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Rybnikov SR, Hübner S, Korol AB. A Numerical Model Supports the Evolutionary Advantage of Recombination Plasticity in Shifting Environments. Am Nat 2024; 203:E78-E91. [PMID: 38358806 DOI: 10.1086/728405] [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: 02/17/2024]
Abstract
AbstractNumerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions. Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario-when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination in individuals developing in a different environment than their parents and, optionally, also in offspring of such individuals. We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may also appear beneficial when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared with the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms, such as chromatin epigenetics remodeling.
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Winbush A, Singh ND. Variation in fine-scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection. G3 GENES|GENOMES|GENETICS 2022; 12:6663992. [PMID: 35961026 PMCID: PMC9526048 DOI: 10.1093/g3journal/jkac208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022]
Abstract
Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection, but the extent to which fine-scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here, we utilize a set of 3 temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes, including recombination rate, based on the temperature regime in which they evolved. Using whole-genome sequencing data from these populations, we generated linkage disequilibrium-based fine-scale recombination maps for each population. With these maps, we compare recombination rates and patterns among the 3 populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the 3 populations. Lastly, we show variation in localized regions of enhanced recombination rates, termed warm spots, between the populations with these warm spots and associated genes overlapping areas previously shown to have diverged in the 3 populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.
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Affiliation(s)
- Ari Winbush
- Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR 97403, USA
| | - Nadia D Singh
- Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR 97403, USA
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Aggarwal DD, Rybnikov S, Sapielkin S, Rashkovetsky E, Frenkel Z, Singh M, Michalak P, Korol AB. Seasonal changes in recombination characteristics in a natural population of Drosophila melanogaster. Heredity (Edinb) 2021; 127:278-287. [PMID: 34163036 PMCID: PMC8405755 DOI: 10.1038/s41437-021-00449-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Environmental seasonality is a potent evolutionary force, capable of maintaining polymorphism, promoting phenotypic plasticity and causing bet-hedging. In Drosophila, environmental seasonality has been reported to affect life-history traits, tolerance to abiotic stressors and immunity. Oscillations in frequencies of alleles underlying fitness-related traits were also documented alongside SNPs across the genome. Here, we test for seasonal changes in two recombination characteristics, crossover rate and crossover interference, in a natural D. melanogaster population from India using morphological markers of the three major chromosomes. We show that winter flies, collected after the dry season, have significantly higher desiccation tolerance than their autumn counterparts. This difference proved to hold also for hybrids with three independent marker stocks, suggesting its genetic rather than plastic nature. Significant between-season changes are documented for crossover rate (in 9 of 13 studied intervals) and crossover interference (in four of eight studied pairs of intervals); both single and double crossovers were usually more frequent in the winter cohort. The winter flies also display weaker plasticity of both recombination characteristics to desiccation. We ascribe the observed differences to indirect selection on recombination caused by directional selection on desiccation tolerance. Our findings suggest that changes in recombination characteristics can arise even after a short period of seasonal adaptation (~8-10 generations).
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Affiliation(s)
- Dau Dayal Aggarwal
- Department of Zoology, Banaras Hindu University, Varanasi, India.
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.
| | - Sviatoslav Rybnikov
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
| | - Shaul Sapielkin
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Manvender Singh
- Department of Biotechnology, UIET, MD University, Rohtak, India
| | - Pawel Michalak
- Institute of Evolution, University of Haifa, Haifa, Israel
- Edward Via College of Osteopathic Medicine, Monroe, LA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
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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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Abstract
Sex, as well as meiotic recombination between homologous chromosomes, is nearly ubiquitous among eukaryotes. In those species that use it, recombination is important for chromosome segregation during gamete production, and thus for fertility. Strikingly, although in most species only one crossover event per chromosome is required to ensure proper segregation, recombination rates vary considerably above this minimum and show variation within and among species. However, whether this variation in recombination is adaptive or neutral and what might shape it remain unclear. Empirical studies and theory support the idea that recombination is generally beneficial but can also have costs. Here, we review variation in genome-wide recombination rates, explore what might cause this, and discuss what is known about its mechanistic basis. We end by discussing the environmental sensitivity of meiosis and recombination rates, how these features may relate to adaptation, and their implications for a broader understanding of recombination rate evolution. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
| | - Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, 8092 Zürich, Switzerland;
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Weitz AP, Dukic M, Zeitler L, Bomblies K. Male meiotic recombination rate varies with seasonal temperature fluctuations in wild populations of autotetraploid Arabidopsis arenosa. Mol Ecol 2021; 30:4630-4641. [PMID: 34273213 PMCID: PMC9292783 DOI: 10.1111/mec.16084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022]
Abstract
Meiosis, the cell division by which eukaryotes produce haploid gametes, is essential for fertility in sexually reproducing species. This process is sensitive to temperature, and can fail outright at temperature extremes. At less extreme values, temperature affects the genome‐wide rate of homologous recombination, which has important implications for evolution and population genetics. Numerous studies in laboratory conditions have shown that recombination rate plasticity is common, perhaps nearly universal, among eukaryotes. These studies have also shown that variation in the length or timing of stresses can strongly affect results, raising the important question whether these findings translate to more variable field conditions. Moreover, lower or higher recombination rate could cause certain kinds of meiotic aberrations, especially in polyploid species—raising the additional question whether temperature fluctuations in field conditions cause problems. Here, we tested whether (1) recombination rate varies across a season in the wild in two natural populations of autotetraploid Arabidopsis arenosa, (2) whether recombination rate correlates with temperature fluctuations in nature, and (3) whether natural temperature fluctuations might cause meiotic aberrations. We found that plants in two genetically distinct populations showed a similar plastic response with recombination rate increases correlated with both high and low temperatures. In addition, increased recombination rate correlated with increased multivalent formation, especially at lower temperature, hinting that polyploids in particular may suffer meiotic problems in conditions they encounter in nature. Our results show that studies of recombination rate plasticity done in laboratory settings inform our understanding of what happens in nature.
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Affiliation(s)
- Andrew P Weitz
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Department of Environmental Sciences, Western Washington University, Bellingham, Washington, USA
| | - Marinela Dukic
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Leo Zeitler
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Department of Biology, Ecological Genomics, Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Kirsten Bomblies
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
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Rybnikov S, Frenkel Z, Korol AB. The evolutionary advantage of fitness-dependent recombination in diploids: A deterministic mutation-selection balance model. Ecol Evol 2020; 10:2074-2084. [PMID: 32128139 PMCID: PMC7042682 DOI: 10.1002/ece3.6040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/26/2019] [Accepted: 01/02/2020] [Indexed: 12/20/2022] Open
Abstract
Recombination's omnipresence in nature is one of the most intriguing problems in evolutionary biology. The question of why recombination exhibits certain general features is no less interesting than that of why it exists at all. One such feature is recombination's fitness dependence (FD). The so far developed population genetics models have focused on the evolution of FD recombination mainly in haploids, although the empirical evidence for this phenomenon comes mostly from diploids. Using numerical analysis of modifier models for infinite panmictic populations, we show here that FD recombination can be evolutionarily advantageous in diploids subjected to purifying selection. We ascribe this advantage to the differential rate of disruption of lower- versus higher-fitness genotypes, which can be manifested in selected systems with at least three loci. We also show that if the modifier is linked to such selected system, it can additionally benefit from modifying this linkage in a fitness-dependent manner. The revealed evolutionary advantage of FD recombination appeared robust to crossover interference within the selected system, either positive or negative. Remarkably, FD recombination was often favored in situations where any constant nonzero recombination was evolutionarily disfavored, implying a relaxation of the rather strict constraints on major parameters (e.g., selection intensity and epistasis) required for the evolutionary advantage of nonzero recombination formulated by classical models.
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Affiliation(s)
- Sviatoslav Rybnikov
- Institute of EvolutionUniversity of HaifaHaifaIsrael
- Department of Evolutionary and Environmental BiologyUniversity of HaifaHaifaIsrael
| | - Zeev Frenkel
- Department of Mathematics and Computational ScienceAriel UniversityArielIsrael
| | - Abraham B. Korol
- Institute of EvolutionUniversity of HaifaHaifaIsrael
- Department of Evolutionary and Environmental BiologyUniversity of HaifaHaifaIsrael
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