scholarly journals Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

2017 ◽  
Vol 26 (16) ◽  
pp. 4158-4172 ◽  
Author(s):  
Takeshi Kawakami ◽  
Carina F. Mugal ◽  
Alexander Suh ◽  
Alexander Nater ◽  
Reto Burri ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Rate Variation ◽  
Whole Genome ◽  
Fine Scale ◽  
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 Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)

2019 ◽  
Author(s):  
Rami-Petteri Apuli ◽  
Carolina Bernhardsson ◽  
Bastian Schiffthaler ◽  
Kathryn M. Robinson ◽  
Stefan Jansson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Map ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Populus Tremula ◽  
Rate Variation ◽  
Recombination Rates ◽  
Genomic Features ◽  
European Aspen ◽  
Recombination Rate Variation

AbstractThe rate of meiotic recombination is one of the central factors determining levels of linkage disequilibrium and the efficiency of natural selection, and many organisms show a positive correlation between local rates of recombination and levels of nucleotide diversity indicating that linked selection is an important factor determining genome-wide levels of nucleotide diversity. Several methods for estimating recombination rates from segregating polymorphisms in natural populations have recently been developed. These methods have been extensively used in part because they are relatively simple to implement even in many non-model organisms, but also because they potentially offer higher resolution than traditional map-based methods. However, thorough comparisons of LD and map-based estimates of recombination are not readily available in plants. Here we present a new, high-resolution linkage map for Populus tremula and use this to estimate variation in recombination rates across the P. tremula genome. We compare these results to recombination rates estimated based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with 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 identify a number of genomic regions with very high recombination rates that the map-based method fail 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.

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 Exploration of fine-scale recombination rate variation in the domestic horse

2019 ◽  
Vol 29 (10) ◽  
pp. 1744-1752 ◽  
Author(s):  
Samantha K. Beeson ◽  
James R. Mickelson ◽  
Molly E. McCue
Keyword(s):  
Recombination Rate ◽  
Rate Variation ◽  
Domestic Horse ◽  
Fine Scale ◽  
Recombination Rate Variation
Sign in / Sign up

Export Citation Format

Share Document