13:e1002112. [PMID: 25859758 PMCID: PMC4393120 DOI: 10.1371/journal.pbio.1002112] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.
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Affiliation(s)
- Russell B. Corbett-Detig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Massachusetts, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Massachusetts, United States of America
| | - Timothy B. Sackton
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Massachusetts, United States of America
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45
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Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc Natl Acad Sci U S A 2014; 111:15138-43. [PMID: 25277973 DOI: 10.1073/pnas.1404341111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cancer progression is an example of a rapid adaptive process where evolving new traits is essential for survival and requires a high mutation rate. Precancerous cells acquire a few key mutations that drive rapid population growth and carcinogenesis. Cancer genomics demonstrates that these few driver mutations occur alongside thousands of random passenger mutations--a natural consequence of cancer's elevated mutation rate. Some passengers are deleterious to cancer cells, yet have been largely ignored in cancer research. In population genetics, however, the accumulation of mildly deleterious mutations has been shown to cause population meltdown. Here we develop a stochastic population model where beneficial drivers engage in a tug-of-war with frequent mildly deleterious passengers. These passengers present a barrier to cancer progression describable by a critical population size, below which most lesions fail to progress, and a critical mutation rate, above which cancers melt down. We find support for this model in cancer age-incidence and cancer genomics data that also allow us to estimate the fitness advantage of drivers and fitness costs of passengers. We identify two regimes of adaptive evolutionary dynamics and use these regimes to understand successes and failures of different treatment strategies. A tumor's load of deleterious passengers can explain previously paradoxical treatment outcomes and suggest that it could potentially serve as a biomarker of response to mutagenic therapies. The collective deleterious effect of passengers is currently an unexploited therapeutic target. We discuss how their effects might be exacerbated by current and future therapies.
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46
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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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47
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Roerink SF, van Schendel R, Tijsterman M. Polymerase theta-mediated end joining of replication-associated DNA breaks in C. elegans. Genome Res 2014; 24:954-62. [PMID: 24614976 PMCID: PMC4032859 DOI: 10.1101/gr.170431.113] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/04/2014] [Indexed: 11/24/2022]
Abstract
DNA lesions that block replication fork progression are drivers of cancer-associated genome alterations, but the error-prone DNA repair mechanisms acting on collapsed replication are incompletely understood, and their contribution to genome evolution largely unexplored. Here, through whole-genome sequencing of animal populations that were clonally propagated for more than 50 generations, we identify a distinct class of deletions that spontaneously accumulate in C. elegans strains lacking translesion synthesis (TLS) polymerases. Emerging DNA double-strand breaks are repaired via an error-prone mechanism in which the outermost nucleotide of one end serves to prime DNA synthesis on the other end. This pathway critically depends on the A-family polymerase theta, which protects the genome against gross chromosomal rearrangements. By comparing the genomes of isolates of C. elegans from different geographical regions, we found that in fact most spontaneously evolving structural variations match the signature of polymerase theta-mediated end joining (TMEJ), illustrating that this pathway is an important source of genetic diversification.
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Affiliation(s)
| | | | - Marcel Tijsterman
- Department of Toxicogenetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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48
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Experimental evolution and the dynamics of genomic mutation rate modifiers. Heredity (Edinb) 2014; 113:375-80. [PMID: 24849169 DOI: 10.1038/hdy.2014.49] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 04/11/2014] [Accepted: 04/15/2014] [Indexed: 01/01/2023] Open
Abstract
Because genes that affect mutation rates are themselves subject to mutation, mutation rates can be influenced by natural selection and other evolutionary forces. The population genetics of mutation rate modifier alleles has been a subject of theoretical interest for many decades. Here, we review experimental contributions to our understanding of mutation rate modifier dynamics. Numerous evolution experiments have shown that mutator alleles (modifiers that elevate the genomic mutation rate) can readily rise to high frequencies via genetic hitchhiking in non-recombining microbial populations. Whereas these results certainly provide an explanatory framework for observations of sporadically high mutation rates in pathogenic microbes and in cancer lineages, it is nonetheless true that most natural populations have very low mutation rates. This raises the interesting question of how mutator hitchhiking is suppressed or its phenotypic effect reversed in natural populations. Very little experimental work has addressed this question; with this in mind, we identify some promising areas for future experimental investigation.
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49
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Honma H, Hirai M, Nakamura S, Hakimi H, Kawazu SI, Palacpac NMQ, Hisaeda H, Matsuoka H, Kawai S, Endo H, Yasunaga T, Ohashi J, Mita T, Horii T, Furusawa M, Tanabe K. Generation of rodent malaria parasites with a high mutation rate by destructing proofreading activity of DNA polymerase δ. DNA Res 2014; 21:439-46. [PMID: 24670267 PMCID: PMC4131837 DOI: 10.1093/dnares/dsu009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Plasmodium falciparum malaria imposes a serious public health concern throughout the tropics. Although genetic tools are principally important to fully investigate malaria parasites, currently available forward and reverse tools are fairly limited. It is expected that parasites with a high mutation rate can readily acquire novel phenotypes/traits; however, they remain an untapped tool for malaria biology. Here, we generated a mutator malaria parasite (hereinafter called a ‘malaria mutator’), using site-directed mutagenesis and gene transfection techniques. A mutator Plasmodium berghei line with a defective proofreading 3′ → 5′ exonuclease activity in DNA polymerase δ (referred to as PbMut) and a control P. berghei line with wild-type DNA polymerase δ (referred to as PbCtl) were maintained by weekly passage in ddY mice for 122 weeks. High-throughput genome sequencing analysis revealed that two PbMut lines had 175–178 mutations and a 86- to 90-fold higher mutation rate than that of a PbCtl line. PbMut, PbCtl, and their parent strain, PbWT, showed similar course of infection. Interestingly, PbMut lost the ability to form gametocytes during serial passages. We believe that the malaria mutator system could provide a novel and useful tool to investigate malaria biology.
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Affiliation(s)
- Hajime Honma
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Makoto Hirai
- Department of Parasitology, Graduate School of Medicine, Gunma University, Maebashi, Gunma 371-8511, Japan
| | - Shota Nakamura
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hassan Hakimi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Shin-Ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Nirianne M Q Palacpac
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hajime Hisaeda
- Department of Parasitology, Graduate School of Medicine, Gunma University, Maebashi, Gunma 371-8511, Japan
| | - Hiroyuki Matsuoka
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Satoru Kawai
- Laboratory of Tropical Medicine and Parasitology, Institute of International Education and Research, Dokkyo Medical University, Shimotsuga, Tochigi 321-0293, Japan
| | - Hiroyoshi Endo
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University School of Medicine, Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Teruo Yasunaga
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Jun Ohashi
- Faculty of Medicine, University of Tsukuba, Ibaragi 305-8575, Japan
| | - Toshihiro Mita
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University School of Medicine, Kawada-cho, Shinjuku, Tokyo 162-8666, Japan Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Hongo, Bunkyo, Tokyo 113-8421, Japan
| | - Toshihiro Horii
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mitsuru Furusawa
- Neo-Morgan Laboratory, Inc., Nogawa, Miyamae, Kawasaki, Kanagawa 216-0001, Japan
| | - Kazuyuki Tanabe
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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50
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Pélabon C, Larsen LK, Bolstad GH, Viken Å, Fleming IA, Rosenqvist G. The effects of sexual selection on life-history traits: an experimental study on guppies. J Evol Biol 2014; 27:404-16. [PMID: 24417444 DOI: 10.1111/jeb.12309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/18/2013] [Accepted: 11/24/2013] [Indexed: 11/26/2022]
Abstract
Sexual selection is often prevented during captive breeding in order to maximize effective population size and retain genetic diversity. However, enforcing monogamy and thereby preventing sexual selection may affect population fitness either negatively by preventing the purging of deleterious mutations or positively by reducing sexual conflicts. To better understand the effect of sexual selection on the fitness of small populations, we compared components of female fitness and the expression of male secondary sexual characters in 19 experimental populations of guppies (Poecilia reticulata) maintained under polygamous or monogamous mating regimes over nine generations. In order to generate treatments that solely differed by their level of sexual selection, the middle-class neighbourhood breeding design was enforced in the monogamous populations, while in the polygamous populations, all females contributed similarly to the next generation with one male and one female offspring. This experimental design allowed potential sexual conflicts to increase in the polygamous populations because selection could not operate on adult-female traits. Clutch size and offspring survival showed a weak decline from generation to generation but did not differ among treatments. Offspring size, however, declined across generations, but more in monogamous than polygamous populations. By generation eight, orange- and black-spot areas were larger in males from the polygamous treatment, but these differences were not statistically significant. Overall, these results suggest that neither sexual conflict nor the purging of deleterious mutation had important effects on the fitness of our experimental populations. However, only few generations of enforced monogamy in a benign environment were sufficient to negatively affect offspring size, a trait potentially crucial for survival in the wild. Sexual selection may therefore, under certain circumstances, be beneficial over enforced monogamy during captive breeding.
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Affiliation(s)
- C Pélabon
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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