Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

Veller, Carl; Edelman, Nathaniel B.; Muralidhar, Pavitra; Nowak, Martin A.

doi:10.1534/genetics.120.303680

Cited by 11 publications

(12 citation statements)

References 40 publications

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“…Furthermore, crossing over is absent in males. In Veller et al (2020), we estimated a sex-averaged autosomal value of for D. melanogaster , substantially less than the theoretical maximum of 1 / 2. In contrast, humans have 22 autosomes, the independent assortment of which generates much genetic shuffling.…”

Section: Species Differences In the Genome-wide Rate Of Purgingmentioning

confidence: 82%

“…From Eq. (1) in Veller et al (2020), among those gametes produced by generation-1 hybrids, where is the average recombination rate across all pairs of loci in the genome (Veller et al 2019). When the recombination process differs between the sexes—as is usually the case (Lenormand and Dutheil 2005; Sardell and Kirkpatrick 2020)—the sex-averaged value of applies in Eq.…”

Section: Species Differences In the Genome-wide Rate Of Purgingmentioning

confidence: 99%

“…Each generation-t individual with introgressed ancestry descends from a single introgressing ancestor in generation 0, and, because selection has not appreciably affected the distribution of genetic ancestry among these generation-t individuals, the ancestry variance among them is equal to the variance of a random individual's genetic relatedness to one of its t-th degree great-grandparents. This quantity is calculated in Veller et al (2020):…”

Section: Long-term Purging Of Introgressed Dnamentioning

confidence: 99%

“…(2) An investigation of the rate of purging of introgressed DNA following admixture, based in part on results from part (1). Part (1) has since been published as Veller et al (2020). The present manuscript has been reconfigured to focus on part (2).…”

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Recombination and selection against introgressed DNA

Veller

Edelman

Muralidhar

et al. 2019

Preprint

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The genomic proportion that two relatives share identically by descent-their genetic relatednesscan vary depending on the patterns of recombination and segregation in their pedigree. Here, we calculate the precise connection between genome-wide genetic shuffling and variance in genetic relatedness. For the relationships of grandparent-grandoffspring and siblings, the variance in genetic relatedness is a simple decreasing function ofr, the average proportion of locus pairs that recombine in gametogenesis. These formulations explain several recent observations about variance in genetic relatedness. They further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling F2-based tests for various kinds of selection, such as Dobzhansky-Muller incompatibilities and hybrid vigor. Our calculations also allow us to characterize how recombination affects the rate at which selection eliminates deleterious introgressed DNA after hybridization-by modulating the variance of introgressed ancestry across individuals. Species with low aggregate recombination rates, like Drosophila, purge introgressed DNA more rapidly and more completely than species with high aggregate recombination rates, like humans. These conclusions also hold for different genomic regions. Within the genomes of several species, positive correlations have been observed between local recombination rate and introgressed ancestry. Our results imply that these correlations can be driven more by recombination's effect on the purging of deleterious introgressed alleles than its effect in unlinking neutral introgressed alleles from deleterious alleles. In general, our results demonstrate that the aggregate recombination process-as quantified byr and analogs-acts as a variable barrier to gene flow between species.

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Section: Species Differences In the Genome-wide Rate Of Purgingmentioning

confidence: 82%

Section: Species Differences In the Genome-wide Rate Of Purgingmentioning

confidence: 99%

Section: Long-term Purging Of Introgressed Dnamentioning

confidence: 99%

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confidence: 99%

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Recombination and selection against introgressed DNA

Veller

Edelman

Muralidhar

et al. 2019

Preprint

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“…This lower per chromosome recombination rate may be favored in certain circumstances. For example, fusions may aid adaptation if recombination is reduced between coadapted alleles at multiple loci ( Guerrero and Kirkpatrick 2014 ; Veller et al 2019 , 2020 ). A beneficial alteration of the recombination landscape might explain why chromosomal fusions could become fixed despite initial deleterious impacts on meiosis in species with monocentric chromosomes ( Lunt et al 2014 ; Fradin et al 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size

Cicconardi

Lewis

Martin

et al. 2021

Molecular Biology and Evolution

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Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with a recent chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 20 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. When fused, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.

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Predicting recombination frequency from map distance

et al. 2022

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Map distance is one of the key measures in genetics and indicates the expected number of crossovers between two loci. Map distance is estimated from the observed recombination frequency using mapping functions, the most widely used of those, Haldane and Kosambi, being developed at the time when the number of markers was low and unobserved crossovers had a substantial effect on the recombination fractions. In contemporary high-density marker data, the probability of multiple crossovers between adjacent loci is negligible and different mapping functions yield the same result, that is, the recombination frequency between adjacent loci is equal to the map distance in Morgans. However, high-density linkage maps contain an interpretation problem: the map distance over a long interval is additive and its association with recombination frequency is not defined. Here, we demonstrate with high-density linkage maps from humans and stickleback fishes that the inverses of Haldane’s and Kosambi’s mapping functions systematically underpredict recombination frequencies from map distance. To remedy this, we formulate a piecewise function that yields more accurate predictions of recombination frequency from map distance. Our results demonstrate that the association between map distance and recombination frequency is context-dependent and without a universal solution.

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Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

Cited by 11 publications

References 40 publications

Recombination and selection against introgressed DNA

Recombination and selection against introgressed DNA

Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size

Predicting recombination frequency from map distance

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