scholarly journals Fine-scale crossover rate variation on the C. elegans X chromosome

2016 ◽  
Author(s):  
Max R. Bernstein ◽  
Matthew V. Rockman
Keyword(s):  
X Chromosome ◽  
Nucleosome Occupancy ◽  
Gc Content ◽  
Genotypic Diversity ◽  
Rate Variation ◽  
Open Chromatin ◽  
Fine Scale ◽  
Recombination Rates ◽  
Crossover Rate ◽  
Scale Variation

AbstractMeiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa and the distribution of crossovers can differ significantly among populations and between sexes. Crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination hotspots. However, several species appear to lack hotspots despite significant crossover heterogeneity. The nematode Caenorhabditis elegans was previously found to have the least fine-scale variation in crossover distribution among organisms studied to date. It is unclear whether this pattern extends to the X chromosome given its unique compaction through the pachytene stage of meiotic prophase in hermaphrodites. We generated 798 recombinant nested near-isogenic lines (NILs) with crossovers in a 1.41 Mb region on the left arm of the X chromosome to determine if its recombination landscape is similar to that of the autosomes. We find that the fine-scale variation in crossover rate is lower than that of other model species and is inconsistent with hotspots. The relationship of genomic features to crossover rate is dependent on scale, with GC content, histone modifications, and nucleosome occupancy being negatively associated with crossovers. We also find that the abundances of 4-6 base pair DNA motifs significantly explain crossover density. These results are consistent with recombination occurring at unevenly distributed sites of open chromatin.

scholarly journals Evidence for substantial fine-scale variation in recombination rates across the human genome

2004 ◽  
Vol 36 (7) ◽  
pp. 700-706 ◽  
Author(s):  
Dana C Crawford ◽  
Tushar Bhangale ◽  
Na Li ◽  
Garrett Hellenthal ◽  
Mark J Rieder ◽  
...  
Keyword(s):  
Human Genome ◽  
Fine Scale ◽  
Recombination Rates ◽  
Scale Variation

scholarly journals Fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish

2018 ◽  
Author(s):  
Alice F. Shanfelter ◽  
Sophie L. Archambeault ◽  
Michael A. White
Keyword(s):  
Gasterosteus Aculeatus ◽  
Demographic History ◽  
Strong Association ◽  
Threespine Stickleback ◽  
Open Chromatin ◽  
Fine Scale ◽  
Recombination Rates ◽  
Transcription Start Sites ◽  
Marine Population ◽  
Recombination Hotspots

AbstractMeiotic recombination is a highly conserved process that has profound effects on genome evolution. Recombination rates can vary drastically at a fine-scale across genomes and often localize to small recombination “hotspots” with highly elevated rates surrounded by regions with little recombination. Hotspot targeting to specific genomic locations is variable across species. In some mammals, hotspots have divergent landscapes between closely related species which is directed by the binding of the rapidly evolving protein, PRDM9. In many species outside of mammals, hotspots are generally conserved and tend to localize to regions with open chromatin such as transcription start sites. It remains unclear if the location of recombination hotspots diverge in taxa outside of mammals. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using an LD-based approach, we found recombination rates varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had divergent landscapes between stickleback populations, where only ~15% were shared, though part of this divergence could be due to demographic history. Additionally, we did not detect a strong association of PRDM9 with recombination hotspots in threespine stickleback fish. Our results suggest fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish and argue for additional molecular characterization to verify the extent of the divergence.

scholarly journals Evolutionary implications of recombination differences across diverging populations of Anopheles

2021 ◽  
Author(s):  
Joel T. Nelson ◽  
Omar E. Cornejo ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Rate Variation ◽  
Anopheles Coluzzii ◽  
Fine Scale ◽  
Recombination Rates ◽  
Population Genetic Differentiation ◽  
Recombination Hotspots

AbstractRecombination is one of the main evolutionary mechanisms responsible for changing the genomic architecture of populations; and in essence, it is the main mechanism by which novel combinations of alleles, haplotypes, are formed. A clear picture that has emerged across study systems is that recombination is highly variable, even among closely related species. However, it is only until very recently that we have started to understand how recombination variation between populations of the same species impact genetic diversity and divergence. Here, we used whole-genome sequence data to build fine-scale recombination maps for nine populations within two species of Anopheles, Anopheles gambiae and Anopheles coluzzii. The genome-wide recombination averages were on the same order of magnitude for all populations except one. Yet, we identified significant differences in fine-scale recombination rates among all population comparisons. We report that effective population sizes, and presence of a chromosomal inversion has major contribution to recombination rate variation along the genome and across populations. We identified over 400 highly variable recombination hotspots across all populations, where only 9.6% are shared between two or more populations. Additionally, our results are consistent with recombination hotspots contributing to both genetic diversity and absolute divergence (dxy) between populations and species of Anopheles. However, we also show that recombination has a small impact on population genetic differentiation as estimated with FST. The minimal impact that recombination has on genetic differentiation across populations represents the first empirical evidence against recent theoretical work suggesting that variation in recombination along the genome can mask or impair our ability to detect signatures of selection. Our findings add new understanding to how recombination rates vary within species, and how this major evolutionary mechanism can maintain and contribute to genetic variation and divergence within a prominent malaria vector.

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