Pervasive gene conversion in chromosomal inversion heterozygotes

Korunes, Katharine L; Noor, Mohamed A. F.

doi:10.1111/mec.14921

Cited by 76 publications

(114 citation statements)

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“…Overall, the pattern of differentiation within the Formica supergene differs strikingly from the predictions of the expanding strata model (Figures 2-4). We propose that the Formica supergene results from a long history of rare recombination [25] and/or gene conversion [26,27]) between alternative haplotypes in different lineages ( Figure 4).…”

Section: Resultsmentioning

confidence: 99%

An Ancient and Eroded Social Supergene Is Widespread across Formica Ants

et al. 2020

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Section: Resultsmentioning

confidence: 99%

An Ancient and Eroded Social Supergene Is Widespread across Formica Ants

et al. 2020

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“…The rationale for this approach is that recombination suppression should produce very high LD among SNPs within inversions. Although gene conversion and double recombination can break down LD in the middle of old and large inversions, such as that observed for some inversions in Drosophila (Korunes and Noor, 2019), whether this is common in plants is unclear. Other mechanisms that reduce recombination, such as pericentromeric heterochromatin, will also lead to high LD regions.…”

Section: Population Genomic Approachesmentioning

confidence: 99%

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

2020

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Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.

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“…Along with the candidate gene approach to examine associations with genome-wide recombination rate, we also investigated the possibility that small-scale differences in genomic structure between the inbred lines may explain differences in recombination rate. This may be of particular importance given that our design required measuring recombination rate in F 1 individuals (inbred line × tester line), and that structural heterozygosity has a well-known negative association with recombination rate (Morgan et al ., 2017; Crown et al ., 2018; Korunes & Noor, 2019).…”

Section: Methodsmentioning

confidence: 99%

Natural selection shapes variation in genome-wide recombination rate inDrosophila pseudoobscura

Samuk

Manzano‐Winkler

Ritz

et al. 2019

Preprint

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AbstractWhile recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations (2) interpopulation differences in recombination rate may be the result of local adaptation, and (3) the observed variation among individuals in recombination rate is primarily driven by global regulators of crossover rate, with little detected variation in recombination rate among strains across specific tracts of individual chromosomes.

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Pervasive gene conversion in chromosomal inversion heterozygotes

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as

Cited by 76 publications

References 77 publications

An Ancient and Eroded Social Supergene Is Widespread across Formica Ants

An Ancient and Eroded Social Supergene Is Widespread across Formica Ants

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

Natural selection shapes variation in genome-wide recombination rate inDrosophila pseudoobscura

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