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 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.

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.

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 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 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.

Sign in / Sign up

Export Citation Format

Share Document