Recombination and selection against introgressed DNA

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

doi:10.1101/846147

Cited by 28 publications

(57 citation statements)

References 89 publications

(176 reference statements)

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“…Variance in genetic relatedness has also been hypothesized to have important evolutionary consequences, including driving the evolution of karyotypes and recombination rates in some clades (Sherman 1979;Wilfert et al 2007). Moreover, as we show elsewhere, variance in genetic relatedness plays a key role in selection against deleterious introgressed DNA following hybridization (Veller et al 2019a).…”

Section: Introductionsupporting

confidence: 57%

Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

et al. 2020

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The genomic proportion that two relatives share identically by descent-their genetic relatedness-can vary depending on the history of recombination and segregation in their pedigree. Previous calculations of the variance of genetic relatedness have defined genetic relatedness as the proportion of total genetic map length (cM) shared by relatives, and have neglected crossover interference and sex differences in recombination. Here, we consider genetic relatedness as the proportion of the total physical genome (bp) shared by relatives, and calculate its variance for general pedigree relationships, making no assumptions about the recombination process. For the relationships of grandparent-grandoffspring and siblings, the variance of genetic relatedness is a simple decreasing function of r̄, the average proportion of locus pairs that recombine in meiosis. For general pedigree relationships, the variance of genetic relatedness is a function of metrics analogous to r̄. Therefore, features of the aggregate recombination process that affect r̄ and analogs also affect variance in genetic relatedness. Such features include the number of chromosomes and heterogeneity in their size, the number of crossovers and their spatial organization along chromosomes, and sex differences in recombination. Our calculations help to explain several recent observations about variance in genetic relatedness, including that it is reduced by crossover interference (which is known to increase r̄). Our methods further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling precise statistical inference in F2-based tests for various kinds of selection.

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Section: Introductionsupporting

confidence: 57%

Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

et al. 2020

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“…Dashed lineordinary least squares fit.Evidence for introgression is weaker between more diverged species One of the expectations of hybridization is that as divergence increases between the parental species, the number of incompatibilities increases at a fast pace(Satokangas, et al 2020). Since the amount of residual introgression after hybridization has been hypothesized to be affected by the density of hybrid incompatibilities(Veller, et al 2019), then hybridization between more divergent species should lead to lower signals of admixture(Wiens, et al 2006;Hamlin, et al 2020). We next annotated our dataset with genetic distances between pairs of species showing evidence for introgression.…”

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confidence: 99%

15 years of introgression studies: quantifying gene flow across Eukaryotes

Peede

et al. 2021

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With the rise of affordable next generation sequencing technology, introgression - or the exchange of genetic materials between taxa - is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Patterson's D, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most-often used introgression statistic, Patterson's D, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.

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“…In total, this suggests that all OOA populations have experienced some level of gene flow with Central Africa, West Africa, and HD, but flies from the SE United States may have experienced a second, and independent pulse of West African ancestry (as has been hypothesized by [27, 28]). The lack of distinction may also be caused by rapid purging of introgressed alleles, reducing any signals of introgression in a short time-span [67].…”

Section: Resultsmentioning

confidence: 99%

Patterns of and processes shaping population structure and introgression among recently differentiated Drosophila melanogaster populations

Coughlan¹,

Dagilis²,

Serrato-Capuchina

et al. 2021

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Understanding the factors that produce and maintain genetic variation is a central goal of evolutionary biology. Despite a century of genetic analysis, the evolutionary history underlying patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic and phenotypic variation is partitioned across global D. melanogaster populations, and specifically in its putative ancestral range in Subtropical Africa, remains unresolved. Here, we integrate genomic and behavioral analyses to assess patterns of population genetic structure, admixture, mate preference, and genetic incompatibility throughout the range of this model organism. Our analysis includes 174 new accessions from novel and under-sampled regions within Subtropical Africa. We find that while almost all Out of Africa genomes correspond to a single genetic ancestry, different geographic regions within Africa contain multiple distinct ancestries, including the presence of substantial cryptic diversity within Subtropical Africa. We find evidence for significant admixture- and variation in admixture rates-between geographic regions within Africa, as well as between African and non-African lineages. By combining behavioral analysis with population genomics, we demonstrate that female mate choice is highly polymorphic, behavioral types are not monophyletic, and that genomic differences between behavioral types correspond to many regions across the genome. These include regions associated with neurological development, behavior, olfactory perception, and learning. Finally, we discovered that many individual pairs of putative incompatibility loci likely evolved during or after the expansion of D. melanogaster out of Africa. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the distribution of reproductive barriers that are polymorphic within species.

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Recombination and selection against introgressed DNA

Cited by 28 publications

References 89 publications

Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

15 years of introgression studies: quantifying gene flow across Eukaryotes

Patterns of and processes shaping population structure and introgression among recently differentiated Drosophila melanogaster populations

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