1
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Olito C, Ponnikas S, Hansson B, Abbott JK. Consequences of partially recessive deleterious genetic variation for the evolution of inversions suppressing recombination between sex chromosomes1. Evolution 2024:qpae060. [PMID: 38853722 DOI: 10.1093/evolut/qpae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/26/2024] [Accepted: 04/25/2024] [Indexed: 06/11/2024]
Abstract
The evolution of suppressed recombination between sex chromosomes is widely hypothesized to be driven by sexually antagonistic selection (SA), where tighter linkage between the sex-determining gene(s) and nearby SA loci is favored when it couples male-beneficial alleles to the proto-Y chromosome, and female-beneficial alleles to the proto-X. Although difficult to test empirically, the SA selection hypothesis overshadows several alternatives, including an incomplete but often-repeated "sheltering" hypothesis which suggests that expansion of the sex-linked region (SLR) reduces the homozygous expression of deleterious mutations at selected loci. Here, we use population genetic models to evaluate the consequences of partially recessive deleterious mutational variation for the evolution of otherwise neutral chromosomal inversions expanding the SLR on proto-Y chromosomes. Both autosomal and SLR-expanding inversions face a race against time: lightly-loaded inversions are initially beneficial, but eventually become deleterious as they accumulate new mutations, after which their chances of fixing become negligible. In contrast, initially unloaded inversions eventually become neutral as their deleterious load reaches the same equilibrium as non-inverted haplotypes. Despite the differences in inheritance and indirect selection, SLR-expanding inversions exhibit similar evolutionary dynamics to autosomal inversions over many biologically plausible parameter conditions. Differences emerge when the population average mutation load is quite high; in this case large autosomal inversions that are lucky enough to be mutation-free can rise to intermediate to high frequencies where selection in homozygotes becomes important (Y-linked inversions never appear as homozygous karyotypes); conditions requiring either high mutation rates, highly recessive deleterious mutations, weak selection, or a combination thereof.
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Affiliation(s)
- Colin Olito
- Department of Biology, Lund University, Lund, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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2
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Buffalo V, Kern AD. A quantitative genetic model of background selection in humans. PLoS Genet 2024; 20:e1011144. [PMID: 38507461 PMCID: PMC10984650 DOI: 10.1371/journal.pgen.1011144] [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: 09/17/2023] [Revised: 04/01/2024] [Accepted: 01/19/2024] [Indexed: 03/22/2024] Open
Abstract
Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This "linked selection signal" reflects the impact of selection according to the physical placement of functional regions and recombination rates along chromosomes. Previous work has shown that purifying selection acting against the steady influx of new deleterious mutations at functional portions of the genome shapes patterns of genomic variation. To date, statistical efforts to estimate purifying selection parameters from linked selection models have relied on classic Background Selection theory, which is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of linked selection, that models how polygenic additive fitness variance distributed along the genome increases the rate of stochastic allele frequency change. By jointly predicting the equilibrium fitness variance and substitution rate due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three geographically distinct human samples. While our model can accommodate weaker selection, we find evidence of strong selection operating similarly across all human samples. Although our quantitative genetic model of linked selection fits better than previous models, substitution rates of the most constrained sites disagree with observed divergence levels. We find that a model incorporating selective interference better predicts observed divergence in conserved regions, but overall our results suggest uncertainty remains about the processes generating fitness variation in humans.
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Affiliation(s)
- Vince Buffalo
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Andrew D. Kern
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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3
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Elena SF. Bridging quasispecies theory and social evolution models for sociovirology insights: a commentary on Leeks et al. 2023. J Evol Biol 2023; 36:1590-1594. [PMID: 37975502 DOI: 10.1111/jeb.14229] [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: 08/24/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna (Valencia), Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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4
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Chardès V, Mazzolini A, Mora T, Walczak AM. Evolutionary stability of antigenically escaping viruses. Proc Natl Acad Sci U S A 2023; 120:e2307712120. [PMID: 37871216 PMCID: PMC10622963 DOI: 10.1073/pnas.2307712120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/24/2023] [Indexed: 10/25/2023] Open
Abstract
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the coevolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other nonantigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of nonantigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low.
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Affiliation(s)
- Victor Chardès
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
- Center for Computational Biology, Flatiron Institute, New York, NY10010
| | - Andrea Mazzolini
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
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5
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Avila P, Lehmann L. Life history and deleterious mutation rate coevolution. J Theor Biol 2023; 573:111598. [PMID: 37598761 DOI: 10.1016/j.jtbi.2023.111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
The cost of germline maintenance gives rise to a trade-off between lowering the deleterious mutation rate and investing in life history functions. Therefore, life history and the mutation rate coevolve, but this coevolution is not well understood. We develop a mathematical model to analyse the evolution of resource allocation traits, which simultaneously affect life history and the deleterious mutation rate. First, we show that the invasion fitness of such resource allocation traits can be approximated by the basic reproductive number of the least-loaded class; the expected lifetime production of offspring without deleterious mutations born to individuals without deleterious mutations. Second, we apply the model to investigate (i) the coevolution of reproductive effort and germline maintenance and (ii) the coevolution of age-at-maturity and germline maintenance. This analysis provides two resource allocation predictions when exposure to environmental mutagens is higher. First, selection favours higher allocation to germline maintenance, even if it comes at the expense of life history functions, and leads to a shift in allocation towards reproduction rather than survival. Second, life histories tend to be faster, characterised by individuals with shorter lifespans and smaller body sizes at maturity. Our results suggest that mutation accumulation via the cost of germline maintenance can be a major force shaping life-history traits.
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Affiliation(s)
- Piret Avila
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland.
| | - Laurent Lehmann
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland
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6
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Matheson J, Bertram J, Masel J. Human deleterious mutation rate implies high fitness variance, with declining mean fitness compensated by rarer beneficial mutations of larger effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555871. [PMID: 37732183 PMCID: PMC10508744 DOI: 10.1101/2023.09.01.555871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Each new human has an expected Ud = 2 - 10 new deleterious mutations. This deluge of deleterious mutations cannot all be purged, and therefore accumulate in a declining fitness ratchet. Using a novel simulation framework designed to efficiently handle genome-wide linkage disequilibria across many segregating sites, we find that rarer, beneficial mutations of larger effect are sufficient to compensate fitness declines due to the fixation of many slightly deleterious mutations. Drift barrier theory posits a similar asymmetric pattern of fixations to explain ratcheting genome size and complexity, but in our theory, the cause is Ud > 1 rather than small population size. In our simulations, Ud ~2 - 10 generates high within-population variance in relative fitness; two individuals will typically differ in fitness by 15-40%. Ud ~2 - 10 also slows net adaptation by ~13%-39%. Surprisingly, fixation rates are more sensitive to changes in the beneficial than the deleterious mutation rate, e.g. a 10% increase in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.
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Affiliation(s)
- Joseph Matheson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology, Behavior, and Evolution, University of California San Diego, San Diego, CA, 92093, USA
| | - Jason Bertram
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Mathematics, University of Western Ontario, London ON, Canada
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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7
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Lobinska G, Pilpel Y, Ram Y. Phenotype switching of the mutation rate facilitates adaptive evolution. Genetics 2023; 225:iyad111. [PMID: 37293818 PMCID: PMC10471227 DOI: 10.1093/genetics/iyad111] [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: 02/05/2023] [Revised: 02/05/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The mutation rate plays an important role in adaptive evolution. It can be modified by mutator and anti-mutator alleles. Recent empirical evidence hints that the mutation rate may vary among genetically identical individuals: evidence from bacteria suggests that the mutation rate can be affected by expression noise of a DNA repair protein and potentially also by translation errors in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to a mutator phenotype that is independent from mutator alleles. Here, we investigate mathematically how the rate of adaptive evolution is affected by the rate of mutation rate phenotype switching. We model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. We find that switching rates that correspond to so-far empirically described non-genetic systems of inheritance of the mutation rate lead to higher rates of adaptation on both artificial and natural fitness landscapes. These switching rates can maintain within the same individuals both a mutator phenotype and intermediary mutations, a combination that facilitates adaptation. Moreover, non-genetic inheritance increases the proportion of mutators in the population, which in turn increases the probability of hitchhiking of the mutator phenotype with adaptive mutations. This in turns facilitates the acquisition of additional adaptive mutations. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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8
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Accumulation and maintenance of information in evolution. Proc Natl Acad Sci U S A 2022; 119:e2123152119. [PMID: 36037343 PMCID: PMC9457054 DOI: 10.1073/pnas.2123152119] [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] [Indexed: 11/18/2022] Open
Abstract
Selection accumulates information in the genome-it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback-Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright-Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.
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9
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Chen DS, Clark AG, Wolfner MF. Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster. Genetics 2022; 221:6613932. [PMID: 35736370 DOI: 10.1093/genetics/iyac097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/04/2022] [Indexed: 11/14/2022] Open
Abstract
In polyandrous internally fertilizing species, a multiply-mated female can use stored sperm from different males in a biased manner to fertilize her eggs. The female's ability to assess sperm quality and compatibility is essential for her reproductive success, and represents an important aspect of postcopulatory sexual selection. In Drosophila melanogaster, previous studies demonstrated that the female nervous system plays an active role in influencing progeny paternity proportion, and suggested a role for octopaminergic/tyraminergic Tdc2 neurons in this process. Here, we report that inhibiting Tdc2 neuronal activity causes females to produce a higher-than-normal proportion of first-male progeny. This difference is not due to differences in sperm storage or release, but instead is attributable to the suppression of second-male sperm usage bias that normally occurs in control females. We further show that a subset of Tdc2 neurons innervating the female reproductive tract is largely responsible for the progeny proportion phenotype that is observed when Tdc2 neurons are inhibited globally. On the contrary, overactivation of Tdc2 neurons does not further affect sperm storage and release or progeny proportion. These results suggest that octopaminergic/tyraminergic signaling allows a multiply-mated female to bias sperm usage, and identify a new role for the female nervous system in postcopulatory sexual selection.
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Affiliation(s)
- Dawn S Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14853, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14853, USA
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10
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Sachdeva H, Olusanya O, Barton N. Genetic load and extinction in peripheral populations: the roles of migration, drift and demographic stochasticity. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210010. [PMID: 35067097 PMCID: PMC8784927 DOI: 10.1098/rstb.2021.0010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a 'semi-deterministic' analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.
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Affiliation(s)
- Himani Sachdeva
- Department of Mathematics, University of Vienna, Vienna 1090, Austria
| | | | - Nick Barton
- Institute of Science and Technology Austria, Am Campus, 1, Klosterneuburg 3400, Austria
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11
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Goodman J, Brand J, Laptev G, Auld SKJR. Radiation‐mediated supply of genetic variation outweighs the effects of selection and drift in Chernobyl
Daphnia
populations. J Evol Biol 2022; 35:413-422. [PMID: 35048452 PMCID: PMC9303301 DOI: 10.1111/jeb.13983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Jessica Goodman
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| | - June Brand
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| | | | - Stuart K. J. R. Auld
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
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12
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Rybnikov S, Weissman DB, Hübner S, Korol AB. Fitness dependence preserves selection for recombination across diverse mixed mating strategies. J Theor Biol 2021; 528:110849. [PMID: 34331961 DOI: 10.1016/j.jtbi.2021.110849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/13/2021] [Accepted: 07/24/2021] [Indexed: 12/16/2022]
Abstract
Meiotic recombination and the factors affecting its rate and fate in nature have inspired many studies in theoretical evolutionary biology. Classical theoretical models have inferred that recombination can be favored under a rather restricted parameter range. Thus, the ubiquity of recombination in nature remains an open question. However, these models assumed constant recombination with an equal rate across all individuals within the population, whereas empirical evidence suggests that recombination may display certain sensitivity to ecological stressors and/or genotype fitness. Models assuming condition-dependent recombination show that such a strategy can often be favored over constant recombination. Moreover, in our recent model with panmictic populations subjected to purifying selection, fitness-dependent recombination was quite often favored even when any constant recombination was rejected. By using numerical modeling, we test whether such a 'recombination-rescuing potential' of fitness dependence holds also beyond panmixia, given the recognized effect of mating strategy on the evolution of recombination. We show that deviations from panmixia generally increase the recombination-rescuing potential of fitness dependence, with the strongest effect under intermediate selfing or high clonality. We find that under partial clonality, the evolutionary advantage of fitness-dependent recombination is determined mostly by selection against heterozygotes and additive-by-additive epistasis, while under partial selfing, additive-by-dominance epistasis is also a driver.
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Affiliation(s)
- Sviatoslav Rybnikov
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel.
| | | | - Sariel Hübner
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; Galilee Research Institute (MIGAL), Tel-Hai College, Upper Galilee 1220800, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
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13
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Connallon T, Olito C. Natural selection and the distribution of chromosomal inversion lengths. Mol Ecol 2021; 31:3627-3641. [PMID: 34297880 DOI: 10.1111/mec.16091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/28/2022]
Abstract
Chromosomal inversions contribute substantially to genome evolution, yet the processes governing their evolutionary dynamics remain poorly understood. Theory suggests that a readily measurable property of inversions-their length-can potentially affect their evolutionary fates. Emerging data on the lengths of polymorphic and fixed inversions may therefore provide clues to the evolutionary processes promoting inversion establishment. However, formal predictions for the distribution of inversion lengths remain incomplete, making empirical patterns difficult to interpret. We model the relation between inversion length and establishment probability for four inversion types: (1) neutral, (2) underdominant, (3) directly beneficial, and (4) indirectly beneficial, with selection favouring the latter because they capture locally adapted alleles at migration-selection balance and suppress recombination between them. We also consider how deleterious mutations affect the lengths of established inversions. We show that length distributions of common polymorphic and fixed inversions systematically differ among inversion types. Small rearrangements contribute the most to genome evolution under neutral and underdominant scenarios of selection, with the lengths of neutral inversion substitutions increasing, and those of underdominant substitutions decreasing, with effective population size. Among directly beneficial inversions, small rearrangements are preferentially fixed, whereas intermediate-to-large inversions are maintained as balanced polymorphisms via associative overdominance. Finally, inversions established under the local adaptation scenario are predominantly intermediate-to-large. Such inversions remain polymorphic or approach fixation within the local populations where they are favoured. Our models clarify how inversion length distributions relate to processes of inversion establishment, providing a platform for testing how natural selection shapes the evolution of genome structure.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences and Centre for Geometric Biology, Monash University, Clayton, Victoria, Australia
| | - Colin Olito
- Department of Biology, Section for Evolutionary Ecology, Lund University, Lund, Sweden
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14
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Sandler G, Wright SI, Agrawal AF. Patterns and Causes of Signed Linkage Disequilibria in Flies and Plants. Mol Biol Evol 2021; 38:4310-4321. [PMID: 34097067 PMCID: PMC8476167 DOI: 10.1093/molbev/msab169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most empirical studies of linkage disequilibrium (LD) study its magnitude, ignoring its sign. Here, we examine patterns of signed LD in two population genomic data sets, one from Capsella grandiflora and one from Drosophila melanogaster. We consider how processes such as drift, admixture, Hill–Robertson interference, and epistasis may contribute to these patterns. We report that most types of mutations exhibit positive LD, particularly, if they are predicted to be less deleterious. We show with simulations that this pattern arises easily in a model of admixture or distance-biased mating, and that genome-wide differences across site types are generally expected due to differences in the strength of purifying selection even in the absence of epistasis. We further explore how signed LD decays on a finer scale, showing that loss of function mutations exhibit particularly positive LD across short distances, a pattern consistent with intragenic antagonistic epistasis. Controlling for genomic distance, signed LD in C. grandiflora decays faster within genes, compared with between genes, likely a by-product of frequent recombination in gene promoters known to occur in plant genomes. Finally, we use information from published biological networks to explore whether there is evidence for negative synergistic epistasis between interacting radical missense mutations. In D. melanogaster networks, we find a modest but significant enrichment of negative LD, consistent with the possibility of intranetwork negative synergistic epistasis.
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Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.,Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.,Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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15
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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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16
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Khudiakova KA, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller's ratchet. J Theor Biol 2021; 524:110729. [PMID: 33901507 DOI: 10.1016/j.jtbi.2021.110729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/31/2020] [Accepted: 04/15/2021] [Indexed: 11/29/2022]
Abstract
We report complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This suggests that fixation of a deleterious allele that follows a click of the Muller's ratchet is governed by natural selection, instead of random drift.
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Affiliation(s)
- Ksenia A Khudiakova
- Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow 119992, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia; IST Austria (Institute of Science and Technology Austria), Am Campus 1, A-3400 Klosterneuburg, Austria.
| | - Tatiana Yu Neretina
- Department of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey S Kondrashov
- Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow 119992, Russia; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Lesaffre T, Billiard S. On Deleterious Mutations in Perennials: Inbreeding Depression, Mutation Load, and Life-History Evolution. Am Nat 2021; 197:E143-E155. [PMID: 33908825 DOI: 10.1086/713499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractIn angiosperms, perennials typically present much higher levels of inbreeding depression than annuals. One hypothesis to explain this pattern stems from the observation that inbreeding depression is expressed across multiple life stages in angiosperms. It posits that increased inbreeding depression in more long-lived species could be explained by differences in the way mutations affect fitness, through the life stages at which they are expressed. In this study, we investigate this hypothesis. We combine a physiological growth model and multilocus population genetics approaches to describe a full genotype-to-phenotype-to-fitness map. We study the behavior of mutations affecting growth or survival and explore their consequences in terms of inbreeding depression and mutation load. Although our results agree with empirical data only within a narrow range of conditions, we argue that they may point us toward the type of traits capable of generating high inbreeding depression in long-lived species-that is, traits under sufficiently strong selection, on which selection decreases sharply as life expectancy increases. Then we study the role deleterious mutations maintained at mutation-selection balance may play in the joint evolution of growth and survival strategies.
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18
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Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster. Sci Rep 2020; 10:22415. [PMID: 33376238 PMCID: PMC7772335 DOI: 10.1038/s41598-020-79720-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/11/2020] [Indexed: 01/27/2023] Open
Abstract
European and African natural populations of Drosophila melanogaster have been the focus of several studies aiming at inferring demographic and adaptive processes based on genetic variation data. However, in these analyses little attention has been given to gene flow between African and European samples. Here we present a dataset consisting of 14 fully sequenced haploid genomes sampled from a natural population from the northern species range (Umeå, Sweden). We co-analyzed this new data with an African population to compare the likelihood of several competing demographic scenarios for European and African populations and show that gene flow improves the fit of demographic models to data.
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19
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Skums P, Tsyvina V, Zelikovsky A. Inference of clonal selection in cancer populations using single-cell sequencing data. Bioinformatics 2020; 35:i398-i407. [PMID: 31510696 PMCID: PMC6612866 DOI: 10.1093/bioinformatics/btz392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Summary Intra-tumor heterogeneity is one of the major factors influencing cancer progression and treatment outcome. However, evolutionary dynamics of cancer clone populations remain poorly understood. Quantification of clonal selection and inference of fitness landscapes of tumors is a key step to understanding evolutionary mechanisms driving cancer. These problems could be addressed using single-cell sequencing (scSeq), which provides an unprecedented insight into intra-tumor heterogeneity allowing to study and quantify selective advantages of individual clones. Here, we present Single Cell Inference of FItness Landscape (SCIFIL), a computational tool for inference of fitness landscapes of heterogeneous cancer clone populations from scSeq data. SCIFIL allows to estimate maximum likelihood fitnesses of clone variants, measure their selective advantages and order of appearance by fitting an evolutionary model into the tumor phylogeny. We demonstrate the accuracy our approach, and show how it could be applied to experimental tumor data to study clonal selection and infer evolutionary history. SCIFIL can be used to provide new insight into the evolutionary dynamics of cancer. Availability and implementation Its source code is available at https://github.com/compbel/SCIFIL.
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Affiliation(s)
- Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Viachaslau Tsyvina
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, GA, USA.,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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20
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Willink B, Duryea MC, Wheat C, Svensson EI. Changes in gene expression during female reproductive development in a color polymorphic insect. Evolution 2020; 74:1063-1081. [DOI: 10.1111/evo.13979] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 03/19/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Beatriz Willink
- Department of Biology, Evolutionary Ecology Unit, Ecology BuildingLund University Lund 223–62 Sweden
- Current Address: School of BiologyUniversity of Costa Rica San José 11501–2060 Costa Rica
| | | | | | - Erik I. Svensson
- Department of Biology, Evolutionary Ecology Unit, Ecology BuildingLund University Lund 223–62 Sweden
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21
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Laurentino TG, Moser D, Roesti M, Ammann M, Frey A, Ronco F, Kueng B, Berner D. Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish. Nat Commun 2020; 11:1928. [PMID: 32317640 PMCID: PMC7174299 DOI: 10.1038/s41467-020-15657-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/19/2020] [Indexed: 11/29/2022] Open
Abstract
How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use pooled whole-genome sequence data from the original populations to identify hundreds of candidate genome regions likely under divergent selection between these habitats. Next, we generate F2 hybrids from the same lake-stream population pair in the laboratory and release thousands of juveniles into a natural stream habitat. Comparing the individuals surviving one year of stream selection to a reference sample of F2 hybrids allows us to detect frequency shifts across the candidate regions toward the genetic variants typical of the stream population-an experimental outcome consistent with polygenic directional selection. Our study reveals that adaptation in nature can be detected as a genome-wide signal over just a single generation.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Dario Moser
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Matthias Ammann
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Anja Frey
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Benjamin Kueng
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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22
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Ruan Y, Wang H, Chen B, Wen H, Wu CI. Mutations Beget More Mutations-Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation. Mol Biol Evol 2020; 37:1007-1019. [PMID: 31778175 DOI: 10.1093/molbev/msz283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haiyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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23
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Baselga-Cervera B, García-Balboa C, Díaz-Alejo HM, Costas E, López-Rodas V. Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles. MICROBIAL ECOLOGY 2020; 79:576-587. [PMID: 31463663 DOI: 10.1007/s00248-019-01431-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic extreme environments are emphasized as interesting sites for the study of evolutionary pathways, biodiversity, and extremophile bioprospection. Organisms that grow under these conditions are usually regarded as extremophiles; however, the extreme novelty of these environments may have favor adaptive radiations of facultative extremophiles. At the Iberian Peninsula, uranium mining operations have rendered highly polluted extreme environments in multiple locations. In this study, we examined the phytoplankton diversity, community structure, and possible determining factors in separate uranium mining-impacted waters. Some of these human-induced extreme environments may be able to sustain indigenous facultative extremophile phytoplankton species, as well as alleged obligate extremophiles. Therefore, we investigated the adaptation capacity of three laboratory strains, two Chlamydomonas reinhardtii and a Dictyosphaerium chlorelloides, to uranium-polluted waters. The biodiversity among the sampled waters was very low, and despite presenting unique taxonomic records, ecological patterns can be identified. The microalgae adaptation experiments indicated a gradient of ecological novelty and different phenomena of adaptation, from acclimation in some waters to non-adaptation in the harshest anthropogenic environment. Certainly, phytoplankton extremophiles might have been often overlooked, and the ability to flourish in extreme environments might be a functional feature in some neutrophilic species. Evolutionary biology and microbial biodiversity can benefit the study of recently evolved systems such as uranium-polluted waters. Moreover, anthropogenic extremophiles can be harnessed for industrial applications.
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Affiliation(s)
- Beatriz Baselga-Cervera
- Animal Science (Genetics), School of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
- Ecology, Evolution and Behavior Department, University of Minnesota, St. Paul, MN, 55108, USA
| | - Camino García-Balboa
- Animal Science (Genetics), School of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Héctor M Díaz-Alejo
- Animal Science (Genetics), School of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Eduardo Costas
- Animal Science (Genetics), School of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Victoria López-Rodas
- Animal Science (Genetics), School of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
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24
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Abstract
Fitness interactions between mutations can influence a population's evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.
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Affiliation(s)
- Christelle Fraïsse
- 1 Institut des Sciences de l'Evolution, CNRS-UM-IRD , Montpellier , France.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK.,3 Institute of Science and Technology Austria , Am Campus 1, Klosterneuburg 3400 , Austria
| | - John J Welch
- 2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
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25
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Yeh DJ, Fogarty L, Kandler A. Cultural linkage: the influence of package transmission on cultural dynamics. Proc Biol Sci 2019; 286:20191951. [PMID: 31795868 PMCID: PMC6939269 DOI: 10.1098/rspb.2019.1951] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Many cultural traits are not transmitted independently, but together as a package. This can happen because, for example, media may store information together making it more likely to be transmitted together, or through cognitive mechanisms such as causal reasoning. Evolutionary biology suggests that physical linkage of genes (being on the same chromosome) allows neutral and maladaptive genes to spread by hitchhiking on adaptive genes, while the pairwise difference between neutral genes is unaffected. Whether packaging may lead to similar dynamics in cultural evolution is unclear. To understand the effect of cultural packages on cultural evolutionary dynamics, we built an agent-based simulation that allows links to form and break between cultural traits. During transmission, one trait and others that are directly or indirectly connected to it are transmitted together in a package. We compare variation in cultural traits between different rates of link formation and breakage and find that an intermediate frequency of links can lower cultural diversity, which can be misinterpreted as a signature of payoff bias or conformity. Further, cultural hitchhiking can occur when links are common.
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Affiliation(s)
- D Justin Yeh
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Laurel Fogarty
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Kandler
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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26
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Martín-Clemente E, Melero-Jiménez IJ, Bañares-España E, Flores-Moya A, García-Sánchez MJ. Adaptation dynamics and evolutionary rescue under sulfide selection in cyanobacteria: a comparative study between Microcystis aeruginosa and Oscillatoria sp. (cyanobacteria). JOURNAL OF PHYCOLOGY 2019; 55:1348-1360. [PMID: 31393602 DOI: 10.1111/jpy.12911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Experimental evolution studies using cyanobacteria as model organisms are scarce despite the role of cyanobacteria in the evolution of photosynthesis. Three different experimental evolution approaches have been applied to shed light on the sulfide adaptation process, which played a key role in the evolution of this group. We used a Microcystis aeruginosa sulfide-sensitive strain, unable to grow above ~0.1 mM, and an Oscillatoria sp. strain, isolated from a sulfureous spa (~0.2 mM total sulfide). First, performing a fluctuation analysis design using the spa waters as selective agent, we proved that M. aeruginosa was able to adapt to this sulfide level by rare spontaneous mutations. Second, applying a ratchet protocol, we tested if the limit of adaptation to sulfide of the two taxa was dependent on their initial sulfide tolerance, finding that M. aeruginosa adapted to 0.4 mM sulfide, and Oscillatoria sp. to ~2 mM sulfide, twice it highest tolerance level. Third, using an evolutionary rescue approach, we observed that both speed of exposure to increasing sulfide concentrations (deterioration rate) and populations' genetic variation determined the survival of M. aeruginosa at lethal sulfide levels, with a higher dependence on genetic diversity. In conclusion, sulfide adaptation of sensitive cyanobacterial strains is possible by rare spontaneous mutations and the adaptation limits depend on the sulfide level present in strain's original habitat. The high genetic diversity of a sulfide-sensitive strain, even at fast environmental deterioration rates, could increase its possibility of survival even to a severe sulfide stress.
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Affiliation(s)
- Elena Martín-Clemente
- Departamento de Botánica y Fisiología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - Ignacio J Melero-Jiménez
- Departamento de Botánica y Fisiología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - Elena Bañares-España
- Departamento de Botánica y Fisiología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - Antonio Flores-Moya
- Departamento de Botánica y Fisiología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - María J García-Sánchez
- Departamento de Botánica y Fisiología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
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27
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Brown KE, Kelly JK. Severe inbreeding depression is predicted by the “rare allele load” in
Mimulus guttatus
*. Evolution 2019; 74:587-596. [DOI: 10.1111/evo.13876] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Keely E. Brown
- Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
| | - John K. Kelly
- Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
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28
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Griswold CK. Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species. Evol Bioinform Online 2019; 15:1176934319883612. [PMID: 31723319 PMCID: PMC6831972 DOI: 10.1177/1176934319883612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/25/2019] [Indexed: 11/17/2022] Open
Abstract
In polymerase chain reaction (PCR)-based DNA sequencing studies, there is the
possibility that mutations at the binding sites of primers result in no primer
binding and therefore no amplification. In this article, we call such mutations
PCR dropouts and present a coalescent-based theory of the distribution of
segregating PCR dropout mutations within a species. We show that dropout
mutations typically occur along branch sections that are at or near the base of
a coalescent tree, if at all. Given that a dropout mutation occurs along a
branch section near the base of a tree, there is a good chance that it causes
the alleles of a large fraction of a species to go unamplified, which distorts
the tree shape. Expected coalescence times and distributions of pairwise
sequence differences in the presence of PCR dropout mutations are derived under
the assumptions of both neutrality and background selection. These expectations
differ from when PCR dropout mutations are absent and may form the basis of
inferential approaches to detect the presence of dropout mutations, as well as
the development of unbiased estimators of statistics associated with
population-level genetic variation.
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29
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He C, Liang D, Zhang P. Asymmetric Distribution of Gene Trees Can Arise under Purifying Selection If Differences in Population Size Exist. Mol Biol Evol 2019; 37:881-892. [DOI: 10.1093/molbev/msz232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AbstractIncomplete lineage sorting (ILS) is an important factor that causes gene tree discordance. For gene trees of three species, under neutrality, random mating, and the absence of interspecific gene flow, ILS creates a symmetric distribution of gene trees: the gene tree that accords with the species tree has the highest frequency, and the two discordant trees are equally frequent. If the neutral condition is violated, the impact of ILS may change, altering the gene tree distribution. Here, we show that under purifying selection, even assuming that the fitness effect of mutations is constant throughout the species tree, if differences in population size exist among species, asymmetric distributions of gene trees will arise, which is different from the expectation under neutrality. In extremes, one of the discordant trees rather than the concordant tree becomes the most frequent gene tree. In addition, we found that in a real case, the position of Scandentia relative to Primate and Glires, the symmetry in the gene tree distribution can be influenced by the strength of purifying selection. In current phylogenetic inference, the impact of purifying selection on the gene tree distribution is rarely considered by researchers. This study highlights the necessity of considering this impact.
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Affiliation(s)
- Chong He
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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30
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Kemble H, Nghe P, Tenaillon O. Recent insights into the genotype-phenotype relationship from massively parallel genetic assays. Evol Appl 2019; 12:1721-1742. [PMID: 31548853 PMCID: PMC6752143 DOI: 10.1111/eva.12846] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022] Open
Abstract
With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep mutational scanning assays, capable of scoring comprehensive libraries of genotypes for fitness and a variety of phenotypes in massively parallel fashion. The resulting empirical genotype-fitness maps pave the way to predictive models, potentially accelerating our ability to anticipate the behaviour of pathogen and cancerous cell populations from sequencing data. Besides from cellular fitness, phenotypes of direct application in industry (e.g. enzyme activity) and medicine (e.g. antibody binding) can be quantified and even selected directly by these assays. This review discusses the technological basis of and recent developments in massively parallel genetics, along with the trends it is uncovering in the genotype-phenotype relationship (distribution of mutation effects, epistasis), their possible mechanistic bases and future directions for advancing towards the goal of predictive genetics.
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Affiliation(s)
- Harry Kemble
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Unité Mixte de Recherche 1137Université Paris Diderot, Université Paris NordParisFrance
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), UMR CNRS‐ESPCI CBI 8231PSL Research UniversityParis Cedex 05France
| | - Philippe Nghe
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), UMR CNRS‐ESPCI CBI 8231PSL Research UniversityParis Cedex 05France
| | - Olivier Tenaillon
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Unité Mixte de Recherche 1137Université Paris Diderot, Université Paris NordParisFrance
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31
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Hodač L, Klatt S, Hojsgaard D, Sharbel TF, Hörandl E. A little bit of sex prevents mutation accumulation even in apomictic polyploid plants. BMC Evol Biol 2019; 19:170. [PMID: 31412772 PMCID: PMC6694583 DOI: 10.1186/s12862-019-1495-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/08/2019] [Indexed: 01/30/2023] Open
Abstract
Background In the absence of sex and recombination, genomes are expected to accumulate deleterious mutations via an irreversible process known as Muller’s ratchet, especially in the case of polyploidy. In contrast, no genome-wide mutation accumulation was detected in a transcriptome of facultative apomictic, hexaploid plants of the Ranunculus auricomus complex. We hypothesize that mutations cannot accumulate in flowering plants with facultative sexuality because sexual and asexual development concurrently occurs within the same generation. We assume a strong effect of purging selection on reduced gametophytes in the sexual developmental pathway because previously masked recessive deleterious mutations would be exposed to selection. Results We test this hypothesis by modeling mutation elimination using apomictic hexaploid plants of the R. auricomus complex. To estimate mean recombination rates, the mean number of recombinants per generation was calculated by genotyping three F1 progeny arrays with six microsatellite markers and character incompatibility analyses. We estimated the strength of purging selection in gametophytes by calculating abortion rates of sexual versus apomictic development at the female gametophyte, seed and offspring stage. Accordingly, we applied three selection coefficients by considering effects of purging selection against mutations on (1) male and female gametophytes in the sexual pathway (additive, s = 1.000), (2) female gametophytes only (s = 0.520), and (3) on adult plants only (sporophytes, s = 0.212). We implemented recombination rates into a mathematical model considering the three different selection coefficients, and a genomic mutation rate calculated from genome size of our plants and plant-specific mutation rates. We revealed a mean of 6.05% recombinants per generation. This recombination rate eliminates mutations after 138, 204 or 246 generations, depending on the respective selection coefficients (s = 1.000, 0.520, and 0.212). Conclusions Our results confirm that the empirically observed frequencies of facultative recombination suffice to prevent accumulation of deleterious mutations via Muller’s ratchet even in a polyploid genome. The efficiency of selection is in flowering plants strongly increased by acting on the haplontic (reduced) gametophyte stage. Electronic supplementary material The online version of this article (10.1186/s12862-019-1495-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ladislav Hodač
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Goettingen, Germany
| | - Simone Klatt
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Goettingen, Germany
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Goettingen, Germany
| | - Timothy F Sharbel
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Goettingen, Germany.
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32
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Ram Y, Hadany L. Evolution of Stress-Induced Mutagenesis in the Presence of Horizontal Gene Transfer. Am Nat 2019; 194:73-89. [PMID: 31251650 DOI: 10.1086/703457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Stress-induced mutagenesis has been observed in multiple species of bacteria and yeast. It has been suggested that in asexual populations, a mutator allele that increases the mutation rate during stress can sweep to fixation with the beneficial mutations it generates. However, even asexual microbes can undergo horizontal gene transfer and rare recombination, which typically interfere with the spread of mutator alleles. Here we examine the effect of horizontal gene transfer on the evolutionary advantage of stress-induced mutator alleles. Our results demonstrate that stress-induced mutator alleles are favored by selection even in the presence of horizontal gene transfer and more so when the mutator alleles also increase the rate of horizontal gene transfer. We suggest that when regulated by stress, mutation and horizontal gene transfer can be complementary rather than competing adaptive strategies and that stress-induced mutagenesis has important implications for evolutionary biology, ecology, and epidemiology, even in the presence of horizontal gene transfer and rare recombination.
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Jain K. Interference Effects of Deleterious and Beneficial Mutations in Large Asexual Populations. Genetics 2019; 211:1357-1369. [PMID: 30700529 PMCID: PMC6456326 DOI: 10.1534/genetics.119.301960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/25/2019] [Indexed: 01/29/2023] Open
Abstract
Linked beneficial and deleterious mutations are known to decrease the fixation probability of a favorable mutation in large asexual populations. While the hindering effect of strongly deleterious mutations on adaptive evolution has been well studied, how weakly deleterious mutations, either in isolation or with superior beneficial mutations, influence the rate of adaptation has not been fully explored. When the selection against the deleterious mutations is weak, the beneficial mutant can fix in many genetic backgrounds, besides the one it arose on. Here, taking this factor into account, I obtain an accurate analytical expression for the fixation probability of a beneficial mutant in an asexual population at mutation-selection balance. I then exploit this result along with clonal interference theory to investigate the joint effect of linked beneficial and deleterious mutations on the rate of adaptation, and identify parameter regions where it is reduced due to interference by either beneficial or deleterious or both types of mutations. I also study the evolution of mutation rates in adapting asexual populations, and find that linked beneficial mutations have a stronger influence than the deleterious mutations on mutator fixation.
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Affiliation(s)
- Kavita Jain
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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34
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Goodman J, Copplestone D, Laptev GV, Gashchak S, Auld SKJR. Variation in chronic radiation exposure does not drive life history divergence among Daphnia populations across the Chernobyl Exclusion Zone. Ecol Evol 2019; 9:2640-2650. [PMID: 30891205 PMCID: PMC6405491 DOI: 10.1002/ece3.4931] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/20/2018] [Accepted: 12/31/2018] [Indexed: 11/12/2022] Open
Abstract
Ionizing radiation is a mutagen with known negative impacts on individual fitness. However, much less is known about how these individual fitness effects translate into population-level variation in natural environments that have experienced varying levels of radiation exposure. In this study, we sampled genotypes of the freshwater crustacean, Daphnia pulex, from the eight inhabited lakes across the Chernobyl Exclusion Zone (CEZ). Each lake has experienced very different levels of chronic radiation exposure since a nuclear power reactor exploded there over thirty years ago. The sampled Daphnia genotypes represent genetic snapshots of current populations and allowed us to examine fitness-related traits under controlled laboratory conditions at UK background dose rates. We found that whilst there was variation in survival and schedules of reproduction among populations, there was no compelling evidence that this was driven by variation in exposure to radiation. Previous studies have shown that controlled exposure to radiation at dose rates included in the range measured in the current study reduce survival, or fecundity, or both. One limitation of this study is the lack of available sites at high dose rates, and future work could test life history variation in various organisms at other high radiation areas. Our results are nevertheless consistent with the idea that other ecological factors, for example competition, predation or parasitism, are likely to play a much bigger role in driving variation among populations than exposure to the high radiation dose rates found in the CEZ. These findings clearly demonstrate that it is important to examine the potential negative effects of radiation across wild populations that are subject to many and varied selection pressures as a result of complex ecological interactions.
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Affiliation(s)
- Jessica Goodman
- Biological and Environmental Sciences, Faculty of Natural SciencesStirling UniversityStirlingUK
| | - David Copplestone
- Biological and Environmental Sciences, Faculty of Natural SciencesStirling UniversityStirlingUK
| | | | - Sergey Gashchak
- International Chornobyl Center 11SlavutychKyiv RegionUkraine
| | - Stuart K. J. R. Auld
- Biological and Environmental Sciences, Faculty of Natural SciencesStirling UniversityStirlingUK
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35
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Fitness and Genomic Consequences of Chronic Exposure to Low Levels of Copper and Nickel in Daphnia pulex Mutation Accumulation Lines. G3-GENES GENOMES GENETICS 2019; 9:61-71. [PMID: 30389796 PMCID: PMC6325897 DOI: 10.1534/g3.118.200797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays. After over 100 generations of mutation accumulation, we found no effects of metal exposure on the rates of single nucleotide mutations and of loss of heterozygosity events, the two mutation classes that occurred in sufficient numbers to allow statistical analysis. Similarly, rates of decline in fitness, as measured by intrinsic rate of population increase and of body size at first reproduction, were negligibly affected by metal exposure. We can reject the possibility that Daphnia were insufficiently stressed to invoke genetic responses as we have previously shown rates of large-scale deletions and duplications are elevated under metal exposure in this experiment. Overall, the mutation accumulation lines did not significantly depart from initial values for phenotypic traits measured, indicating the lineage used was broadly mutationally robust. Taken together, these results indicate that the mutagenic effects of chronic low-level exposure to these metals are restricted to certain mutation classes and that fitness consequences are likely minor and therefore unlikely to be relevant in determining the evolutionary responses of populations exposed to these stressors.
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36
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Zhao L, Abbasi AB, Illingworth CJR. Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evol 2019; 5:vez008. [PMID: 31024738 PMCID: PMC6476161 DOI: 10.1093/ve/vez008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mutational load is known to be of importance for the evolution of RNA viruses, the combination of a high mutation rate and large population size leading to an accumulation of deleterious mutations. However, while the effects of mutational load on global viral populations have been considered, its quantitative effects at the within-host scale of infection are less well understood. We here show that even on the rapid timescale of acute disease, mutational load has an effect on within-host viral adaptation, reducing the effective selection acting upon beneficial variants by ∼10 per cent. Furthermore, mutational load induces considerable stochasticity in the pattern of evolution, causing a more than five-fold uncertainty in the effective fitness of a transmitted beneficial variant. Our work aims to bridge the gap between classic models from population genetic theory and the biology of viral infection. In an advance on some previous models of mutational load, we replace the assumption of a constant variant fitness cost with an experimentally-derived distribution of fitness effects. Expanding previous frameworks for evolutionary simulation, we introduce the Wright-Fisher model with continuous mutation, which describes a continuum of possible modes of replication within a cell. Our results advance our understanding of adaptation in the context of strong selection and a high mutation rate. Despite viral populations having large absolute sizes, critical events in viral adaptation, including antigenic drift and the onset of drug resistance, arise through stochastic evolutionary processes.
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Affiliation(s)
- Lei Zhao
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ali B Abbasi
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Christopher J R Illingworth
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
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37
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Fabreti LG, Castro D, Gorzoni B, Janini LMR, Antoneli F. Stochastic Modeling and Simulation of Viral Evolution. Bull Math Biol 2018; 81:1031-1069. [PMID: 30552628 DOI: 10.1007/s11538-018-00550-4] [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: 12/22/2017] [Accepted: 12/03/2018] [Indexed: 12/11/2022]
Abstract
RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversity is generated and maintained is fundamental when approaching viral persistence and pathobiology in infected hosts. In this paper, we access quasispecies theory through a mathematical model based on the theory of multitype branching processes, to better understand the roles of mechanisms resulting in viral diversity, persistence and extinction. We accomplish this understanding by a combination of computational simulations and the theoretical analysis of the model. In order to perform the simulations, we have implemented the mathematical model into a computational platform capable of running simulations and presenting the results in a graphical format in real time. Among other things, we show that the establishment of virus populations may display four distinct regimes from its introduction into new hosts until achieving equilibrium or undergoing extinction. Also, we were able to simulate different fitness distributions representing distinct environments within a host which could either be favorable or hostile to the viral success. We addressed the most used mechanisms for explaining the extinction of RNA virus populations called lethal mutagenesis and mutational meltdown. We were able to demonstrate a correspondence between these two mechanisms implying the existence of a unifying principle leading to the extinction of RNA viruses.
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Affiliation(s)
- Luiza Guimarães Fabreti
- Programa de Pós-Graduação em Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Diogo Castro
- Programa de Pós-Graduação em Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Bruno Gorzoni
- Programa de Pós-Graduação em Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Luiz Mario Ramos Janini
- Departamentos de Microbiologia, Imunologia, Parasitologia and Medicina, Laboratório de Retrovirologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernando Antoneli
- Departamento de Informática em Saúde, Laboratório de Biocomplexidade e Genômica Evolutiva, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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38
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Generation of variation and a modified mean fitness principle: Necessity is the mother of genetic invention. Theor Popul Biol 2018; 123:1-8. [DOI: 10.1016/j.tpb.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 02/05/2023]
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39
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Vanhoenacker E, Sandell L, Roze D. Stabilizing selection, mutational bias, and the evolution of sex*. Evolution 2018; 72:1740-1758. [DOI: 10.1111/evo.13547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/20/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Eloïse Vanhoenacker
- CNRS UMI 3614 Evolutionary Biology and Ecology of Algae 29688 Roscoff France
- Sorbonne Université 29688 Roscoff France
| | - Linnéa Sandell
- Department of Zoology University of British Columbia Vancouver BC V6T1Z4 Canada
| | - Denis Roze
- CNRS UMI 3614 Evolutionary Biology and Ecology of Algae 29688 Roscoff France
- Sorbonne Université 29688 Roscoff France
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40
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Abstract
Genetic differences between species and within populations are two sides of the same coin under the neutral theory of molecular evolution. This theory posits that a vast majority of evolutionary substitutions, which appear as differences between species, are (nearly) neutral, that is, these substitutions are permitted without a significantly adverse impact on a species' survival. We refer to them as evolutionarily permissible (ePerm) variation. Evolutionary permissibility of any possible variant can be inferred from multispecies sequence alignments by applying sophisticated statistical methods to the evolutionary tree of species. Here, we explore the evolutionary permissibility of amino acid variants associated with genetic diseases and those observed in personal exomes. Consistent with the predictions of the neutral theory, disease associated amino acid variants are rarely ePerm, much more biochemically radical, and found predominantly at more conserved positions than their non-disease counterparts. Only 10% of amino acid mutations are ePerm, but these variants rise to become two-thirds of all substitutions in the human lineage (a 6-fold enrichment). In contrast, only a minority of the variants in a personal exome are ePerm, a seemingly counterintuitive pattern that results from a combination of mutational and evolutionary processes that are, in fact, broadly consistent with the neutral theory. Evolutionarily forbidden variants outnumber detrimental variants in individual exomes and may play an underappreciated role in protecting against disease. We discuss these observations and conclude that the long-term evolutionary history of species can illuminate functional biomedical properties of variation present in personal exomes.
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Affiliation(s)
- Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ravi Patel
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
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41
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Dapper AL, Payseur BA. Connecting theory and data to understand recombination rate evolution. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0469. [PMID: 29109228 DOI: 10.1098/rstb.2016.0469] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2017] [Indexed: 02/03/2023] Open
Abstract
Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Amy L Dapper
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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42
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The Effect of Strong Purifying Selection on Genetic Diversity. Genetics 2018; 209:1235-1278. [PMID: 29844134 DOI: 10.1534/genetics.118.301058] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/25/2018] [Indexed: 12/15/2022] Open
Abstract
Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backward-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.
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43
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Kondrashov AS. Through Sex, Nature Is Telling Us Something Important. Trends Genet 2018; 34:352-361. [DOI: 10.1016/j.tig.2018.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 01/05/2018] [Indexed: 11/28/2022]
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44
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Jaffe K. Synergy from reproductive division of labor and genetic complexity drive the evolution of sex. J Biol Phys 2018; 44:317-329. [PMID: 29663185 DOI: 10.1007/s10867-018-9485-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 03/16/2018] [Indexed: 11/28/2022] Open
Abstract
Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating. Looking at the evolution of sex as a complex system through individual-based simulations explains better the diversity of sexual strategies known to exist in nature, compared to classical analytical models.
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Affiliation(s)
- Klaus Jaffe
- Universidad Simón Bolivar, Caracas, Venezuela.
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45
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Sprouffske K, Aguilar-Rodríguez J, Sniegowski P, Wagner A. High mutation rates limit evolutionary adaptation in Escherichia coli. PLoS Genet 2018; 14:e1007324. [PMID: 29702649 PMCID: PMC5942850 DOI: 10.1371/journal.pgen.1007324] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 05/09/2018] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Mutation is fundamental to evolution, because it generates the genetic variation on which selection can act. In nature, genetic changes often increase the mutation rate in systems that range from viruses and bacteria to human tumors. Such an increase promotes the accumulation of frequent deleterious or neutral alleles, but it can also increase the chances that a population acquires rare beneficial alleles. Here, we study how up to 100-fold increases in Escherichia coli's genomic mutation rate affect adaptive evolution. To do so, we evolved multiple replicate populations of asexual E. coli strains engineered to have four different mutation rates for 3000 generations in the laboratory. We measured the ability of evolved populations to grow in their original environment and in more than 90 novel chemical environments. In addition, we subjected the populations to whole genome population sequencing. Although populations with higher mutation rates accumulated greater genetic diversity, this diversity conveyed benefits only for modestly increased mutation rates, where populations adapted faster and also thrived better than their ancestors in some novel environments. In contrast, some populations at the highest mutation rates showed reduced adaptation during evolution, and failed to thrive in all of the 90 alternative environments. In addition, they experienced a dramatic decrease in mutation rate. Our work demonstrates that the mutation rate changes the global balance between deleterious and beneficial mutational effects on fitness. In contrast to most theoretical models, our experiments suggest that this tipping point already occurs at the modest mutation rates that are found in the wild.
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Affiliation(s)
- Kathleen Sprouffske
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - José Aguilar-Rodríguez
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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46
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Abu Awad D, Roze D. Effects of partial selfing on the equilibrium genetic variance, mutation load, and inbreeding depression under stabilizing selection. Evolution 2018; 72:751-769. [DOI: 10.1111/evo.13449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/17/2018] [Indexed: 01/06/2023]
Affiliation(s)
| | - Denis Roze
- CNRS; UMI 3614 Evolutionary Biology and Ecology of Algae,; 29688 Roscoff France
- Sorbonne Universités; UPMC Université Paris VI,; 29688 Roscoff France
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47
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Sohail M, Vakhrusheva OA, Sul JH, Pulit SL, Francioli LC, van den Berg LH, Veldink JH, de Bakker PIW, Bazykin GA, Kondrashov AS, Sunyaev SR. Negative selection in humans and fruit flies involves synergistic epistasis. Science 2018; 356:539-542. [PMID: 28473589 DOI: 10.1126/science.aah5238] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/28/2016] [Accepted: 04/14/2017] [Indexed: 12/22/2022]
Abstract
Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection. However, it is not known whether deleterious alleles affect fitness independently, so that cumulative fitness loss depends exponentially on the number of deleterious alleles, or synergistically, so that each additional deleterious allele results in a larger decrease in relative fitness. Negative selection with synergistic epistasis should produce negative linkage disequilibrium between deleterious alleles and, therefore, an underdispersed distribution of the number of deleterious alleles in the genome. Indeed, we detected underdispersion of the number of rare loss-of-function alleles in eight independent data sets from human and fly populations. Thus, selection against rare protein-disrupting alleles is characterized by synergistic epistasis, which may explain how human and fly populations persist despite high genomic mutation rates.
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48
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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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49
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Brown KE, Kelly JK. Antagonistic pleiotropy can maintain fitness variation in annual plants. J Evol Biol 2017; 31:46-56. [DOI: 10.1111/jeb.13192] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 01/24/2023]
Affiliation(s)
- K. E. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - J. K. Kelly
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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50
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LaBar T, Adami C. Evolution of drift robustness in small populations. Nat Commun 2017; 8:1012. [PMID: 29044114 PMCID: PMC5647343 DOI: 10.1038/s41467-017-01003-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/10/2017] [Indexed: 11/09/2022] Open
Abstract
Most mutations are deleterious and cause a reduction in population fitness known as the mutational load. In small populations, weakened selection against slightly-deleterious mutations results in an additional fitness reduction. Many studies have established that populations can evolve a reduced mutational load by evolving mutational robustness, but it is uncertain whether small populations can evolve a reduced susceptibility to drift-related fitness declines. Here, using mathematical modeling and digital experimental evolution, we show that small populations do evolve a reduced vulnerability to drift, or ‘drift robustness’. We find that, compared to genotypes from large populations, genotypes from small populations have a decreased likelihood of small-effect deleterious mutations, thus causing small-population genotypes to be drift-robust. We further show that drift robustness is not adaptive, but instead arises because small populations can only maintain fitness on drift-robust fitness peaks. These results have implications for genome evolution in organisms with small effective population sizes. Genetic drift can reduce fitness in small populations by counteracting selection against deleterious mutations. Here, LaBar and Adami demonstrate through a mathematical model and simulations that small populations tend to evolve to drift-robust fitness peaks, which have a low likelihood of slightly-deleterious mutations.
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Affiliation(s)
- Thomas LaBar
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Christoph Adami
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. .,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, 48824, USA. .,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, MI, 48824, USA.
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