scholarly journals Gene buddies: Linked balanced polymorphisms reinforce each other even in the absence of epistasis

2017 ◽  
Author(s):  
Jacob A Tennessen
Keyword(s):  
Recombination Rate ◽  
Evolutionary Dynamics ◽  
Balancing Selection ◽  
Natural Populations ◽  
Adaptive Variation ◽  
Recombination Rates ◽  
Future Studies ◽  
Close Physical Proximity ◽  
Selection For ◽  
Independent Effects

The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However, genes harboring adaptive variation can occur in close physical proximity while generating independent effects on fitness. Here, I present a model in which two linked loci without epistasis are both under balancing selection for unrelated reasons. Using forward-time simulations, I show that recombination rate strongly influences the retention of adaptive polymorphism, especially for intermediate selection coefficients. A locus is more likely to retain adaptive variation if it is closely linked to another locus under balancing selection, even if the two loci have no interaction. Thus, two linked polymorphisms can both be retained indefinitely even when they would both be lost to drift if unlinked. Such clusters of mutually reinforcing genes may underlie phenotypic variation in natural populations. Future studies that measure selection coefficients and recombination rates among closely linked genes will be fruitful for characterizing the extent of this phenomenon.

scholarly journals Gene buddies: linked balanced polymorphisms reinforce each other even in the absence of epistasis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5110 ◽  
Author(s):  
Jacob A. Tennessen
Keyword(s):  
Genetic Architecture ◽  
Evolutionary Dynamics ◽  
Balancing Selection ◽  
Natural Populations ◽  
Adaptive Variation ◽  
Recombination Rates ◽  
Future Studies ◽  
Close Physical Proximity ◽  
Selection For ◽  
Independent Effects

The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However, genes harboring adaptive variation can occur in close physical proximity while generating independent effects on fitness. Here, I present a model in which two linked loci without epistasis are both under balancing selection for unrelated reasons. Using forward-time simulations, I show that recombination rate strongly influences the retention of adaptive polymorphism, especially for intermediate selection coefficients. A locus is more likely to retain adaptive variation if it is closely linked to another locus under balancing selection, even if the two loci have no interaction. Thus, two linked polymorphisms can both be retained indefinitely even when they would both be lost to drift if unlinked. While these results may be intuitive, they have important implications for genetic architecture: clusters of mutually reinforcing genes may underlie phenotypic variation in natural populations, and such genes cannot be assumed to be functionally associated. Future studies that measure selection coefficients and recombination rates among closely linked genes will be fruitful for characterizing the extent of this phenomenon.

scholarly journals Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

2019 ◽  
Vol 36 (9) ◽  
pp. 2029-2039 ◽  
Author(s):  
Steven Dreissig ◽  
Martin Mascher ◽  
Stefan Heckmann
Keyword(s):  
Environmental Conditions ◽  
Recombination Rate ◽  
Wild Barley ◽  
Natural Populations ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Positive Linear Correlation ◽  
Short And Long Term ◽  
Underlying Mechanisms ◽  
Chromosome Regions

Abstract Meiotic recombination generates genetic diversity upon which selection can act. Recombination rates are highly variable between species, populations, individuals, sexes, chromosomes, and chromosomal regions. The underlying mechanisms are controlled at the genetic and epigenetic level and show plasticity toward the environment. Environmental plasticity may be divided into short- and long-term responses. We estimated recombination rates in natural populations of wild barley and domesticated landraces using a population genetics approach. We analyzed recombination landscapes in wild barley and domesticated landraces at high resolution. In wild barley, high recombination rates are found in more interstitial chromosome regions in contrast to distal chromosome regions in domesticated barley. Among subpopulations of wild barley, natural variation in effective recombination rate is correlated with temperature, isothermality, and solar radiation in a nonlinear manner. A positive linear correlation was found between effective recombination rate and annual precipitation. We discuss our findings with respect to how the environment might shape effective recombination rates in natural populations. Higher recombination rates in wild barley populations subjected to specific environmental conditions could be a means to maintain fitness in a strictly inbreeding species.

scholarly journals Species and Recombination Effects on DNA Variability in the Tomato Genus

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1725-1735 ◽  
Author(s):  
Emmanuelle Baudry ◽  
Carole Kerdelhué ◽  
Hideki Innan ◽  
Wolfgang Stephan
Keyword(s):  
Mating System ◽  
Recombination Rate ◽  
Sequence Variation ◽  
Single Copy ◽  
Recombination Rates ◽  
Dna Sequence Variation ◽  
Incompatibility Alleles ◽  
Selection For ◽  
Weak Influence ◽  
Selfing Species

Abstract Population genetics theory predicts that strong selection for rare, beneficial mutations or against frequent, deleterious mutations reduces polymorphism at linked neutral (or weakly selected) sites. The reduction of genetic variation is expected to be more severe when recombination rates are lower. In outbreeding species, low recombination rates are usually confined to certain chromosomal regions, such as centromeres and telomeres. In contrast, in predominantly selfing species, the rarity of double heterozygotes leads to a reduced effective recombination rate in the whole genome. We investigated the effects of restricted recombination on DNA polymorphism in these two cases, analyzing five Lycopersicon species with contrasting mating systems: L. chilense, L. hirsutum, L. peruvianum, L. chmielewskii, and L. pimpinellifolium, of which only the first three species have self-incompatibility alleles. In each species, we determined DNA sequence variation of five single-copy genes located in chromosomal regions with either high or low recombination rate. We found that the mating system has a highly significant effect on the level of polymorphism, whereas recombination has only a weak influence. The effect of recombination on levels of polymorphism in Lycopersicon is much weaker than in other well-studied species, including Drosophila. To explain these observations, we discuss a number of hypotheses, invoking selection, recombination, and demographic factors associated with the mating system. We also provide evidence that L. peruvianum, showing a level of polymorphism (almost 3%) that is comparable to the level of divergence in the whole genus, is the ancestral species from which the other species of the genus Lycopersicon have originated relatively recently.

Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee

2019 ◽  
Vol 36 (10) ◽  
pp. 2277-2291 ◽  
Author(s):  
Julia C Jones ◽  
Andreas Wallberg ◽  
Matthew J Christmas ◽  
Karen M Kapheim ◽  
Matthew T Webster
Keyword(s):  
Recombination Rate ◽  
Rate Variation ◽  
Sequencing Data ◽  
Recombination Rates ◽  
Evolution Of Sociality ◽  
Leafcutter Bee ◽  
Selection For ◽  
Worker Caste ◽  
Recombination Rate Variation ◽  
Genomic Recombination

Abstract Social insect genomes exhibit the highest rates of crossing over observed in plants and animals. The evolutionary causes of these extreme rates are unknown. Insight can be gained by comparing recombination rate variation across the genomes of related social and solitary insects. Here, we compare the genomic recombination landscape of the highly social honey bee, Apis mellifera, with the solitary alfalfa leafcutter bee, Megachile rotundata, by analyzing patterns of linkage disequilibrium in population-scale genome sequencing data. We infer that average recombination rates are extremely elevated in A. mellifera compared with M. rotundata. However, our results indicate that similar factors control the distribution of crossovers in the genomes of both species. Recombination rate is significantly reduced in coding regions in both species, with genes inferred to be germline methylated having particularly low rates. Genes with worker-biased patterns of expression in A. mellifera and their orthologs in M. rotundata have higher than average recombination rates in both species, suggesting that selection for higher diversity in genes involved in worker caste functions in social taxa is not the explanation for these elevated rates. Furthermore, we find no evidence that recombination has modulated the efficacy of selection among genes during bee evolution, which does not support the hypothesis that high recombination rates facilitated positive selection for new functions in social insects. Our results indicate that the evolution of sociality in insects likely entailed selection on modifiers that increased recombination rates genome wide, but that the genomic recombination landscape is determined by the same factors.

scholarly journals GENETIC MODIFICATION OF RECOMBINATION RATE IN TRIBOLIUM CASTANEUM

Genetics ◽  
1975 ◽  
Vol 81 (3) ◽  
pp. 537-552
Author(s):  
Andrew A Dewees
Keyword(s):  
Tribolium Castaneum ◽  
Recombination Rate ◽  
Similar Response ◽  
Response Patterns ◽  
Recombination Rates ◽  
Polygenic Control ◽  
New Gene ◽  
In Trans ◽  
Selection For ◽  
In Cis

ABSTRACT Asymmetrical responses were obtained in a replicated study of 15 generations of two-way selection for recombination rate between the ruby (rb) and jet (j) loci in Tribolium castaneum. Recombination rates in the two replicate high lines increased from an average of 0.22 in the base populations to an average of 0.42 at generation 15. Recombination rate pooled over the 15 generations of selection in each low line was significantly less than the control but there was no clear downward trend in response to selection for decreased recombination rate. The realized heritabilities were 0.16 ± 0.03 and 0.17 ± 0.02 in the two high lines, and were not significantly different from zero in the two low lines. Selection was based on crossing over in cis females only; however, rates measured in cis males after 12 generations showed the same response patterns as female rates. Similar response patterns were also determined for recombination measured in trans males and females at generation 18 following three generations of relaxed selection. The distribution of recombination rates measured in backcross beetles [(H × L) × H and (H × L) × L] at generation 12 indicated polygenic control with those genes decreasing recombination rate being dominant. Detailed analysis of recombination rates in F1's produced by interline crosses at generation 15 confirmed the directional dominance findings. Under a polygenic model of recombination modifiers in which low recombination is dominant to high, average recombination rates will increase as inbreeding progresses, thus providing a mechanism for the production of new gene combinations in small populations.

scholarly journals Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii

2020 ◽  
Vol 12 (4) ◽  
pp. 370-380 ◽  
Author(s):  
Ahmed R Hasan ◽  
Rob W Ness
Keyword(s):  
Linkage Disequilibrium ◽  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Effective Rate ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

scholarly journals EXPECTED LINKAGE DISEQUILIBRIUM FOR A NEUTRAL LOCUS LINKED TO A CHROMOSOMAL ARRANGEMENT

Genetics ◽  
1983 ◽  
Vol 103 (3) ◽  
pp. 545-555
Author(s):  
Curtis Strobeck
Keyword(s):  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Natural Populations ◽  
Transient Behavior ◽  
Random Drift ◽  
Strong Linkage ◽  
Linkage Disequilibria ◽  
Chromosomal Arrangement ◽  
Neutral Locus ◽  
Selection For

ABSTRACT The expected value of the squared linkage disequilibrium is derived for a neutral locus associated with a chromosomal arrangement that is maintained in the population by strong balancing selection. For a given value of recombination, the expected squared linkage disequilibrium is shown to decrease as the intensity of selection maintaining the arrangement increases. The transient behavior of the expected square linkage disequilibrium is also derived. This theory applies to loci that are closely linked to inversions in Drosophila species and to loci closely linked to the differential segments of the translocation complexes in ring-forming species of Oenothera. In both cases the strong linkage disequilibria that have been observed in natural populations can be explained by random drift.

Frontiers in Metapopulation Biology: The Legacy of Ilkka Hanski

2018 ◽  
Vol 49 (1) ◽  
pp. 231-252 ◽  
Author(s):  
Otso Ovaskainen ◽  
Marjo Saastamoinen
Keyword(s):  
Evolutionary Dynamics ◽  
Molecular Level ◽  
Extinction Risk ◽  
Natural Populations ◽  
Special Focus ◽  
Trait Variation ◽  
Ecological Aspects ◽  
Dispersal Traits ◽  
Selection For ◽  
Natural Laboratory

This review of metapopulation biology has a special focus on Professor Ilkka Hanski's (1953–2016) research. Hanski made seminal contributions to both empirical and theoretical metapopulation biology throughout his scientific career. Hanski's early research focused on ecological aspects of metapopulation biology, in particular how the spatial structure of a landscape influences extinction thresholds and how habitat loss and fragmentation can result in extinction debt. Hanski then used the Glanville fritillary system as a natural laboratory within which he studied genetic and evolutionary processes, such as the influence of inbreeding on extinction risk and variation in selection for dispersal traits generated by landscape variation. During the last years of his career, Hanski's work was in the forefront of the rapidly developing field of eco-evolutionary dynamics. Hanski was a pioneer in showing how molecular-level underpinnings of trait variation can explain why evolutionary change can occur rapidly in natural populations and how these changes can subsequently influence ecological dynamics.

scholarly journals Selective Sweeps in the Presence of Interference Among Partially Linked Loci

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 389-398 ◽  
Author(s):  
Yuseob Kim ◽  
Wolfgang Stephan
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Substantial Reduction ◽  
Natural Populations ◽  
High Rate ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Analytical Approximations ◽  
Fixation Probabilities ◽  
Beneficial Allele

Abstract Recurrent directional selection on a partially recombining chromosome may cause a substantial reduction of standing genetic variation in natural populations. Previous studies of this effect, commonly called selective sweeps, assumed that at most one beneficial allele is on the way to fixation at a given time. However, for a high rate of selected substitutions and a low recombination rate, this assumption can easily be violated. We investigated this problem using full-forward simulations and analytical approximations. We found that interference between linked beneficial alleles causes a reduction of their fixation probabilities. The hitchhiking effect on linked neutral variation for a given substitution also slightly decreases due to interference. As a result, the strength of recurrent selective sweeps is weakened. However, this effect is significant only in chromosomal regions of relatively low recombination rates where the level of variation is greatly reduced. Therefore, previous results on recurrent selective sweeps although derived for a restricted parameter range are still valid. Analytical approximations are obtained for the case of complete linkage for which interference between competing beneficial alleles is maximal.

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.

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