Research Topic

Genomic Footprints of Meiotic Recombination

About this Research Topic

Recent development of single nucleotide polymorphism (SNP) genotyping arrays with up to hundreds of thousands of markers, together with the application of whole-genome re-sequencing to the estimation of fine-scale recombination rates have revolutionized the study of recombination rate variation. It has not only become evident that the extent of meiotic recombination differs between species, chromosomes, and sexes, but also extensive regional heterogeneity along chromosomes has been observed. Such variation in recombination rate causes variation in genomic footprints associated with meiotic recombination.

Genomic footprints of meiotic recombination are at least twofold. First, meiotic recombination has direct effects at the genomic location, where it takes place. Recombination can be mutagenic and is associated with a conversion mechanism. Recombination-initiating double-strand breaks (DSBs) are repaired through gene conversion, with the paradoxical consequence that the sequences inducing the DSBs are progressively lost through conversion (the so-called recombination hotspot paradox). GC-biased gene conversion (gBGC) is a another process that takes place during meiotic recombination, where the preferential repair of G:C base pairs over A:T base pairs at sites heterozygous for G:C/A:T alleles favors the fixation of G:C alleles at the population scale. The association between meiotic recombination and gBGC manifests in a positive correlation between the local GC content and the rate of recombination. Moreover, shifts in the site frequency spectrum (SFS) of G:C/A:T polymorphisms in high-recombining regions towards higher frequencies of G:C alleles mimic signatures of directional selection and/or demographic changes. As a consequence, studies of natural selection and demography that rely on the SFS might be biased if gBGC is not accounted for.

Second, meiotic recombination has indirect effects by reshuffling alleles on homologous chromosomes. Recombination can create novel and potentially advantageous combinations of alleles, which can increase in frequency in a population, at the same time as recombination can break up existing advantageous combinations. The effect of recombination on the pattern of selection is therefore context dependent. In addition, the efficacy of natural selection is decreased by genetic linkage of selected alleles, a process known as Hill-Robertson interference. Moreover, selective sweeps and background selection reduce genetic variation at neutral sites linked to targets of selection. The effects of these processes are positively related to the density of targets of selection and negatively to the rate of recombination. This creates a positive association between the rate of recombination and local effective population size, which in turn leads to locally accelerated lineage sorting of shared ancestral polymorphisms during the process of speciation in regions of low recombination. Therefore, meiotic recombination has been suggested to play an important role in shaping the differentiation landscape and recombination rate variation is a key parameter in the study of speciation and adaptation.

The aim of the Research Topic “Genomic footprints of meiotic recombination” is to promote the awareness of the diverse impacts of meiotic recombination on genome evolution. The Topic Editors are particularly interested in attracting contributions from a wide range of both empirical and theoretical researchers with innovative ways of incorporating recombination rate variation in genomic studies.


Keywords: recombination, GC-biased gene conversion, genome evolution, genetic linkage, linked selection


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Recent development of single nucleotide polymorphism (SNP) genotyping arrays with up to hundreds of thousands of markers, together with the application of whole-genome re-sequencing to the estimation of fine-scale recombination rates have revolutionized the study of recombination rate variation. It has not only become evident that the extent of meiotic recombination differs between species, chromosomes, and sexes, but also extensive regional heterogeneity along chromosomes has been observed. Such variation in recombination rate causes variation in genomic footprints associated with meiotic recombination.

Genomic footprints of meiotic recombination are at least twofold. First, meiotic recombination has direct effects at the genomic location, where it takes place. Recombination can be mutagenic and is associated with a conversion mechanism. Recombination-initiating double-strand breaks (DSBs) are repaired through gene conversion, with the paradoxical consequence that the sequences inducing the DSBs are progressively lost through conversion (the so-called recombination hotspot paradox). GC-biased gene conversion (gBGC) is a another process that takes place during meiotic recombination, where the preferential repair of G:C base pairs over A:T base pairs at sites heterozygous for G:C/A:T alleles favors the fixation of G:C alleles at the population scale. The association between meiotic recombination and gBGC manifests in a positive correlation between the local GC content and the rate of recombination. Moreover, shifts in the site frequency spectrum (SFS) of G:C/A:T polymorphisms in high-recombining regions towards higher frequencies of G:C alleles mimic signatures of directional selection and/or demographic changes. As a consequence, studies of natural selection and demography that rely on the SFS might be biased if gBGC is not accounted for.

Second, meiotic recombination has indirect effects by reshuffling alleles on homologous chromosomes. Recombination can create novel and potentially advantageous combinations of alleles, which can increase in frequency in a population, at the same time as recombination can break up existing advantageous combinations. The effect of recombination on the pattern of selection is therefore context dependent. In addition, the efficacy of natural selection is decreased by genetic linkage of selected alleles, a process known as Hill-Robertson interference. Moreover, selective sweeps and background selection reduce genetic variation at neutral sites linked to targets of selection. The effects of these processes are positively related to the density of targets of selection and negatively to the rate of recombination. This creates a positive association between the rate of recombination and local effective population size, which in turn leads to locally accelerated lineage sorting of shared ancestral polymorphisms during the process of speciation in regions of low recombination. Therefore, meiotic recombination has been suggested to play an important role in shaping the differentiation landscape and recombination rate variation is a key parameter in the study of speciation and adaptation.

The aim of the Research Topic “Genomic footprints of meiotic recombination” is to promote the awareness of the diverse impacts of meiotic recombination on genome evolution. The Topic Editors are particularly interested in attracting contributions from a wide range of both empirical and theoretical researchers with innovative ways of incorporating recombination rate variation in genomic studies.


Keywords: recombination, GC-biased gene conversion, genome evolution, genetic linkage, linked selection


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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31 January 2018 Abstract
31 May 2018 Manuscript

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Topic Editors

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Submission Deadlines

31 January 2018 Abstract
31 May 2018 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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