1
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Hartfield M, Glémin S. Polygenic selection to a changing optimum under self-fertilisation. PLoS Genet 2024; 20:e1011312. [PMID: 39018328 DOI: 10.1371/journal.pgen.1011312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/29/2024] [Accepted: 05/21/2024] [Indexed: 07/19/2024] Open
Abstract
Many traits are polygenic, affected by multiple genetic variants throughout the genome. Selection acting on these traits involves co-ordinated allele-frequency changes at these underlying variants, and this process has been extensively studied in random-mating populations. Yet many species self-fertilise to some degree, which incurs changes to genetic diversity, recombination and genome segregation. These factors cumulatively influence how polygenic selection is realised in nature. Here, we use analytical modelling and stochastic simulations to investigate to what extent self-fertilisation affects polygenic adaptation to a new environment. Our analytical solutions show that while selfing can increase adaptation to an optimum, it incurs linkage disequilibrium that can slow down the initial spread of favoured mutations due to selection interference, and favours the fixation of alleles with opposing trait effects. Simulations show that while selection interference is present, high levels of selfing (at least 90%) aids adaptation to a new optimum, showing a higher long-term fitness. If mutations are pleiotropic then only a few major-effect variants fix along with many neutral hitchhikers, with a transient increase in linkage disequilibrium. These results show potential advantages to self-fertilisation when adapting to a new environment, and how the mating system affects the genetic composition of polygenic selection.
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Affiliation(s)
- Matthew Hartfield
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sylvain Glémin
- Université de Rennes, Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) - Unité Mixte de Recherche (UMR) 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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2
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Johnson MTJ, Arif I, Marchetti F, Munshi-South J, Ness RW, Szulkin M, Verrelli BC, Yauk CL, Anstett DN, Booth W, Caizergues AE, Carlen EJ, Dant A, González J, Lagos CG, Oman M, Phifer-Rixey M, Rennison DJ, Rosenberg MS, Winchell KM. Effects of urban-induced mutations on ecology, evolution and health. Nat Ecol Evol 2024; 8:1074-1086. [PMID: 38641700 DOI: 10.1038/s41559-024-02401-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 04/21/2024]
Abstract
Increasing evidence suggests that urbanization is associated with higher mutation rates, which can affect the health and evolution of organisms that inhabit cities. Elevated pollution levels in urban areas can induce DNA damage, leading to de novo mutations. Studies on mutations induced by urban pollution are most prevalent in humans and microorganisms, whereas studies of non-human eukaryotes are rare, even though increased mutation rates have the potential to affect organisms and their populations in contemporary time. Our Perspective explores how higher mutation rates in urban environments could impact the fitness, ecology and evolution of populations. Most mutations will be neutral or deleterious, and higher mutation rates associated with elevated pollution in urban populations can increase the risk of cancer in humans and potentially other species. We highlight the potential for urban-driven increased deleterious mutational loads in some organisms, which could lead to a decline in population growth of a wide diversity of organisms. Although beneficial mutations are expected to be rare, we argue that higher mutation rates in urban areas could influence adaptive evolution, especially in organisms with short generation times. Finally, we explore avenues for future research to better understand the effects of urban-induced mutations on the fitness, ecology and evolution of city-dwelling organisms.
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Affiliation(s)
- Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada.
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Irtaqa Arif
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, Armonk, NY, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Marta Szulkin
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Warren Booth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, MO, USA
| | - Anthony Dant
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - César González Lagos
- Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Madeleine Oman
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Diana J Rennison
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
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3
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Lamka GF, Willoughby JR. Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations. PLoS One 2024; 19:e0304276. [PMID: 38814889 PMCID: PMC11139274 DOI: 10.1371/journal.pone.0304276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024] Open
Abstract
As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05-0.10) compared to the historical recipient population (average FST range 0.23-0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.
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Affiliation(s)
- Gina F. Lamka
- College of Forestry, Wildlife, and Environment, Auburn University, Auburn, Alabama, United States of America
| | - Janna R. Willoughby
- College of Forestry, Wildlife, and Environment, Auburn University, Auburn, Alabama, United States of America
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4
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Chen J, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567139. [PMID: 38045239 PMCID: PMC10690195 DOI: 10.1101/2023.11.14.567139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. Their phenotypic impacts and evolutionary pattern over time, however, remain elusive in humans due to the technical and ethical complexities in functional studies. By combining human gene age dating and Mendelian disease phenotyping, our research reveals a gradual increase in disease gene proportions with gene age. Logistic regression modeling indicates that this increase could be related to longer protein lengths and higher burdens of deleterious de novo germline variants (DNVs) for older genes. We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a "pleiotropy-barrier" model that delineates higher potentials of phenotypic innovation for young genes than for older genes, a process subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Affiliation(s)
- Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Alexander Guzzetta
- Department of Pathology, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Jared Atlas
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
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Kyriazis CC, Lohmueller KE. Constraining models of dominance for nonsynonymous mutations in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.582010. [PMID: 38463985 PMCID: PMC10925099 DOI: 10.1101/2024.02.25.582010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Dominance is a fundamental parameter in genetics, determining the dynamics of natural selection on deleterious and beneficial mutations, the patterns of genetic variation in natural populations, and the severity of inbreeding depression in a population. Despite this importance, dominance parameters remain poorly known, particularly in humans or other non-model organisms. A key reason for this lack of information about dominance is that it is extremely challenging to disentangle the selection coefficient (s) of a mutation from its dominance coefficient (h). Here, we explore dominance and selection parameters in humans by fitting models to the site frequency spectrum (SFS) for nonsynonymous mutations. When assuming a single dominance coefficient for all nonsynonymous mutations, we find that numerous h values can fit the data, so long as h is greater than ~0.15. Moreover, we also observe that theoretically-predicted models with a negative relationship between h and s can also fit the data well, including models with h=0.05 for strongly deleterious mutations. Finally, we use our estimated dominance and selection parameters to inform simulations revisiting the question of whether the out-of-Africa bottleneck has led to differences in genetic load between African and non-African human populations. These simulations suggest that the relative burden of genetic load in non-African populations depends on the dominance model assumed, with slight increases for more weakly recessive models and slight decreases shown for more strongly recessive models. Moreover, these results also demonstrate that models of partially recessive nonsynonymous mutations can explain the observed severity of inbreeding depression in humans, bridging the gap between molecular population genetics and direct measures of fitness in humans. Our work represents a comprehensive assessment of dominance and deleterious variation in humans, with implications for parameterizing models of deleterious variation in humans and other mammalian species.
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Affiliation(s)
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, USA
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6
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Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
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7
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Chen J. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. RESEARCH SQUARE 2023:rs.3.rs-3632644. [PMID: 38045389 PMCID: PMC10690325 DOI: 10.21203/rs.3.rs-3632644/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impact on humans, however, remains elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals that new genes associated with disease phenotypes steadily integrate into the human genome at a rate of ~ 0.07% every million years over macroevolutionary timescales. Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures between young and old genes. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, bipedal locomotion, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a "pleiotropy-barrier" model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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8
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Hwang HY, Wang J. Effect of recombination on genetic diversity of Caenorhabditis elegans. Sci Rep 2023; 13:16425. [PMID: 37777524 PMCID: PMC10542817 DOI: 10.1038/s41598-023-42600-5] [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: 07/20/2022] [Accepted: 09/12/2023] [Indexed: 10/02/2023] Open
Abstract
Greater molecular divergence and genetic diversity are present in regions of high recombination in many species. Studies describing the correlation between variant abundance and recombination rate have long focused on recombination in the context of linked selection models, whereby interference between linked sites under positive or negative selection reduces genetic diversity in regions of low recombination. Here, we show that indels, especially those of intermediate sizes, are enriched relative to single nucleotide polymorphisms in regions of high recombination in C. elegans. To explain this phenomenon, we reintroduce an alternative model that emphasizes the mutagenic effect of recombination. To extend the analysis, we examine the variants with a phylogenetic context and discuss how different models could be examined together. The number of variants generated by recombination in natural populations could be substantial including possibly the majority of some indel subtypes. Our work highlights the potential importance of a mutagenic effect of recombination, which could have a significant role in the shaping of natural genetic diversity.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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9
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Pérez‐Pereira N, Quesada H, Caballero A. An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions. Evol Appl 2023; 16:1302-1315. [PMID: 37492144 PMCID: PMC10363801 DOI: 10.1111/eva.13568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/27/2023] Open
Abstract
Inbreeding depression (ID), the reduction in fitness due to inbreeding, is typically measured by the regression of the phenotypic values of individuals for a particular trait on their corresponding inbreeding coefficients (F). While genealogical records can provide these coefficients, they may be unavailable or incomplete, making molecular markers a useful alternative. The power to detect ID and its accuracy depend on the variation of F values of individuals, the sample sizes available, and the accuracy in the estimation of individual fitness traits and F values. In this study, we used Drosophila melanogaster to evaluate the effectiveness of molecular markers in estimating ID under suboptimal conditions. We generated two sets of 100 pairs of unrelated individuals from a large panmictic population and mated them for two generations to produce non-inbred and unrelated individuals (F = 0) and inbred individuals (full-sib progeny; F = 0.25). Using these expected genealogical F values, we calculated inbreeding depression for two fitness-related traits, pupae productivity and competitive fitness. We then sequenced the males from 17 non-inbred pairs and 17 inbred pairs to obtain their genomic inbreeding coefficients and estimate ID for the two traits. The scenario assumed was rather restrictive in terms of estimation of ID because: (1) the individuals belonged to the same generation of a large panmictic population, leading to low variation in individual F coefficients; (2) the sample sizes were small; and (3) the traits measured depended on both males and females while only males were sequenced. Despite the challenging conditions of our study, we found that molecular markers provided estimates of ID that were comparable to those obtained from simple pedigree estimations with larger sample sizes. The results therefore suggest that genomic measures of inbreeding are useful to provide estimates of inbreeding depression even under very challenging scenarios.
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Affiliation(s)
- Noelia Pérez‐Pereira
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Humberto Quesada
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Armando Caballero
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
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10
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Wade EE, Kyriazis CC, Cavassim MIA, Lohmueller KE. Quantifying the fraction of new mutations that are recessive lethal. Evolution 2023; 77:1539-1549. [PMID: 37074880 PMCID: PMC10309970 DOI: 10.1093/evolut/qpad061] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/20/2023]
Abstract
The presence and impact of recessive lethal mutations have been widely documented in diploid outcrossing species. However, precise estimates of the proportion of new mutations that are recessive lethal remain limited. Here, we evaluate the performance of Fit∂a∂i, a commonly used method for inferring the distribution of fitness effects (DFE), in the presence of lethal mutations. Using simulations, we demonstrate that in both additive and recessive cases, inference of the deleterious nonlethal portion of the DFE is minimally affected by a small proportion (<10%) of lethal mutations. Additionally, we demonstrate that while Fit∂a∂i cannot estimate the fraction of recessive lethal mutations, Fit∂a∂i can accurately infer the fraction of additive lethal mutations. Finally, as an alternative approach to estimate the proportion of mutations that are recessive lethal, we employ models of mutation-selection-drift balance using existing genomic parameters and estimates of segregating recessive lethals for humans and Drosophila melanogaster. In both species, the segregating recessive lethal load can be explained by a very small fraction (<1%) of new nonsynonymous mutations being recessive lethal. Our results refute recent assertions of a much higher proportion of mutations being recessive lethal (4%-5%), while highlighting the need for additional information on the joint distribution of selection and dominance coefficients.
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Affiliation(s)
- Emma E Wade
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, United States
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
| | - Maria Izabel A Cavassim
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
- Interdepartmental Program in Bioinformatics, University of California–Los Angeles, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, CA, United States
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11
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Kyriazis CC, Robinson JA, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Taylor BL, Lohmueller KE, Morin PA. Models based on best-available information support a low inbreeding load and potential for recovery in the vaquita. Heredity (Edinb) 2023; 130:183-187. [PMID: 36941409 PMCID: PMC10076335 DOI: 10.1038/s41437-023-00608-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Affiliation(s)
- Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav); Irapuato, Guanajuato, Mexico
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Michael C Fontaine
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA.
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12
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Arcuschin CD, Pinkasz M, Schor IE. Mechanisms of robustness in gene regulatory networks involved in neural development. Front Mol Neurosci 2023; 16:1114015. [PMID: 36814969 PMCID: PMC9940843 DOI: 10.3389/fnmol.2023.1114015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
The functions of living organisms are affected by different kinds of perturbation, both internal and external, which in many cases have functional effects and phenotypic impact. The effects of these perturbations become particularly relevant for multicellular organisms with complex body patterns and cell type heterogeneity, where transcriptional programs controlled by gene regulatory networks determine, for example, the cell fate during embryonic development. Therefore, an essential aspect of development in these organisms is the ability to maintain the functionality of their genetic developmental programs even in the presence of genetic variation, changing environmental conditions and biochemical noise, a property commonly termed robustness. We discuss the implication of different molecular mechanisms of robustness involved in neurodevelopment, which is characterized by the interplay of many developmental programs at a molecular, cellular and systemic level. We specifically focus on processes affecting the function of gene regulatory networks, encompassing transcriptional regulatory elements and post-transcriptional processes such as miRNA-based regulation, but also higher order regulatory organization, such as gene network topology. We also present cases where impairment of robustness mechanisms can be associated with neurodevelopmental disorders, as well as reasons why understanding these mechanisms should represent an important part of the study of gene regulatory networks driving neural development.
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Affiliation(s)
- Camila D. Arcuschin
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marina Pinkasz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ignacio E. Schor
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina,*Correspondence: Ignacio E. Schor ✉
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Kyriazis CC, Beichman AC, Brzeski KE, Hoy SR, Peterson RO, Vucetich JA, Vucetich LM, Lohmueller KE, Wayne RK. Genomic Underpinnings of Population Persistence in Isle Royale Moose. Mol Biol Evol 2023; 40:7024794. [PMID: 36729989 PMCID: PMC9927576 DOI: 10.1093/molbev/msad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.
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Affiliation(s)
| | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Sarah R Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Rolf O Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Leah M Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
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14
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Why does the X chromosome lag behind autosomes in GWAS findings? PLoS Genet 2023; 19:e1010472. [PMID: 36848382 PMCID: PMC9997976 DOI: 10.1371/journal.pgen.1010472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/09/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
The X-chromosome is among the largest human chromosomes. It differs from autosomes by a number of important features including hemizygosity in males, an almost complete inactivation of one copy in females, and unique patterns of recombination. We used data from the Catalog of Published Genome Wide Association Studies to compare densities of the GWAS-detected SNPs on the X-chromosome and autosomes. The density of GWAS-detected SNPs on the X-chromosome is 6-fold lower compared to the density of the GWAS-detected SNPs on autosomes. Differences between the X-chromosome and autosomes cannot be explained by differences in the overall SNP density, lower X-chromosome coverage by genotyping platforms or low call rate of X-chromosomal SNPs. Similar differences in the density of GWAS-detected SNPs were found in female-only GWASs (e.g. ovarian cancer GWASs). We hypothesized that the lower density of GWAS-detected SNPs on the X-chromosome compared to autosomes is not a result of a methodological bias, e.g. differences in coverage or call rates, but has a real underlying biological reason-a lower density of functional SNPs on the X-chromosome versus autosomes. This hypothesis is supported by the observation that (i) the overall SNP density of X-chromosome is lower compared to the SNP density on autosomes and that (ii) the density of genic SNPs on the X-chromosome is lower compared to autosomes while densities of intergenic SNPs are similar.
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15
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Gutiérrez F, Valdesoiro F. The evolution of personality disorders: A review of proposals. Front Psychiatry 2023; 14:1110420. [PMID: 36793943 PMCID: PMC9922784 DOI: 10.3389/fpsyt.2023.1110420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/12/2023] [Indexed: 02/02/2023] Open
Abstract
Personality disorders (PDs) are currently considered dysfunctions. However, personality differences are older than humanity and are ubiquitous in nature, from insects to higher primates. This suggests that a number of evolutionary mechanisms-other than dysfunctions-may be able to maintain stable behavioral variation in the gene pool. First of all, apparently maladaptive traits may actually improve fitness by enabling better survival or successful mating or reproduction, as exemplified by neuroticism, psychopathy, and narcissism. Furthermore, some PDs may harm important biological goals while facilitating others, or may be globally beneficial or detrimental depending on environmental circumstances or body condition. Alternatively, certain traits may form part of life history strategies: Coordinated suites of morphological, physiological and behavioral characters that optimize fitness through alternative routes and respond to selection as a whole. Still others may be vestigial adaptations that are no longer beneficial in present times. Finally, variation may be adaptative in and by itself, as it reduces competition for finite resources. These and other evolutionary mechanisms are reviewed and illustrated through human and non-human examples. Evolutionary theory is the best-substantiated explanatory framework across the life sciences, and may shed light on the question of why harmful personalities exist at all.
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Affiliation(s)
- Fernando Gutiérrez
- Hospital Clínic de Barcelona, Institute of Neuroscience, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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16
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Sexual selection for males with beneficial mutations. Sci Rep 2022; 12:12613. [PMID: 35871224 PMCID: PMC9308816 DOI: 10.1038/s41598-022-16002-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 07/04/2022] [Indexed: 11/08/2022] Open
Abstract
Sexual selection is the process by which traits providing a mating advantage are favoured. Theoretical treatments of the evolution of sex by sexual selection propose that it operates by reducing the load of deleterious mutations. Here, we postulate instead that sexual selection primarily acts through females preferentially mating with males carrying beneficial mutations. We used simulation and analytical modelling to investigate the evolutionary dynamics of beneficial mutations in the presence of sexual selection. We found that female choice for males with beneficial mutations had a much greater impact on genetic quality than choice for males with low mutational load. We also relaxed the typical assumption of a fixed mutation rate. For deleterious mutations, mutation rate should always be minimized, but when rare beneficial mutations can occur, female choice for males with those rare beneficial mutations could overcome a decline in average fitness and allow an increase in mutation rate. We propose that sexual selection for beneficial mutations could overcome the ‘two-fold cost of sex’ much more readily than choice for males with low mutational load and may therefore be a more powerful explanation for the prevalence of sexual reproduction than the existing theory. If sexual selection results in higher fitness at higher mutation rates, and if the variability produced by mutation itself promotes sexual selection, then a feedback loop between these two factors could have had a decisive role in driving adaptation.
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17
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Connallon T, Beasley IJ, MDonough Y, Ruzicka F. How much does the unguarded X contribute to sex differences in life span? Evol Lett 2022; 6:319-329. [PMID: 35937469 PMCID: PMC9346086 DOI: 10.1002/evl3.292] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/22/2022] [Accepted: 06/12/2022] [Indexed: 11/09/2022] Open
Abstract
Females and males often have markedly different mortality rates and life spans, but it is unclear why these forms of sexual dimorphism evolve. The unguarded X hypothesis contends that dimorphic life spans arise from sex differences in X or Z chromosome copy number (i.e., one copy in the “heterogametic” sex; two copies in the “homogametic” sex), which leads to a disproportionate expression of deleterious mutations by the heterogametic sex (e.g., mammalian males; avian females). Although data on adult sex ratios and sex‐specific longevity are consistent with predictions of the unguarded X hypothesis, direct experimental evidence remains scant, and alternative explanations are difficult to rule out. Using a simple population genetic model, we show that the unguarded X effect on sex differential mortality is a function of several reasonably well‐studied evolutionary parameters, including the proportion of the genome that is sex linked, the genomic deleterious mutation rate, the mean dominance of deleterious mutations, the relative rates of mutation and strengths of selection in each sex, and the average effect of mutations on survival and longevity relative to their effects on fitness. We review published estimates of these parameters, parameterize our model with them, and show that unguarded X effects are too small to explain observed sex differences in life span across species. For example, sex differences in mean life span are known to often exceed 20% (e.g., in mammals), whereas our parameterized models predict unguarded X effects of a few percent (e.g., 1–3% in Drosophila and mammals). Indeed, these predicted unguarded X effects fall below statistical thresholds of detectability in most experiments, potentially explaining why direct tests of the hypothesis have generated little support for it. Our results suggest that evolution of sexually dimorphic life spans is predominantly attributable to other mechanisms, potentially including “toxic Y” effects and sexual dimorphism for optimal investment in survival versus reproduction. Females and males are dimorphic for a wide range of traits, including the average lengths of their life spans. Sex differences in life span are both conspicuous and variable among species. For example, in mammals, females live ∼20% longer than males (on average), whereas in birds, males live ∼10% longer than females. One leading explanation for these patterns—the unguarded X hypothesis—argues that sex differences in life span emerge from the distinct sex chromosomes that females and males inherit. For many species, one sex (e.g., female mammals; male birds) carries two copies of each X‐linked gene, whereas the other carries one. Because harmful mutations are partially recessive, the sex with only one copy of the X is more prone to expressing them, and that sex should therefore have a shorter average life span. This prediction of the unguarded X hypothesis is qualitatively consistent with observations of sex‐ratio bias in adults and sexual dimorphism for longevity (e.g., mammalian males have one copy of the X and have shorter lives than females). However, there are other possible explanations for these patterns, making it unclear how much the unguarded X explains species diversity for sex‐specific longevity. We developed a mathematical model for the contribution of unguarded X effects to sex differences in survival and life span, and used data on mutation rates and their effects on survival and fitness to quantify the importance of the unguarded X across species. The model, when combined with current data, suggests that the unguarded X hypothesis cannot explain the conspicuous sex differences in life span that are commonly reported in animal species, particularly vertebrates. Our results suggest that the unguarded X is an unlikely general explanation for the evolution of sexually dimorphic life spans, which gives weight to alternative mechanisms, including “toxic Y” effects and sex differential selection via trade‐offs between survival and reproduction.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences Monash University Clayton VIC 3800 Australia
| | - Isobel J. Beasley
- School of BioSciences The University of Melbourne Parkville VIC 3010 Australia
- Melbourne Integrative Genomics The University of Melbourne Parkville VIC 3010 Australia
- St. Vincent's Institute of Medical Research Fitzroy VIC 3065 Australia
| | - Yasmine MDonough
- School of Biological Sciences Monash University Clayton VIC 3800 Australia
| | - Filip Ruzicka
- School of Biological Sciences Monash University Clayton VIC 3800 Australia
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18
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Shen Y, Lian D, Shi K, Gao Y, Hu X, Yu K, Zhao Q, Feng C. Cancer Risk and Mutational Patterns Following Organ Transplantation. Front Cell Dev Biol 2022; 10:956334. [PMID: 35837331 PMCID: PMC9274140 DOI: 10.3389/fcell.2022.956334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid development of medical technology and widespread application of immunosuppressive drugs have improved the success rate of organ transplantation significantly. However, the use of immunosuppressive agents increases the frequency of malignancy greatly. With the prospect of “precision medicine” for tumors and development of next-generation sequencing technology, more attention has been paid to the application of high-throughput sequencing technology in clinical oncology research, which is mainly applied to the early diagnosis of tumors and analysis of tumor-related genes. All generations of cancers carry somatic mutations, meanwhile, significant differences were observed in mutational signatures across tumors. Systematic sequencing of cancer genomes from patients after organ transplantation can reveal DNA damage and repair processes in exposed cancer cells and their precursors. In this review, we summarize the application of high-throughput sequencing and organoids in the field of organ transplantation, the mutational patterns of cancer genomes, and propose a new research strategy for understanding the mechanism of cancer following organ transplantation.
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Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuefeng Gao
- College of Applied Engineering, Henan University of Science and Technology, Sanmenxia, China
- Sanmenxia Polytechnic, Sanmenxia, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kun Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
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19
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van Oosterhout C, Marcu D, Immler S. Accounting for the genetic load in assisted reproductive technology. Clin Transl Med 2022; 12:e864. [PMID: 35613708 PMCID: PMC9132725 DOI: 10.1002/ctm2.864] [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: 04/15/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
The genetic load in the human genome has important ramifications for assisted reproductive technology (ART), human reproduction and fertility more generally. Here, we discuss these topics in the light of evolutionary genetic theory, the technological revolution in ART and the advances in the fields of genomics and bioinformatics.
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Affiliation(s)
| | - Daniel Marcu
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Simone Immler
- School of Biological SciencesUniversity of East AngliaNorwichUK
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20
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Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD. Recommendations for improving statistical inference in population genomics. PLoS Biol 2022; 20:e3001669. [PMID: 35639797 PMCID: PMC9154105 DOI: 10.1371/journal.pbio.3001669] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population genetic insights outpaced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous nonadaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Charles F. Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Peter D. Keightley
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susanne P. Pfeifer
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
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21
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The relative fitness of the de novo variants in general Lithuanian population vs. in individuals with intellectual disability. Eur J Hum Genet 2022; 30:332-338. [PMID: 34363065 PMCID: PMC8904440 DOI: 10.1038/s41431-021-00915-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 11/08/2022] Open
Abstract
The effect of a variant on an organism is always multifaceted and can be considered from multiple perspectives-biochemical, medical, or evolutionary. However, the relationship between the effects of amino acid substitution on protein activity, human health, and an individual's evolutionary fitness is not trivial. We uncover that the general Lithuanian population is characterized by a "mirror reflection" of the de novo variant fitness effect, confirming the theory of neutrality. Meanwhile, in the group of individuals with intellectual disability, compared with the reference exome de novo variants significantly changed the composition of the amino acid. Therefore, it predicts that, both in terms of the number of amino acids and changes in their relative fitness, the structure of the proteins encoded by the studied amino acids undergo significant changes following the de novo variant, leading to possible changes in protein function associated with phenotypic traits. These results suggest that the analysis of relative fitness of exome sequences with de novo variants can predict the future phenotype. Therefore even in those cases, then only a few of all functional prediction analysis tools predict a variant as damaging, the negative relative fitness or even adaptability of the genome variant should be carefully evaluated considering both its direct function and the global background of the possible disease-associated mechanism regardless of the phenotype being studied.
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22
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López-Cortegano E, Craig RJ, Chebib J, Samuels T, Morgan AD, Kraemer SA, Böndel KB, Ness RW, Colegrave N, Keightley PD. De Novo Mutation Rate Variation and Its Determinants in Chlamydomonas. Mol Biol Evol 2021; 38:3709-3723. [PMID: 33950243 PMCID: PMC8383909 DOI: 10.1093/molbev/msab140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
De novo mutations are central for evolution, since they provide the raw material for natural selection by regenerating genetic variation. However, studying de novo mutations is challenging and is generally restricted to model species, so we have a limited understanding of the evolution of the mutation rate and spectrum between closely related species. Here, we present a mutation accumulation (MA) experiment to study de novo mutation in the unicellular green alga Chlamydomonas incerta and perform comparative analyses with its closest known relative, Chlamydomonas reinhardtii. Using whole-genome sequencing data, we estimate that the median single nucleotide mutation (SNM) rate in C. incerta is μ = 7.6 × 10-10, and is highly variable between MA lines, ranging from μ = 0.35 × 10-10 to μ = 131.7 × 10-10. The SNM rate is strongly positively correlated with the mutation rate for insertions and deletions between lines (r > 0.97). We infer that the genomic factors associated with variation in the mutation rate are similar to those in C. reinhardtii, allowing for cross-prediction between species. Among these genomic factors, sequence context and complexity are more important than GC content. With the exception of a remarkably high C→T bias, the SNM spectrum differs markedly between the two Chlamydomonas species. Our results suggest that similar genomic and biological characteristics may result in a similar mutation rate in the two species, whereas the SNM spectrum has more freedom to diverge.
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Affiliation(s)
- Eugenio López-Cortegano
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jobran Chebib
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Samuels
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew D Morgan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Katharina B Böndel
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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23
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A simple expression for the strength of selection on recombination generated by interference among mutations. Proc Natl Acad Sci U S A 2021; 118:2022805118. [PMID: 33941695 DOI: 10.1073/pnas.2022805118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
One of the most widely cited hypotheses to explain the evolutionary maintenance of genetic recombination states that the reshuffling of genotypes at meiosis increases the efficiency of natural selection by reducing interference among selected loci. However, and despite several decades of theoretical work, a quantitative estimation of the possible selective advantage of a mutant allele increasing chromosomal map length (the average number of cross-overs at meiosis) remains difficult. This article derives a simple expression for the strength of selection acting on a modifier gene affecting the genetic map length of a whole chromosome or genome undergoing recurrent mutation. In particular, it shows that indirect selection for recombination caused by interference among mutations is proportional to [Formula: see text], where [Formula: see text] is the effective population size, U is the deleterious mutation rate per chromosome, and R is the chromosome map length. Indirect selection is relatively insensitive to the fitness effects of deleterious alleles, epistasis, or the genetic architecture of recombination rate variation and may compensate for substantial costs associated with recombination when linkage is tight. However, its effect generally stays weak in large, highly recombining populations.
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24
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Population Modelling in Affective Disorders. Curr Behav Neurosci Rep 2021; 8:21-27. [PMID: 33875934 PMCID: PMC8047557 DOI: 10.1007/s40473-021-00229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2021] [Indexed: 11/28/2022]
Abstract
Purpose of Review The prevalence of affective disorders is on the rise. This upward trajectory leads to a substantial personal and societal cost. There is growing body of literature demonstrating decision-making impairments associated with affective disorders, and more studies are using computational modelling methods to infer underlying mechanisms of these impairments from participant choice behaviour. However, lack of population modelling suggests that data resources may still be underutilised. Recent Findings A number of recent studies associated major depression with abnormal risky decision-making as well as impairments in temporal discounting and social decision-making. These domains capture relevant aspects of real-life decision-making. Consequently, data from these studies can be used to define behavioural phenotypes for major depression. Summary The manuscript describes a detailed proposal for population modelling to capture changes in the prevalence rate of major depression. The population modelling approach can also identify which decision-making domains can account for a larger part of impairments in psychosocial functioning and how behavioural interventions built on computational principles can target these to improve real-life psychosocial functioning in patient groups.
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25
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Singh RS, Singh KK, Singh SM. Origin of Sex-Biased Mental Disorders: An Evolutionary Perspective. J Mol Evol 2021; 89:195-213. [PMID: 33630117 PMCID: PMC8116267 DOI: 10.1007/s00239-021-09999-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/06/2021] [Indexed: 12/12/2022]
Abstract
Sexual dimorphism or sex bias in diseases and mental disorders have two biological causes: sexual selection and sex hormones. We review the role of sexual selection theory and bring together decades of molecular studies on the variation and evolution of sex-biased genes and provide a theoretical basis for the causes of sex bias in disease and health. We present a Sexual Selection-Sex Hormone theory and show that male-driven evolution, including sexual selection, leads to: (1) increased male vulnerability due to negative pleiotropic effects associated with male-driven sexual selection and evolution; (2) increased rates of male-driven mutations and epimutations in response to early fitness gains and at the cost of late fitness; and (3) enhanced female immunity due to antagonistic responses to mutations that are beneficial to males but harmful to females, reducing female vulnerability to diseases and increasing the thresholds for disorders such as autism. Female-driven evolution, such as reproduction-related fluctuation in female sex hormones in association with stress and social condition, has been shown to be associated with increased risk of certain mental disorders such as major depression disorder in women. Bodies have history, cells have memories. An evolutionary framework, such as the Sexual Selection–Sex Hormone theory, provides a historical perspective for understanding how the differences in the sex-biased diseases and mental disorders have evolved over time. It has the potential to direct the development of novel preventive and treatment strategies.
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Affiliation(s)
- Rama S Singh
- Department of Biology, McMaster University, Hamilton, Canada.
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Canada.,Krembil Research Institute, University Health Network, Toronto, Canada
| | - Shiva M Singh
- Department of Biology, University of Western Ontario, London, Canada
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26
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Pentzold C, Kokal M, Pentzold S, Weise A. Sites of chromosomal instability in the context of nuclear architecture and function. Cell Mol Life Sci 2020; 78:2095-2103. [PMID: 33219838 PMCID: PMC7966619 DOI: 10.1007/s00018-020-03698-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 10/31/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase. We conclude that nuclear architecture shapes the activity profile of the cell, i.e. replication timing and transcriptional activity, thereby influencing genomic integrity during interphase with the potential to cause fragility in mitosis. We further propose fragile sites as examples of regions specifically positioned in the interphase nucleus with putative anchoring points at the nuclear lamina to enable a tightly regulated replication–transcription profile and diverse signalling functions in the cell. Consequently, fragility starts before the actual display as chromosomal breakage in metaphase to balance the initial contradiction of cellular overgrowth or malfunctioning and maintaining diversity in molecular evolution.
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Affiliation(s)
- Constanze Pentzold
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany.
| | - Miriam Kokal
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Stefan Pentzold
- Research Center Lobeda, Jena University Hospital, 07747, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
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27
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Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. CpG-creating mutations are costly in many human viruses. Evol Ecol 2020; 34:339-359. [PMID: 32508375 PMCID: PMC7245597 DOI: 10.1007/s10682-020-10039-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/11/2020] [Indexed: 01/26/2023]
Abstract
Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.
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Affiliation(s)
- Victoria R. Caudill
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Biology, University of Oregon, Eugene, OR USA
| | - Sarina Qin
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Quantitative Systems Biology, Univeristy of California, Merced, CA USA
| | - Ryan Winstead
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jasmeen Kaur
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Kaho Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - E. Geo Pineda
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Caroline Solis
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Oana Carja
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA USA
| | | | - Roland Regoes
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Scott Roy
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Nicole Allen
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Milo Aviles
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Brittany A. Baker
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - William Bauer
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Shannel Bermudez
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Corey Carlson
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Edgar Castellanos
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Francisca L. Catalan
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Neurological Surgery, University of California, San Francisco, CA USA
| | | | - Jacob Elliot
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Dwayne Evans
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Natalie Fiutek
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Emily Fryer
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA USA
| | - Samuel Melvin Goodfellow
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Health Sciences Center, University of New Mexico, Albuquerque, NM USA
| | - Mordecai Hecht
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Kellen Hopp
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - E. Deshawn Hopson
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Amirhossein Jaberi
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Christen Kinney
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Derek Lao
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Adrienne Le
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jacky Lo
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Alejandro G. Lopez
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Andrea López
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Fernando G. Lorenzo
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Gordon T. Luu
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Andrew R. Mahoney
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Rebecca L. Melton
- Department of Biology, San Francisco State University, San Francisco, CA USA
- UCSD Biomed Sciences PhD Program, University of California, San Diego, CA USA
| | | | - Anjani Pradhananga
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Nicole S. Rodrigues
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, CA USA
| | - Annie Shieh
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jasmine Sims
- Department of Biology, San Francisco State University, San Francisco, CA USA
- UCSF Tetrad Graduate Program, University of California, San Francisco, CA USA
| | - Rima Singh
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Hasan Sulaeman
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Ricky Thu
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Krystal Tran
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Livia Tran
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | | | - Albert Wong
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA USA
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28
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Parrott A, Khoury PR, Shikany AR, Lorts A, Villa CR, Miller EM. Investigation of de novo variation in pediatric cardiomyopathy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:116-123. [PMID: 31912959 DOI: 10.1002/ajmg.c.31764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/20/2022]
Abstract
Pediatric cardiomyopathies can be caused by variants in genes encoding the sarcomere and cytoskeleton in cardiomyocytes. Variants are typically inherited in an autosomal dominant manner with variable expressivity. De novo variants have been reported, however their overall frequency is largely unknown. We sought to determine the rate of de novo, pathogenic and likely pathogenic (P/LP) variants in children with a diagnosis of hypertrophic, dilated, or restrictive cardiomyopathy (HCM, DCM, or RCM), and to compare disease outcomes between individuals with and without a de novo variant. A retrospective record review identified 126 individuals with HCM (55%), DCM (37%), or RCM (8%) ≤18 years of age who had genetic testing. Overall, 50 (40%) had positive genetic testing and 18% of P/LP variants occurred de novo. The rate of de novo variation in those with RCM (80%) was higher than in those with HCM (9%) or DCM (20%). There was evidence of germline mosaicism in one family with RCM. Individuals with de novo variants were more likely than those without to have a history of arrhythmia (p = .049), sudden cardiac arrest (p = .024), hospitalization (p = .041), and cardiac transplantation (p = .030). The likelihood of de novo variation and impact on family risk and screening should be integrated into genetic counseling.
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Affiliation(s)
- Ashley Parrott
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Philip R Khoury
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Amy R Shikany
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Angela Lorts
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chet R Villa
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Erin M Miller
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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29
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Loureiro LO, Engstrom MD, Lim BK. Comparative phylogeography of mainland and insular species of Neotropical molossid bats ( Molossus). Ecol Evol 2020; 10:389-409. [PMID: 31993120 PMCID: PMC6972955 DOI: 10.1002/ece3.5903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023] Open
Abstract
Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype-by-sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.
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Affiliation(s)
- Livia O. Loureiro
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Mark D. Engstrom
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
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30
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Matthey‐Doret R, Whitlock MC. Background selection andFST: Consequences for detecting local adaptation. Mol Ecol 2019; 28:3902-3914. [DOI: 10.1111/mec.15197] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/19/2019] [Accepted: 07/03/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Remi Matthey‐Doret
- Department of Zoology and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Michael C. Whitlock
- Department of Zoology and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
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31
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Kauppila JHK, Bonekamp NA, Mourier A, Isokallio MA, Just A, Kauppila TES, Stewart JB, Larsson NG. Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice. Nucleic Acids Res 2019; 46:6642-6669. [PMID: 29860357 PMCID: PMC6061787 DOI: 10.1093/nar/gky456] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 05/11/2018] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations become more prevalent with age and are postulated to contribute to the ageing process. Point mutations of mtDNA have been suggested to originate from two main sources, i.e. replicative errors and oxidative damage, but the contribution of each of these processes is much discussed. To elucidate the origin of mtDNA mutations, we measured point mutation load in mice with deficient mitochondrial base-excision repair (BER) caused by knockout alleles preventing mitochondrial import of the DNA repair glycosylases OGG1 and MUTYH (Ogg1 dMTS, Mutyh dMTS). Surprisingly, we detected no increase in the mtDNA mutation load in old Ogg1 dMTS mice. As DNA repair is especially important in the germ line, we bred the BER deficient mice for five consecutive generations but found no increase in the mtDNA mutation load in these maternal lineages. To increase reactive oxygen species (ROS) levels and oxidative damage, we bred the Ogg1 dMTS mice with tissue specific Sod2 knockout mice. Although increased superoxide levels caused a plethora of changes in mitochondrial function, we did not detect any changes in the mutation load of mtDNA or mtRNA. Our results show that the importance of oxidative damage as a contributor of mtDNA mutations should be re-evaluated.
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Affiliation(s)
- Johanna H K Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nina A Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Arnaud Mourier
- Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, Bordeaux, France
| | - Marita A Isokallio
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Alexandra Just
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Timo E S Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - James B Stewart
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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32
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Uspenskaya NY, Akopov SB, Snezhkov EV, Sverdlov ED. The Rate of Human Germline Mutations—Variable Factor of Evolution and Diseases. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Charlesworth B. Mutational load, inbreeding depression and heterosis in subdivided populations. Mol Ecol 2018; 27:4991-5003. [DOI: 10.1111/mec.14933] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
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34
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Abstract
DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences.
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Affiliation(s)
- Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
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35
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Hermann NV, Darvann TA, Munch A, Kreiborg S. Parental age in relation to the severity of cleft lip and/or palate. Orthod Craniofac Res 2018; 21:236-241. [PMID: 30188007 DOI: 10.1111/ocr.12241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 06/27/2018] [Accepted: 07/18/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To investigate parental age in relation to the severity of cleft diagnosis in a population-based consecutive sample of individuals with clefts. SETTING/SAMPLE Retrospective, consecutive. MATERIAL/METHODS The sample comprised 545 consecutive cases with nonsyndromic clefts (437 individuals with cleft lip with/without cleft palate [CL ± P] and 106 individuals with isolated cleft palate [CP]) and parental ages recorded. The groups were subdivided according to the extent/severity of cleft. Unilateral clefts were divided according to left/right sidedness. Logistic regression was used to analyse the association between parental age and risk of severe cleft separately for CL ± P and CP, as well as between parental age and risk of right-sided cleft. RESULTS In CL ± P, the risk of a complete cleft in the offspring increases with maternal age when the paternal age exceeds approximately 29 years. Moreover, the risk is higher when both parents are old than when both parents are young. In CP, no statistically significant results were identified. However, there were clear trends that indicated a similar pattern as that for CL ± P. No association was identified between increased parental age and the sidedness of clefts. CONCLUSIONS Parental age seems to contribute to cleft severity, as older parents showed a higher risk of having offspring with a complete cleft than younger parents.
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Affiliation(s)
- Nuno V Hermann
- Section of Pediatric Dentistry and Clinical Genetics, School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,3D Craniofacial Image Research Laboratory (School of Dentistry, University of Copenhagen, Centre of Head and Orthopaedics, Copenhagen University Hospital Rigshospitalet; and Department of Applied Mathematics and Computer Science, Technical University of Denmark), Copenhagen, Denmark
| | - Tron A Darvann
- 3D Craniofacial Image Research Laboratory (School of Dentistry, University of Copenhagen, Centre of Head and Orthopaedics, Copenhagen University Hospital Rigshospitalet; and Department of Applied Mathematics and Computer Science, Technical University of Denmark), Copenhagen, Denmark.,Department of Oral and Maxillofacial Surgery, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anders Munch
- Section of Biostatistics, Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sven Kreiborg
- Section of Pediatric Dentistry and Clinical Genetics, School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,3D Craniofacial Image Research Laboratory (School of Dentistry, University of Copenhagen, Centre of Head and Orthopaedics, Copenhagen University Hospital Rigshospitalet; and Department of Applied Mathematics and Computer Science, Technical University of Denmark), Copenhagen, Denmark
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36
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Role of recombination and faithfulness to partner in sex chromosome degeneration. Sci Rep 2018; 8:8978. [PMID: 29895905 PMCID: PMC5997740 DOI: 10.1038/s41598-018-27219-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/24/2018] [Indexed: 11/08/2022] Open
Abstract
Sex determination in mammals is strongly linked to sex chromosomes. In most cases, females possess two copies of X chromosome while males have one X and one Y chromosome. It is assumed that these chromosomes originated from a pair of homologous autosomes, which diverged when recombination between them was suppressed. However, it is still debated why the sex chromosomes stopped recombining and how this process spread out over most part of the chromosomes. To study this problem, we developed a simulation model, in which the recombination rate between the sex chromosomes can freely evolve. We found that the suppression of recombination between the X and Y is spontaneous and proceeds very quickly during the evolution of population, which leads to the degeneration of the Y in males. Interestingly, the degeneration happens only when mating pairs are unfaithful. This evolutionary strategy purifies the X chromosome from defective alleles and leads to the larger number of females than males in the population. In consequence, the reproductive potential of the whole population increases. Our results imply that both the suppression of recombination and the degeneration of Y chromosome may be associated with reproductive strategy and favoured in polygamous populations with faithless mating partners.
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37
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Graur D. An Upper Limit on the Functional Fraction of the Human Genome. Genome Biol Evol 2017; 9:1880-1885. [PMID: 28854598 PMCID: PMC5570035 DOI: 10.1093/gbe/evx121] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2017] [Indexed: 12/13/2022] Open
Abstract
For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.
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Affiliation(s)
- Dan Graur
- Department of Biology and Biochemistry, University of Houston, TX
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38
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39
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Tatsumoto S, Go Y, Fukuta K, Noguchi H, Hayakawa T, Tomonaga M, Hirai H, Matsuzawa T, Agata K, Fujiyama A. Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing. Sci Rep 2017; 7:13561. [PMID: 29093469 PMCID: PMC5666008 DOI: 10.1038/s41598-017-13919-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/04/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations generate genetic variation and are a major driving force of evolution. Therefore, examining mutation rates and modes are essential for understanding the genetic basis of the physiology and evolution of organisms. Here, we aim to identify germline de novo mutations through the whole-genome surveyance of Mendelian inheritance error sites (MIEs), those not inherited through the Mendelian inheritance manner from either of the parents, using ultra-deep whole genome sequences (>150-fold) from a chimpanzee parent-offspring trio. We identified such 889 MIEs and classified them into four categories based on the pattern of inheritance and the sequence read depth: [i] de novo single nucleotide variants (SNVs), [ii] copy number neutral inherited variants, [iii] hemizygous deletion inherited variants, and [iv] de novo copy number variants (CNVs). From de novo SNV candidates, we estimated a germline de novo SNV mutation rate as 1.48 × 10-8 per site per generation or 0.62 × 10-9 per site per year. In summary, this study demonstrates the significance of ultra-deep whole genome sequencing not only for the direct estimation of mutation rates but also for discerning various mutation modes including de novo allelic conversion and de novo CNVs by identifying MIEs through the transmission of genomes from parents to offspring.
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Affiliation(s)
- Shoji Tatsumoto
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Yasuhiro Go
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan. .,Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan. .,Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 484-8585, Japan.
| | - Kentaro Fukuta
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan.,Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan
| | - Masaki Tomonaga
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan.,Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan.,Language and Intelligence Section, Department of Cognitive Sciences, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Hirohisa Hirai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Tetsuro Matsuzawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan.,Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan.,Language and Intelligence Section, Department of Cognitive Sciences, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan.,Institute of Advanced Study, Kyoto University, Kyoto, 606-8501, Japan
| | - Kiyokazu Agata
- Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.,Laboratory for Molecular Developmental Biology, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.,Graduate Course in Life Science, Gakushuin University, Tokyo, 171-8585, Japan
| | - Asao Fujiyama
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan. .,Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
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40
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Arslan RC, Willführ KP, Frans EM, Verweij KJH, Bürkner PC, Myrskylä M, Voland E, Almqvist C, Zietsch BP, Penke L. Older fathers' children have lower evolutionary fitness across four centuries and in four populations. Proc Biol Sci 2017; 284:rspb.2017.1562. [PMID: 28904145 DOI: 10.1101/042788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/07/2017] [Indexed: 05/25/2023] Open
Abstract
Higher paternal age at offspring conception increases de novo genetic mutations. Based on evolutionary genetic theory we predicted older fathers' children, all else equal, would be less likely to survive and reproduce, i.e. have lower fitness. In sibling control studies, we find support for negative paternal age effects on offspring survival and reproductive success across four large populations with an aggregate N > 1.4 million. Three populations were pre-industrial (1670-1850) Western populations and showed negative paternal age effects on infant survival and offspring reproductive success. In twentieth-century Sweden, we found minuscule paternal age effects on survival, but found negative effects on reproductive success. Effects survived tests for key competing explanations, including maternal age and parental loss, but effects varied widely over different plausible model specifications and some competing explanations such as diminishing paternal investment and epigenetic mutations could not be tested. We can use our findings to aid in predicting the effect increasingly older parents in today's society will have on their children's survival and reproductive success. To the extent that we succeeded in isolating a mutation-driven effect of paternal age, our results can be understood to show that de novo mutations reduce offspring fitness across populations and time periods.
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Affiliation(s)
- Ruben C Arslan
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
| | - Kai P Willführ
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
| | - Emma M Frans
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karin J H Verweij
- Department of Biological Psychology, VU University, 1081 BT Amsterdam, The Netherlands
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | - Mikko Myrskylä
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
- Department of Social Policy, London School of Economics and Political Science, London WC2A 2AE, UK
- Population Research Unit, University of Helsinki, 00100 Helsinki, Finland
| | - Eckart Voland
- Department of Biophilosophy, Justus Liebig University Gießen, 35390 Gießen, Germany
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Brendan P Zietsch
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Lars Penke
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
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Arslan RC, Willführ KP, Frans EM, Verweij KJH, Bürkner PC, Myrskylä M, Voland E, Almqvist C, Zietsch BP, Penke L. Older fathers' children have lower evolutionary fitness across four centuries and in four populations. Proc Biol Sci 2017; 284:20171562. [PMID: 28904145 PMCID: PMC5597845 DOI: 10.1098/rspb.2017.1562] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022] Open
Abstract
Higher paternal age at offspring conception increases de novo genetic mutations. Based on evolutionary genetic theory we predicted older fathers' children, all else equal, would be less likely to survive and reproduce, i.e. have lower fitness. In sibling control studies, we find support for negative paternal age effects on offspring survival and reproductive success across four large populations with an aggregate N > 1.4 million. Three populations were pre-industrial (1670-1850) Western populations and showed negative paternal age effects on infant survival and offspring reproductive success. In twentieth-century Sweden, we found minuscule paternal age effects on survival, but found negative effects on reproductive success. Effects survived tests for key competing explanations, including maternal age and parental loss, but effects varied widely over different plausible model specifications and some competing explanations such as diminishing paternal investment and epigenetic mutations could not be tested. We can use our findings to aid in predicting the effect increasingly older parents in today's society will have on their children's survival and reproductive success. To the extent that we succeeded in isolating a mutation-driven effect of paternal age, our results can be understood to show that de novo mutations reduce offspring fitness across populations and time periods.
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Affiliation(s)
- Ruben C Arslan
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
| | - Kai P Willführ
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
| | - Emma M Frans
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karin J H Verweij
- Department of Biological Psychology, VU University, 1081 BT Amsterdam, The Netherlands
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | - Mikko Myrskylä
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
- Department of Social Policy, London School of Economics and Political Science, London WC2A 2AE, UK
- Population Research Unit, University of Helsinki, 00100 Helsinki, Finland
| | - Eckart Voland
- Department of Biophilosophy, Justus Liebig University Gießen, 35390 Gießen, Germany
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Brendan P Zietsch
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Lars Penke
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
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Martinez J, Braganholi DF, Ambrósio IB, Polverari FS, Cicarelli RMB. Mutation rates for 20 STR loci in a population from São Paulo state, Southeast, Brazil. Ann Hum Biol 2017; 44:659-662. [DOI: 10.1080/03014460.2017.1371222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Juliana Martinez
- Laboratory of Paternity Investigation, São Paulo State University (UNESP), School of Pharmaceutical Sciences, São Paulo, Brazil
| | - Danilo Faustino Braganholi
- Laboratory of Paternity Investigation, São Paulo State University (UNESP), School of Pharmaceutical Sciences, São Paulo, Brazil
| | - Isabela Brunelli Ambrósio
- Laboratory of Paternity Investigation, São Paulo State University (UNESP), School of Pharmaceutical Sciences, São Paulo, Brazil
| | - Fernanda Silva Polverari
- Laboratory of Paternity Investigation, São Paulo State University (UNESP), School of Pharmaceutical Sciences, São Paulo, Brazil
| | - Regina Maria Barretto Cicarelli
- Laboratory of Paternity Investigation, São Paulo State University (UNESP), School of Pharmaceutical Sciences, São Paulo, Brazil
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43
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Genome instability: a conserved mechanism of ageing? Essays Biochem 2017; 61:305-315. [PMID: 28550046 DOI: 10.1042/ebc20160082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/18/2017] [Accepted: 05/02/2017] [Indexed: 01/09/2023]
Abstract
DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals. More recently, next-generation sequencing-based methods have been developed to accurately determine the complete landscape of base substitution mutations in single cells. The first results show that the somatic mutation rate is much higher than the germline mutation rate and that base substitution loads in somatic cells are high enough to potentially affect cellular function.
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44
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Du H, Pan B, Chen T. Evaluation of chemical mutagenicity using next generation sequencing: A review. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2017; 35:140-158. [PMID: 28506110 DOI: 10.1080/10590501.2017.1328831] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations are heritable changes in the nucleotide sequence of DNA that can lead to many adverse effects. Genotoxicity assays have been used to identify chemical mutagenicity. Recently, next generation sequencing (NGS) has been used for this purpose. In this review, we present the progress in NGS application for assessing mutagenicity of chemicals, including the methods used for detecting the induced mutations, bioinformatics tools for analyzing the sequencing data, and chemicals whose mutagenicity has been evaluated using NGS. Available information suggests that NGS technology has unparalleled advantages for evaluating mutagenicity of chemicals can be applied for the next generation of mutagenicity tests.
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Affiliation(s)
- Hua Du
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Bohu Pan
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Tao Chen
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
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45
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Vijg J, Dong X, Zhang L. A high-fidelity method for genomic sequencing of single somatic cells reveals a very high mutational burden. Exp Biol Med (Maywood) 2017; 242:1318-1324. [PMID: 28737476 PMCID: PMC5529006 DOI: 10.1177/1535370217717696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Postzygotic mutations in somatic cells lead to genome mosaicism and can be the cause of cancer, possibly other human diseases and aging. Somatic mutations are difficult to detect in bulk tissue samples. Here, we review the available assays for measuring somatic mutations, with a focus on recent single-cell, whole genome sequencing methods. Impact statement Somatic mutations cause cancer, possibly other diseases and aging. Yet, very little is known about the frequency of such mutations in vivo, their distribution across the genome, and their possible functional consequences other than cancer. Even in cancer, we do not know the heterogeneity of mutations within a tumor and if seemingly normal cells in its surroundings already have elevated mutation frequencies. Here, we review a new, whole genome amplification system that allows accurate quantification and characterization of single-cell mutational landscapes in human cells and tissues in relation to disease.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, NY 10461, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, NY 10461, USA
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, NY 10461, USA
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46
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Schaafsma GCP, Vihinen M. Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases. Hum Mutat 2017; 38:839-848. [DOI: 10.1002/humu.23236] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/05/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Gerard C. P. Schaafsma
- Protein Structure and Bioinformatics; Department of Experimental Medical Science; Lund University; Lund Sweden
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47
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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: 437] [Impact Index Per Article: 62.4] [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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48
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da Silva J, Galbraith JD. Hill-Robertson interference maintained by Red Queen dynamics favours the evolution of sex. J Evol Biol 2017; 30:994-1010. [PMID: 28295769 DOI: 10.1111/jeb.13068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 02/17/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022]
Abstract
Although it is well established theoretically that selective interference among mutations (Hill-Robertson interference) favours meiotic recombination, genomewide mean rates of mutation and strengths of selection appear too low to support this as the mechanism favouring recombination in nature. A possible solution to this discrepancy between theory and observation is that selection is at least intermittently very strong due to the antagonistic coevolution between a host and its parasites. The Red Queen theory posits that such coevolution generates fitness epistasis among loci, which generates negative linkage disequilibrium among beneficial mutations, which in turn favours recombination. This theory has received only limited support. However, Red Queen dynamics without epistasis may provide the ecological conditions that maintain strong and frequent selective interference in finite populations that indirectly selects for recombination. This hypothesis is developed here through the simulation of Red Queen dynamics. This approach required the development of a method to calculate the exact frequencies of multilocus haplotypes after recombination. Simulations show that recombination is favoured by the moderately weak selection of many loci involved in the interaction between a host and its parasites, which results in substitution rates that are compatible with empirical estimates. The model also reproduces the previously reported rapid increase in the rate of outcrossing in Caenorhabditis elegans coevolving with a bacterial pathogen.
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Affiliation(s)
- J da Silva
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - J D Galbraith
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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49
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Abu Awad D, Billiard S. The double edged sword: The demographic consequences of the evolution of self-fertilization. Evolution 2017; 71:1178-1190. [DOI: 10.1111/evo.13222] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 02/26/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Diala Abu Awad
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo; F-59000 Lille France
- INRA, UMR AGAP; 2 place Pierre Viala F-34060 Montpellier Cedex 1; France
| | - Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo; F-59000 Lille France
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50
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Woodley of Menie MA, Kanazawa S. Paternal age negatively predicts offspring physical attractiveness in two, large, nationally representative datasets. PERSONALITY AND INDIVIDUAL DIFFERENCES 2017. [DOI: 10.1016/j.paid.2016.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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