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 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 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 Erratum: Rybnikov et al. Selection for Plastic, Pathogen-Inducible Recombination in a Red Queen Model with Diploid Antagonists. Pathogens 2021, 10, 898

Pathogens ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1460
Author(s):  
Sviatoslav Rybnikov ◽  
Zeev Frenkel ◽  
Abraham B. Korol ◽  
Tzion Fahima
Keyword(s):  
Red Queen ◽  
Selection For ◽  
Red Queen Model

In the original article, there was a mistake published in Figure 3 [...]

scholarly journals Recombination hotspots as a point process

2005 ◽  
Vol 360 (1460) ◽  
pp. 1597-1603 ◽  
Author(s):  
Maria De Iorio ◽  
Eric de Silva ◽  
Michael P.H Stumpf
Keyword(s):  
Point Process ◽  
Dna Sequences ◽  
Recombination Rate ◽  
Population Genetic ◽  
Process Model ◽  
Chromosomal Dna ◽  
New Approach ◽  
Recombination Hotspots ◽  
Minimum Number ◽  
Fully Bayesian

The variation of the recombination rate along chromosomal DNA is one of the important determinants of the patterns of linkage disequilibrium. A number of inferential methods have been developed which estimate the recombination rate and its variation from population genetic data. The majority of these methods are based on modelling the genealogical process underlying a sample of DNA sequences and thus explicitly include a model of the demographic process. Here we propose a different inferential procedure based on a previously introduced framework where recombination is modelled as a point process along a DNA sequence. The approach infers regions containing putative hotspots based on the inferred minimum number of recombination events; it thus depends only indirectly on the underlying population demography. A Poisson point process model with local rates is then used to infer patterns of recombination rate estimation in a fully Bayesian framework. We illustrate this new approach by applying it to several population genetic datasets, including a region with an experimentally confirmed recombination hotspot.

scholarly journals Dynamics of recombination modifiers caused by cyclical selection: Interaction of forced and auto-oscillations

1998 ◽  
Vol 72 (2) ◽  
pp. 135-147 ◽  
Author(s):  
A. B. KOROL ◽  
V. M. KIRZHNER ◽  
E. NEVO
Keyword(s):  
Recombination Rate ◽  
Domain Of Attraction ◽  
Forced Oscillations ◽  
Modifier Locus ◽  
Long Period ◽  
Short Period ◽  
Fixed Parameter ◽  
Key Factor ◽  
Limiting Behaviour ◽  
Selection For

Temporally varying selection is considered to be one of the potential mechanisms of recombination evolution. We found earlier that simple cyclical selection for a trait controlled by multiple additive, dominant or semi-dominant loci can result in extremely complex limiting behaviour (CLB) of population trajectories, including ‘supercycles’ and more complex attractors. Recombination rate proved to be a key factor affecting the mode of CLB and the very existence of CLB. Therefore, we considered here a generalized model: the fixed recombination rate was replaced by a polymorphic recombination modifier. The modifier-dependent changes included: (a) supercyclical dynamics due to the recombination modifier in a system that does not manifest CLB when recombination rate is a fixed parameter; (b) appearance of a new level of superoscillations (super-supercycles) in a system that manifests supercycles with a fixed modifier; (c) chaotization of the regular supercyclical dynamics. The domain of attraction of these movements appeared to be quite large. It is noteworthy that the modifier locus is an active participant in the observed non-monotonic limiting movements. Interactions between short-period forced oscillations and the revealed long-period auto-oscillations appeared to result in new regimes of recombination evolution (for some range of linkage between the modifier locus and the selected system), as compared with those caused by the forced oscillations alone.

scholarly journals Selection for recombination in a polygenic model – the mechanism

1988 ◽  
Vol 51 (1) ◽  
pp. 59-63 ◽  
Author(s):  
J. Maynard Smith
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Phenotypic Variability ◽  
Directional Selection ◽  
Polygenic Model ◽  
Infinite Population ◽  
Selection For ◽  
Repulsion Linkage

SummaryA polygenic model has been simulated in order to reveal the process whereby selection in an infinite population can lead to an increase in the frequency of alleles causing higher rates of recombination (CH alleles). Directional selection generates repulsion linkage disequilibrium (+ − + −), which is less strong in CH gametes (gametes carrying CH alleles). In consequence, CH gametes contribute greater phenotypic variability, and therefore respond more to directional selection: that is, they accumulate more selectively favoured alleles. CH alleles then increase in frequency by hitch-hiking. In contrast, normalizing selection, or frequent changes in the direction of selection, favour alleles for a low recombination rate.

scholarly journals Population sequencing enhances understanding of tea plant evolution

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinchao Wang ◽  
Hu Feng ◽  
Yuxiao Chang ◽  
Chunlei Ma ◽  
Liyuan Wang ◽  
...  
Keyword(s):  
Population Genetic ◽  
Tea Plant ◽  
Plant Evolution ◽  
Marker Assisted Breeding ◽  
High Quality ◽  
Domestication Selection ◽  
The World ◽  
High Species Diversity ◽  
Selection For ◽  
Genomic Resequencing

Abstract Tea is an economically important plant characterized by a large genome, high heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality chromosome-scale genome for the ‘Longjing 43’ cultivar of Camellia sinensis var. sinensis. Genomic resequencing of 139 tea accessions from around the world is used to investigate the evolution and phylogenetic relationships of tea accessions. We find that hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations with the spread of tea cultivation. Population genetic and transcriptomic analyses reveal that during domestication, selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. This study provides resources for marker-assisted breeding of tea and sets the foundation for further research on tea genetics and evolution.

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