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At least 19 recordsLinked to original sources
PubMed2005

Positive correlation between evolutionary rate and recombination rate in Drosophila genes with male-biased expression.

Previous studies have shown that genes that are expressed predominantly or exclusively in males tend to evolve rapidly in comparison to other genes. In most cases, however, it is unknown whether this rapid evolution is the result of increased positive (or sexual) selection on male-expressed traits or if it is due to a relaxation of selective constraints. To distinguish between these two possibilities, we analyzed the relationship between the nonsynonymous substitution rate (dN) and local recombination rate for 343 Drosophila genes that were classified as male, female, or nonsex biased in their expression. For the male-biased genes, a positive correlation between dN and recombination rate was observed. This can be explained by an increased rate of adaptive evolution in regions of higher recombination due to a reduction of Hill-Robertson interference. In contrast, the correlation between dN and recombination rate was negative for both female- and nonsex-biased genes, suggesting that these genes are primarily subject to purifying selection, which is expected to be less effective in regions of reduced recombination.

Animals↗
PubMed2003

On the determination of recombination rates in intermated recombinant inbred populations.

The recurrent intermating of F(2) individuals for some number of generations followed by several generations of inbreeding produces an intermated recombinant inbred (IRI) population. Such populations are currently being developed in the plant-breeding community because linkage associations present in an F(2) population are broken down and a population of fixed inbred lines is also created. The increased levels of recombination enable higher-resolution mapping in IRI populations relative to F(2) populations. Herein we derive relationships, under several limiting assumptions, for determining the expected recombination fraction in IRI populations from the crossover rate per meiosis. These relationships are applicable to situations where the inbreeding component of IRI population development is by either self-fertilization or full-sib mating. Additionally, we show that the derived equations can be solved for the crossover rate per meiosis if the recombination fraction is known for the IRI population. Thus, the observed recombination fraction in any IRI population can be expressed on an F(2) basis. The implications of this work on the expansion of genetic maps in IRI populations and limits for detecting linkage between markers are also considered.

Chromosome Mapping↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed1994

How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained?

Different regions of the Drosophila genome have very different rates of recombination. For example, near centromeres and near the tips of chromosomes, the rates of recombination are much lower than in other regions. Several surveys of polymorphisms in Drosophila have now documented that levels of DNA polymorphism are positively correlated with rates of recombination; i.e., regions with low rates of recombination tend to have low levels of DNA polymorphism within populations of Drosophila. Three hypotheses are reviewed that might account for these observations. The first hypothesis is that regions of low recombination have low neutral mutation rates. Under this hypothesis between-species divergences should also be low in regions of low recombination. In fact, regions of low recombination have diverged at the same rate as other regions of the genome. On this basis, this strictly neutral hypothesis is rejected. The second hypothesis is that the process of fixation of favorable mutations leads to the observed correlation between polymorphism and recombination. This occurs via genetic hitchhiking, in which linked regions of the genome are swept along with the selectively favored mutant as it increases in frequency and eventually fixes in the population. This hitchhiking model with fixation of favorable mutations is compatible with major features of the data. By assuming this model is correct, one can estimate the rate of fixation of favorable mutations. The third hypothesis is that selection against continually arising deleterious mutations results in reduced levels of polymorphism at linked loci. Analysis of this background selection model shows that it can produce some reduction in levels of polymorphism but cannot explain some extreme cases that have been observed. Thus, it appears that hitchhiking of favorable mutations and background selection against deleterious mutations must be considered together to correctly account for the patterns of polymorphism that are observed in Drosophila.

Animals↗
PubMed1998

Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima).

The relation between the level of genetic variation and the rate of recombination per physical unit was investigated in sea beet (Beta vulgaris subsp. maritima). The rate of recombination per physical unit was estimated indirectly through marker density in an RFLP linkage map of sugar beet. From this map, we also selected RFLP markers covering two of the nine chromosomes in Beta. The markers were used to estimate the level of genetic variation in three populations of sea beet, two from Italy and one from England. Two estimates of genetic variation were employed, one based on the number of alleles in the sample and the other on heterozygosity. A statistically significant positive correlation was found between recombination rate and genetic variation. Several theoretical explanations for this are discussed, background selection being one. A correlation similar to this has been observed previously in Drosophila, one that was higher than what we obtained for Beta. This is consistent with various biological differences between the two species.

Chenopodiaceae↗
PubMed2001

Consequences of recombination rate variation on quantitative trait locus mapping studies. Simulations based on the Drosophila melanogaster genome.

We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the "small X-effect" that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

Animals↗
PubMed1995

Recombination rates across the HLA complex: use of microsatellites as a rapid screen for recombinant chromosomes.

Meiotic recombination does not appear to occur randomly across chromosomes, but rather seems to be restricted to specific regions. A striking example of this phenomenon is illustrated by the HLA class II region. No recombination within the 100 kb encompassing the DRB1-DQA1-DQB1 loci has been reported, whereas the random association of TAP1 with TAP2 alleles suggests the presence of a hotspot for recombination within the 15 kb separating the closest variant sites of these two loci. Recombination rates between loci may provide clues to the functional properties of haplotypes. Absence of recombination may suggest the necessity to keep alleles of certain genes in phase and, alternatively, high recombination rates may suggest selective pressure to diversify haplotypes within the population. To address this issue, recombination rates across the HLA complex were determined using the 59 Centre d'Etude Polymorphisme Humain (CEPH) pedigrees. The allele frequencies of four microsatellite markers which map at sites ranging from the telomeric to centromeric ends of the complex were determined and the markers were used as a rapid means for identification of recombinant chromosomes. Typing these as well as other polymorphic loci within the HLA class I, II and III regions allowed assignment of the segments where recombination occurred. Recombination rates within the class II region (defined here as DRB1 to DPB1) and class III region (defined here as HLA-B to DRB1) regions were 0.74% and 0.94%, respectively, both of which are within an expected range given the standard of 1% recombination rate per megabase of DNA per meiosis.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed2002

Sex-specific recombination rates in zebrafish (Danio rerio).

In many organisms, the rate of genetic recombination is not uniform along the length of chromosomes or between sexes. To compare the relative recombination rates during meiosis in male and female zebrafish, we constructed a genetic map based on male meiosis. We developed a meiotic mapping panel of 94 androgenetic haploid embryos that were scored for genetic polymorphisms. The resulting male map was compared to female and sex-average maps. We found that the recombination rate in male meiosis is dramatically suppressed relative to that of female meiosis, especially near the centromere. These findings have practical applications for experimental design. The use of exclusively female meiosis in a positional cloning project maximizes the ratio of genetic map distance to physical distance. Alternatively, the use of exclusively male meiosis to localize a mutation initially to a linkage group or to maintain relationships of linked alleles minimizes recombination, thereby facilitating some types of analysis.

Animals↗
PubMed1998

Retroviral recombination rates do not increase linearly with marker distance and are limited by the size of the recombining subpopulation.

Recombination occurs at high frequencies in all examined retroviruses. The previously determined homologous recombination rate in one retroviral replication cycle is 4% for markers 1.0 kb apart in spleen necrosis virus (SNV). This has often been used to suggest that approximately 30 to 40% of the replication-competent viruses with 7- to 10-kb genomes undergo recombination. These estimates were based on the untested assumption that a linear relationship exists between recombination rates and marker distances. To delineate this relationship, we constructed three sets of murine leukemia virus (MLV)-based vectors containing the neomycin phosphotransferase gene (neo) and the hygromycin phosphotransferase B gene (hygro). Each set contained one vector with a functional neo and an inactivated hygro and one vector with a functional hygro and an inactivated neo. The two inactivating mutations in the three sets of vectors were separated by 1.0, 1.9, and 7.1 kb. Recombination rates after one round of replication were 4.7, 7.4, and 8.2% with markers 1.0, 1.9, and 7.1 kb apart, respectively. Thus, the rate of homologous recombination with 1.0 kb of marker distance is similar in MLV and SNV. The recombination rate increases when the marker distance increases from 1.0 to 1.9 kb; however, the recombination rates with marker distances of 1.9 and 7.1 kb are not significantly different. These data refute the previous assumption that recombination is proportional to marker distance and define the maximum recombining population in retroviruses.

Genome, Viral↗
PubMed2007

A haplotype-linkage analysis method for estimating recombination rates using dense SNP trio data.

Meiotic recombination is an important evolution force in shaping human genomes and creating human diversity. Recent explorations suggest that meiotic recombination events tend to happen in certain regions of the genome, leading to the hypothesis of recombination hot spots. To identify such hot spots, we describe an empirical method for estimating the recombination rate, which reflects both historical and current meiotic events, using unphased genotypes from nuclear families, in particular, parents-child trios. The key idea is that use of the haplotypic polymorphisms with multiple adjacent SNPs will increase the number of informative meioses and hence would improve the power of linkage analysis. Since haplotypes of individuals are not directly observed, e.g., in HapMap data, we infer the haplotypes simultaneously while estimating recombination rate. We refer this described method as haplotype-linkage (HALIN) method. Our simulation results show that HALIN gives unbiased estimates of recombination rate. We apply HALIN to analyze the genotype data of chromosome 20 from HapMap data and compare the results to the results using two existing methods, Bayesian coalescent method described by McVean et al. [2004] science 304:581-584 and empirical method by Clarke and Cardon ([2005] Genetics). Results suggest that HALIN identified 75 hot spots on chromosome 20, and 85% of them are also identified by the method by McVean et al. ([2004] science 304:581-584), in addition to a few new hot spots. In comparison with Clarke and Cardon's result, estimated recombination rates (RRs) under these 75 hot spots are significantly greater than those outside of hot spots, which support the general consistency in discovering recombination hot spots between two methods.

Child↗
PubMed2004

Comparative recombination rates in the rat, mouse, and human genomes.

Levels of recombination vary among species, among chromosomes within species, and among regions within chromosomes in mammals. This heterogeneity may affect levels of diversity, efficiency of selection, and genome composition, as well as have practical consequences for the genetic mapping of traits. We compared the genetic maps to the genome sequence assemblies of rat, mouse, and human to estimate local recombination rates across these genomes. Humans have greater overall levels of recombination, as well as greater variance. In rat and mouse, the size of the chromosome and proximity to telomere have less effect on local recombination rate than in human. At the chromosome level, rat and mouse X chromosomes have the lowest recombination rates, whereas human chromosome X does not show the same pattern. In all species, local recombination rate is significantly correlated with several sequence variables, including GC%, CpG density, repetitive elements, and the neutral mutation rate, with some pronounced differences between species. Recombination rate in one species is not strongly correlated with the rate in another, when comparing homologous syntenic blocks of the genome. This comparative approach provides additional insight into the causes and consequences of genomic heterogeneity in recombination.

Animals↗
PubMed1999

Effect of excited states on the ionization balance in plasmas via the enhancement of ionization and recombination rate coefficients.

The effect of excited states on the effective ionization and recombination rate coefficients for the ground states was investigated analytically and by computer simulation. The calculation was done for carbon ions. The results using carbon ions show (1) the contribution from excited states to ionization rate coefficients becomes significant even at an electron density as low as 10(15) cm(-3) and saturated from around N(e) approximately 10(20) cm(-3); (2) the lower the electron temperature, the larger the contribution; (3) in the case of recombination rate coefficients, there is still a non-negligible contribution from excited states even at a very low electron density of 10(10) cm(-3), where the contribution has been considered negligible; (4) this contribution to the recombination rate coefficients increases linearly with the electron density; (5) the enhancements of the ionization and recombination rate coefficients increase as N(e) increases and are saturated to the same value at higher densities; (6) there exists a region of temperature and density where the recombination is effectively hindered. Some of the behaviors of the ionization and recombination rate coefficients in the extreme regions of a very low and high electron density were analytically understood. The calculated ionization and recombination rate coefficients for carbon ions, including the effect of excited states, were used in a one-dimensional magnetohydrodynamic code for the calculation of the ionization balance of carbon ions in a Z-pinch carbon plasma and the gain of C VI H(alpha) (18.2 nm) line. The significant change in the evolution of the ionization balance was observed. The rapid depletion of C VII ions by the increased recombination rate reduces the gain significantly by a factor of approximately 3 compared to the case where the contribution from excited states was neglected. Such calculations can be done for other ions. The characteristics found for carbon ions are generic and applicable to other ions.

Journal Article↗
PubMed2003

The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms.

Genes detected by wheat expressed sequence tags (ESTs) were mapped into chromosome bins delineated by breakpoints of 159 overlapping deletions. These data were used to assess the organizational and evolutionary aspects of wheat genomes. Relative gene density and recombination rate increased with the relative distance of a bin from the centromere. Single-gene loci present once in the wheat genomes were found predominantly in the proximal, low-recombination regions, while multigene loci tended to be more frequent in distal, high-recombination regions. One-quarter of all gene motifs within wheat genomes were represented by two or more duplicated loci (paralogous sets). For 40 such sets, ancestral loci and loci derived from them by duplication were identified. Loci derived by duplication were most frequently located in distal, high-recombination chromosome regions whereas ancestral loci were most frequently located proximal to them. It is suggested that recombination has played a central role in the evolution of wheat genome structure and that gradients of recombination rates along chromosome arms promote more rapid rates of genome evolution in distal, high-recombination regions than in proximal, low-recombination regions.

Chromosome Mapping↗
PubMed1975

Genetic modification of recombination rate in Tribolium castaneum.

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 X L) X H and (H X L) X 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.

Animals↗
PubMed2003

Genetic variation versus recombination rate in a structured population of mice.

The correlation between genetic variation and recombination rate was investigated in a structured mouse population. Nucleotide sequence data from 19 autosomal DNA loci from eight inbred strains of mouse (Mus musculus) sampled from three major subspecies were analyzed. The recombination rate was estimated from the comparison of genetic and physical map distances between markers flanking a 10-cM region of each locus. The strains were categorized into four groups (subpopulations) based on geography. By partitioning the genetic diversity into within-group and among-group variation, we detected a positive correlation between the recombination rate and nucleotide diversity within groups. The level of nucleotide differentiation among groups (G(ST)) showed a negative correlation with the rate of recombination. There was no significant correlation between recombination rate and nucleotide diversity when data from different subpopulations were pooled. No correlation was detected between recombination rate and nucleotide divergence of M. musculus and M. spicilegus. These patterns deviate from the strict neutral expectation under the constant nucleotide substitution rate, and they are likely to have been formed either by a hitchhiking effect of positively selected mutants or by background selection of deleterious mutants occurring in a subdivided population. Our series of comparisons show that because a real population always has some structure, incorporation of its information is important in detecting non-neutral evolution.

Animals↗
PubMed1999

Impact of demographic distribution and population growth rate on haplotypic diversity linked to a disease gene and their consequences for the estimation of recombination rate: example of a French Canadian population.

A disease gene introduced into a rapidly growing population by a single individual remains in strong linkage disequilibrium with the surrounding molecular markers. Mapping strategies taking advantage of this phenomenon allow increased mapping resolution as compared to pedigree analysis. Demographic models underlying these strategies usually assume the population exponential growth approximated by Poisson distribution of the number of children per individual. Knowing the real demographic distribution in the studied French-Canadian population, we analyzed the validity of the Poisson approximation. We adapted the existing model of the Poisson branching process to the case of a rapidly growing population and to non-Poisson distributions. In consequence, we were able to apply maximum-likelihood methods to estimate the recombination rate under various demographic scenarios. Our analysis shows that the growth rate has a higher impact on the estimation of recombination rate than the shape of the demographic distribution. The choice of the demographic model (Poisson vs. non-Poisson) has little effect on the estimation of the recombination rate but affects the expected distribution of haplotype frequencies. This distribution, however, depends much more on the population growth rate. Finally, we also demonstrate the usefulness of the Luria-Delbrück method, which gives a correct estimation of the recombination rate in a growing population, provided the sampling error is taken into account in the confidence intervals.

Confidence Intervals↗
PubMed1998

DNA variability and recombination rates at X-linked loci in humans.

We sequenced 11,365 bp from introns of seven X-linked genes in 10 humans, one chimpanzee, and one orangutan to (i) provide an average estimate of nucleotide diversity (pi) in humans, (ii) investigate whether there is variation in pi among loci, (iii) compare ratios of polymorphism to divergence among loci, and (iv) provide a preliminary test of the hypothesis that heterozygosity is positively correlated with the local rate of recombination. The average value for pi was low 0.063%, SE = 0.036%, about one order of magnitude smaller than for Drosophila melanogaster, the species for which the best data are available. Among loci, pi varied by over one order of magnitude. Statistical tests of neutrality based on ratios of polymorphism to divergence or based on the frequency spectrum of variation within humans failed to reject a neutral, equilibrium model. However, there was a positive correlation between heterozygosity and rate of recombination, suggesting that the joint effects of selection and linkage are important in shaping patterns of nucleotide variation in humans.

Animals↗