scholarly journals The recombination landscape in wild house mice inferred using population genomic data

2017 ◽  
Author(s):  
Tom R. Booker ◽  
Rob W. Ness ◽  
Peter D. Keightley
Keyword(s):  
House Mouse ◽  
Recombination Rate ◽  
Inbred Lines ◽  
House Mice ◽  
Rate Variation ◽  
Recombination Hotspots ◽  
Population Genomic ◽  
Wild House Mice ◽  
Recombination Rate Variation ◽  
Broad Scale

AbstractCharacterizing variation in the rate of recombination across the genome is important for understanding many evolutionary processes. The landscape of recombination has been studied previously in the house mouse, Mus musculus, and it is known that the different subspecies exhibit different suites of recombination hotspots. However, it is not established whether broad-scale variation in the rate of recombination is conserved between the subspecies. In this study, we construct a fine-scale recombination map for the Eastern house mouse subspecies, M. m. castaneus, using 10 individuals sampled from its ancestral range. After inferring phase, we use LDhelmet to construct recombination maps for each autosome. We find that the spatial distribution of recombination rate is strongly positively between our castaneus map and a map constructed using inbred lines of mice derived predominantly from M. m. domesticus. We also find that levels of genetic diversity in M. m. castaneus are positively correlated with the rate of recombination, consistent with pervasive natural selection acting in the genome. Our study suggests that recombination rate variation is conserved at broad scales between M. musculus subspecies.

scholarly journals The Time-Scale of Recombination Rate Evolution in Great Apes

2015 ◽  
Author(s):  
Laurie S Stevison ◽  
August E Woerner ◽  
Jeffrey M Kidd ◽  
Joanna L Kelley ◽  
Krishna R Veeramah ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Time Scale ◽  
Linear Regression Analysis ◽  
Great Apes ◽  
Rate Variation ◽  
Human Populations ◽  
Great Ape ◽  
Recombination Rates ◽  
Recombination Rate Variation ◽  
Broad Scale

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequencing data of 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez et al. 2013). Using species-specific PRDM9 sequences to predict potential binding sites, we identified an important role for PRDM9 in predicting recombination rate variation broadly across great apes. Our results are contrary to previous research that PRDM9 is not associated with recombination in western chimpanzees (Auton et al. 2012). Additionally, we show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time-scale of complete hotspot turnover. We quantified the variation in the biased distribution of recombination rates towards recombination hotspots across great apes. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10‐15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, based on multiple linear regression analysis, we found that various correlates of recombination rate persist throughout primates including repeats, diversity, divergence and local effective population size (Ne). Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.

scholarly journals Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 581-588
Author(s):  
Mohamed A F Noor ◽  
Aimee L Cunningham ◽  
John C Larkin
Keyword(s):  
Quantitative Trait Locus ◽  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Recombination Rate ◽  
Genome Project ◽  
Gene Density ◽  
Rate Variation ◽  
Trait Locus ◽  
Recombination Rate Variation

Abstract 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.

scholarly journals The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals a pronounced effect of linked selection

2018 ◽  
Author(s):  
Ahmed R. Hasan ◽  
Rob W. Ness
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Gc Content ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Entire Genome ◽  
Recombination Rate Variation ◽  
Linked Selection

AbstractRecombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations and facilitating selection. Here, we use genome-wide patterns of LD to infer fine-scale recombination rate variation in the genome of the model green alga Chlamydomonas reinhardtii and estimate rates of LD decay across the entire genome. We observe recombination rate variation of up to two orders of magnitude, finding evidence of recombination hotspots playing a role in the genome. Recombination rate is highest just upstream of genic regions, suggesting the preferential targeting of recombination breakpoints in promoter regions. Furthermore, we observe a positive correlation between GC content and recombination rate, suggesting a role for GC-biased gene conversion or selection on base composition within the GC-rich genome of C. reinhardtii. We also find a positive relationship between nucleotide diversity and recombination, consistent with widespread influence of linked selection in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations of this important model microbe, estimating a sexual cycle roughly every 770 generations. We argue that the relatively infrequent rate of sex and large effective population size creates an population genetic environment that increases the influence of linked selection on the genome.

scholarly journals A High-Resolution Genetic Map of Yellow Monkeyflower Identifies Chemical Defense QTLs and Recombination Rate Variation

2014 ◽  
Vol 4 (5) ◽  
pp. 813-821 ◽  
Author(s):  
Liza M. Holeski ◽  
Patrick Monnahan ◽  
Boryana Koseva ◽  
Nick McCool ◽  
Richard L. Lindroth ◽  
...  
Keyword(s):  
High Resolution ◽  
Chemical Defense ◽  
Genetic Map ◽  
Recombination Rate ◽  
Rate Variation ◽  
Recombination Rate Variation

scholarly journals Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)

2019 ◽  
Vol 10 (1) ◽  
pp. 299-309 ◽  
Author(s):  
Rami-Petteri Apuli ◽  
Carolina Bernhardsson ◽  
Bastian Schiffthaler ◽  
Kathryn M. Robinson ◽  
Stefan Jansson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Map ◽  
Recombination Rate ◽  
Gene Density ◽  
Populus Tremula ◽  
Rate Variation ◽  
Recombination Rates ◽  
Genomic Features ◽  
European Aspen ◽  
Recombination Rate Variation

The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

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’.

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