Recombination is a central biological process with implications for many areas in the life sciences. Yet we are only beginning to appreciate variation in the recombination rate along the genome and among individuals, populations and species. Spurred by technological advances, we are now able to bring variation in this key biological parameter to centre stage. Here, we review the conceptual implications of recombination rate variation and guide the reader through the assumptions, strengths and weaknesses of genomic inference methods, including population-based, pedigree-based and gamete-based approaches. Appreciation of the differences and commonalities of these approaches is a prerequisite to formulate a unifying and comparative framework for understanding the molecular and evolutionary mechanisms shaping, and being shaped by, recombination.
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The authors thank the Dobzhansky Journal Club in the Division of Evolutionary Biology, LMU, Munich, for useful discussion and comments on this review. Funding was provided by the European Research Council (ERCStG-336536 FuncSpecGen) and LMU Munich.
The authors declare no competing interests.
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- Genetic drift
A stochastic change in allele frequency from one generation to the next due to random sampling in finite populations.
- Gene flow
The movement of chromosomes across genetically structured populations.
- Genetic diversity
The total number of non-identical genetic elements in a population.
A set of co-inherited, physically linked genes often contributing to complex phenotypes.
A variation in recombination rates and, accordingly, genetic map length between sexes.
- Heterogametic sex
The sex in which the sex chromosomes differ.
- Structural variants
Any variations in the structure of a chromosome, including insertions, deletions, duplications, inversions or translocations.
- Hill–Robertson interference
The reduction in the efficacy of selection when acting on alleles in physically linked genes.
- Double-strand breaks
(DSBs). Lesions in the DNA double helix induced by a wide range of DNA-damaging agents. Programmed enzymatic induction during meiosis triggers homologous recombination.
- Crossover interference
The non-random occurrence of multiple crossover events relative to each other during meiosis.
- Gene conversion
The process whereby a fragment of DNA sequence is replaced by its homologue.
- Crossover event
When a double-strand break (DSB) during meiosis results in exchange of homologous chromosomal regions. By contrast, a non-crossover event is when a DSB is repaired without homologous exchange of DNA material.
- Recombination landscape
The variation in the local recombination rate plotted against the position along the chromosome.
- Genetic mapping
A marker-based method to identify the order and genetic distance between loci.
- Linkage disequilibrium
The non-random association of alleles at different loci.
A mathematical model describing the stochastic process of random reproduction backwards in time until all gene copies share a common ancestor. It predicts the distribution of gene genealogies of freely recombining segments of the genome.
- Effective population size
(Ne). An abstract population genetic parameter describing the number of individuals in an idealized population in which the effect of genetic drift is representative of that in the real population.
- Ancestral alleles
The allelic state of a locus that originated in the ancestral population. It is generally contrasted to the derived allele that arose by mutation in the evolutionary lineage or population under consideration.
- Infinite sites model
A model in molecular evolution that assumes that there are an infinite number of sites where mutations can occur and that new mutations must occur in a novel site.
- Four-gamete test
A test to detect historic recombination events by locating allelic combinations that could only have arisen as a result of recombination.
- Ancestral recombination graph
A generalization of the coalescence tracing gene genealogies, integrating the recombination history of a population of samples.
The haplotype is inferred from genotype data.
- Genotype likelihoods
The probabilities of genotypes, accounting for potential errors in the sequencing data that occur during sequencing and processing.
- Linkage groups
Genetic markers that are inherited together as a unit, usually representing a chromosome.
- Genetic map
Also known as linkage map. A representation of the order of genetic markers and inter-marker distance derived from the frequency of meiotic recombination.
- Logarithm of the odds scores
(LOD scores). A statistical estimate of the likelihood that two entities are co-inherited, referring to the association of phenotypic and allelic variation or to the association between genotypes.
- Physical map
The physical order of genetic markers along a chromosome.
- Mapping functions
Algorithms to infer the additive genetic distance between two loci from measurable recombination fractions between them.
- Haplotype blocks
Discrete stretches along the chromosome for which the phase can be unequivocally determined.
- Demographic history
The history of a population with regard to change in size, structure and gene flow.
- Whole-genome amplification
Genome-wide amplification of DNA, usually performed from DNA extracted from only one or a few cells.
- Long-read sequencing
A class of DNA sequencing technologies and platforms that currently allows for sequencing of long (>20 kb) stretches of DNA.
- Linked-read sequencing
A DNA library preparation method that incorporates unique barcodes to reads derived from a longer DNA molecule, such that the reads can be bioinformatically reassociated to the original DNA fragment.
- Linked selection
A locus under selection causes corresponding changes in allele frequencies of other nearby loci owing to a lack of recombination between these loci.
- Association mapping
A statistical approach to infer the association between phenotypes and genotypes.
- Nucleotide diversity
A measure of genetic variation within a population or species, reflecting the average number of nucleotide differences between two chromosomes in a population.
- Marker-assisted selection
Artificial selection whereby the founders for the next generation are selected on the basis of the genotype of a particular locus or set of loci underlying the phenotypic trait of interest.
- Quantitative trait locus (QTL) mapping
A specific type of association mapping that focuses on a quantitative trait that is assumed to be encoded by multiple genes.
- Meiotic drive
A mechanism acting during meiosis or gametogenesis that distorts the equal transmission of alleles.
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Peñalba, J.V., Wolf, J.B.W. From molecules to populations: appreciating and estimating recombination rate variation. Nat Rev Genet 21, 476–492 (2020). https://doi.org/10.1038/s41576-020-0240-1
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