scholarly journals The evolutionary advantage of condition-dependent recombination in a Red Queen model with diploid antagonists

2018 ◽  
Author(s):  
Sviatoslav R. Rybnikov ◽  
Zeev M. Frenkel ◽  
Tzion Fahima ◽  
Abraham B. Korol
Keyword(s):  
Recombination Rate ◽  
Theoretical Models ◽  
Condition Dependence ◽  
Red Queen ◽  
Recombination Rates ◽  
Optimal Constant ◽  
Evolutionary Advantage ◽  
Mean Fitness ◽  
Parameter Values ◽  
Red Queen Model

AbstractAntagonistic interaction, like those between a host and its parasite, are known to cause oscillations in genetic structure of both species, usually referred to as Red Queen dynamics (RQD). The RQD is believed to be a plausible explanation for the evolution of sex/recombination, although numerous theoretical models showed that this may happen only under rather restricted parameter values (selection intensity, epistasis, etc.). Here, we consider two diploid antagonists, each with either two or three selected loci; the interaction is based on matching phenotypes model. We use the RQD, whenever it emerges in this system, as a substrate to examine the evolution of one recombination feature, condition dependence in diploids, which still remains an underexplored question. We consider several forms of condition-dependent recombination, with recombination rates in the host being sensitive either to the parasite’s mean fitness, or to the host’s infection status, or to the host’s genotype fitness. We show that all form of condition-dependent recombination can be favored over the corresponding optimal constant recombination rate, even including situations in which the optimal constant recombination rate is zero.

scholarly journals What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160460 ◽  
Author(s):  
Sviatoslav R. Rybnikov ◽  
Zeev M. Frenkel ◽  
Abraham B. Korol
Keyword(s):  
Recombination Rate ◽  
External Environment ◽  
Theoretical Models ◽  
Simulation Modelling ◽  
Condition Dependence ◽  
Rate Variation ◽  
Theoretical Studies ◽  
Recombination Rates ◽  
Modifier Locus ◽  
Recombination Rate Variation

While the evolutionary advantages of non-zero recombination rates have prompted diverse theoretical explanations, the evolution of essential recombination features remains underexplored. We focused on one such feature, the condition dependence of recombination, viewed as the variation in within-generation sensitivity of recombination to external (environment) and/or internal (genotype) conditions. Limited empirical evidence for its existence comes mainly from diploids, whereas theoretical models show that it only easily evolves in haploids. The evolution of condition-dependent recombination can be explained by its advantage for the selected system (indirect effect), or by benefits to modifier alleles, ensuring this strategy regardless of effects on the selected system (direct effect). We considered infinite panmictic populations of diploids exposed to a cyclical two-state environment. Each organism had three selected loci. Examining allele dynamics at a fourth, selectively neutral recombination modifier locus, we frequently observed that a modifier allele conferring condition-dependent recombination between the selected loci displaced the allele conferring the optimal constant recombination rate. Our simulations also confirm the results of theoretical studies showing that condition-dependent recombination cannot evolve in diploids on the basis of direct fitness-dependent effects alone. Therefore, the evolution of condition-dependent recombination in diploids can be driven by indirect effects alone, i.e. by modifier effects on the selected system. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals Selection for Plastic, Pathogen-Inducible Recombination in a Red Queen Model with Diploid Antagonists

Pathogens ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 898
Author(s):  
Sviatoslav Rybnikov ◽  
Zeev Frenkel ◽  
Abraham B. Korol ◽  
Tzion Fahima
Keyword(s):  
Recombination Rate ◽  
Population Genetic ◽  
Infection Prevention ◽  
Theoretical Models ◽  
Prevention Strategy ◽  
Risk Of Infection ◽  
Red Queen ◽  
Selection For ◽  
Red Queen Model ◽  
Antagonistic Interactions

Antagonistic interactions and co-evolution between a host and its parasite are known to cause oscillations in the population genetic structure of both species (Red Queen dynamics). Potentially, such oscillations may select for increased sex and recombination in the host, although theoretical models suggest that this happens under rather restricted values of selection intensity, epistasis, and other parameters. Here, we explore a model in which the diploid parasite succeeds to infect the diploid host only if their phenotypes at the interaction-mediating loci match. Whenever regular oscillations emerge in this system, we test whether plastic, pathogen-inducible recombination in the host can be favored over the optimal constant recombination. Two forms of the host recombination dependence on the parasite pressure were considered: either proportionally to the risk of infection (prevention strategy) or upon the fact of infection (remediation strategy). We show that both forms of plastic recombination can be favored, although relatively infrequently (up to 11% of all regimes with regular oscillations, and up to 20% of regimes with obligate parasitism). This happens under either strong overall selection and high recombination rate in the host, or weak overall selection and low recombination rate in the host. In the latter case, the system’s dynamics are considerably more complex. The prevention strategy is favored more often than the remediation one. It is noteworthy that plastic recombination can be favored even when any constant recombination is rejected, making plasticity an evolutionary mechanism for the rescue of host recombination.

scholarly journals The Red Queen model of recombination hot-spot evolution: a theoretical investigation

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160463 ◽  
Author(s):  
Thibault Latrille ◽  
Laurent Duret ◽  
Nicolas Lartillot
Keyword(s):  
Gene Conversion ◽  
Recombination Rate ◽  
Evolutionary Dynamics ◽  
Genetic Model ◽  
Hot Spot ◽  
Rate Variation ◽  
Red Queen ◽  
Biased Gene Conversion ◽  
Red Queen Model ◽  
The Red Queen

In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs. Thus far, however, this Red Queen model has not been formalized as a quantitative population-genetic model, fully accounting for the intricate interplay between biased gene conversion, mutation, selection, demography and genetic diversity at the PRDM9 locus. Here, we explore the population genetics of the Red Queen model of recombination. A Wright–Fisher simulator was implemented, allowing exploration of the behaviour of the model (mean equilibrium recombination rate, diversity at the PRDM9 locus or turnover rate) as a function of the parameters (effective population size, mutation and erosion rates). In a second step, analytical results based on self-consistent mean-field approximations were derived, reproducing the scaling relations observed in the simulations. Empirical fit of the model to current data from the mouse suggests both a high mutation rate at PRDM9 and strong biased gene conversion on its targets. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals SELECTION ON RECOMBINATION IN CLINES

Genetics ◽  
1979 ◽  
Vol 91 (3) ◽  
pp. 581-589 ◽  
Author(s):  
D Charlesworth ◽  
B Charlesworth
Keyword(s):  
Recombination Rate ◽  
Environmental Changes ◽  
Recombination Rates ◽  
Selection Pressures ◽  
Selection Models ◽  
Linear Sets ◽  
Selection For ◽  
Parameter Values

ABSTRACT Computer runs have been done to examine SLATKIN'S (1975) model for selection on recombination rates in linear sets of populations with environmental changes affecting two loci. In order to determine whether the suggested selection pressures on recombination do, in fact, exist, we follow the changes in frequency at a third locus that is polymorphic for alleles affecting the recombination rate between the two selected loci. With haploid or diploid selection models, there can be selection for increased recombination if the parameter values are chosen suitably, but changes in parameter values often lead to changes in the direction of selection, so that decreased recombination is favored, The selection for increased recombination is usually weak, while that for decreased recombination is frequently much stronger. Weaker selection on the selected loci often leads to increasing selection for decreased recombination.

scholarly journals Connecting theory and data to understand recombination rate evolution

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160469 ◽  
Author(s):  
Amy L. Dapper ◽  
Bret A. Payseur
Keyword(s):  
Recombination Rate ◽  
Empirical Studies ◽  
Theoretical Work ◽  
Rate Variation ◽  
Recombination Rates ◽  
Theoretical Approaches ◽  
Evolutionary Advantage ◽  
New Directions ◽  
The Rich ◽  
Recombination Rate Variation

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’.

scholarly journals Shift-inducible [transgenerational] increase in recombination rate as an evolving strategy in a periodic environment: a numerical model

2021 ◽  
Author(s):  
Sviatoslav Rybnikov ◽  
Sariel Hübner ◽  
Abraham Korol
Keyword(s):  
Recombination Rate ◽  
Physiological Stress ◽  
Empirical Studies ◽  
Theoretical Models ◽  
Epigenetic Factors ◽  
Periodic Environment ◽  
Evolutionary Advantage ◽  
Plastic Changes ◽  
Optimal Recombination ◽  
Evolutionary Role

Numerous empirical studies have witnessed a plastic increase in meiotic recombination rate in organisms experiencing physiological stress due to unfavourable environmental conditions. Yet, it is not clear enough which characteristics of an ecological factor (intensity, duration, variability, etc.) make it stressogenic and therefore recombinogenic for an organism. Several previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more severe, and demonstrated the evolutionary advantage of such recombination strategy. Here we explore another stress-associated recombination strategy, implying a reversible increase in recombination rate each time when the environment alternates. We allow such plastic changes in the organisms, grown in an environment different from that of their parents, and, optionally, also in their offspring. We show that such shift-inducible recombination is always favoured over intermediate constant optimal recombination. Besides, it sometimes outcompetes also zero and free optimal constant recombination, therefore making selection on recombination less polarized. Shift-inducible strategies with a longer, transgenerational plastic effect, are favoured under slightly stronger selection and longer period. These results hold for both panmixia and partial selfing, although selfing makes the dynamics of recombination modifier alleles faster. Our results suggest that epigenetic factors, presumably underlying the environmental plasticity of recombination, may play an important evolutionary role.

scholarly journals Microsatellite Variation and Recombination Rate in the Human Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1285-1298 ◽  
Author(s):  
Bret A Payseur ◽  
Michael W Nachman
Keyword(s):  
Recombination Rate ◽  
Microsatellite Polymorphism ◽  
Published Data ◽  
Strong Positive Correlation ◽  
Background Selection ◽  
Recombination Rates ◽  
Microsatellite Variation ◽  
Positive Correlation ◽  
Genome Recombination ◽  
Neutral Mutations

Abstract Background (purifying) selection on deleterious mutations is expected to remove linked neutral mutations from a population, resulting in a positive correlation between recombination rate and levels of neutral genetic variation, even for markers with high mutation rates. We tested this prediction of the background selection model by comparing recombination rate and levels of microsatellite polymorphism in humans. Published data for 28 unrelated Europeans were used to estimate microsatellite polymorphism (number of alleles, heterozygosity, and variance in allele size) for loci throughout the genome. Recombination rates were estimated from comparisons of genetic and physical maps. First, we analyzed 61 loci from chromosome 22, using the complete sequence of this chromosome to provide exact physical locations. These 61 microsatellites showed no correlation between levels of variation and recombination rate. We then used radiation-hybrid and cytogenetic maps to calculate recombination rates throughout the genome. Recombination rates varied by more than one order of magnitude, and most chromosomes showed significant suppression of recombination near the centromere. Genome-wide analyses provided no evidence for a strong positive correlation between recombination rate and polymorphism, although analyses of loci with at least 20 repeats suggested a weak positive correlation. Comparisons of microsatellites in lowest-recombination and highest-recombination regions also revealed no difference in levels of polymorphism. Together, these results indicate that background selection is not a major determinant of microsatellite variation in humans.

scholarly journals Patterns of DNA Variability at X-Linked Loci in Mus domesticus

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1303-1316
Author(s):  
Michael W Nachman
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
House Mouse ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Mus Domesticus ◽  
Substantial Variation ◽  
Intraspecific Polymorphism ◽  
Recombination Rates ◽  
Interspecific Divergence

Introns of four X-linked genes (Hprt, Plp, Glra2, and Amg) were sequenced to provide an estimate of nucleotide diversity at nuclear genes within the house mouse and to test the neutral prediction that the ratio of intraspecific polymorphism to interspecific divergence is the same for different loci. Hprt and Plp lie in a region of the X chromosome that experiences relatively low recombination rates, while Glra2 and Amg lie near the telomere of the X chromosome, a region that experiences higher recombination rates. A total of 6022 bases were sequenced in each of 10 Mus domesticus and one M. caroli. Average nucleotide diversity (π) for introns within M. domesticus was quite low (π = 0.078%). However, there was substantial variation in the level of heterozygosity among loci. The two telomeric loci, Glra2 and Amg, had higher ratios of polymorphism to divergence than the two loci experiencing lower recombination rates. These results are consistent with the hypothesis that heterozygosity is reduced in regions with lower rates of recombination, although sampling of additional genes is needed to establish whether there is a general correlation between heterozygosity and recombination rate as in Drosophila melanogaster.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

scholarly journals Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161785 ◽  
Author(s):  
Long Wang ◽  
Yanchun Zhang ◽  
Chao Qin ◽  
Dacheng Tian ◽  
Sihai Yang ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Recombination Rate ◽  
Mutation Rates ◽  
Recombination Rates ◽  
Rate Analysis ◽  
A Genome ◽  
Break Points ◽  
New Mutations

Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent–offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination–heterozygozity correlation in peach, we caution against such an interpretation.

Sign in / Sign up

Export Citation Format

Share Document