Seasonal changes in recombination characteristics in a natural population of Drosophila melanogaster

Aggarwal, Dau Dayal; Rybnikov, Sviatoslav; Sapielkin, Shaul; Rashkovetsky, Eugenia; Frenkel, Zeev; Singh, Mahender; Michalak, Pawel; Korol, Abraham B.

doi:10.1038/s41437-021-00449-2

Cited by 8 publications

(12 citation statements)

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“…Recombination rates in Drosophila also not only depend on genetic background, with up to a two-fold difference between North American genotypes (Hunter, et al 2016), but also depend on female age, number of matings, nutrition, temperature, and pathogen exposure (Redfield 1966; Hunter and Singh 2014; Stapley, et al 2017; Aggarwal, et al 2021). However, as all of the female flies used in this experiment were first-generation laboratory flies and were thus similar in age and environmental exposure, the difference in recombination rates more likely resulted from genetic differences.…”

Section: Discussionmentioning

confidence: 99%

“…1.4 cM/Mb (Stocker, et al 2012), D. pseudoobscura of 3.3 - 4.6 cM/Mb, D. miranda of 4.9 – 6.1 cM/Mb (Heil, et al 2015), D. persimilis of 4.1 cM/Mb for autosomes and 5.0 cM/Mb for X chromosome (Stevison and Noor 2010), D. virilis of 4.6 cM/Mb (Hemmer, et al 2020) and D. melanogaster of 2.5 cM/Mb (Comeron, et al 2012). However, experimental studies of Drosophila have rarely looked at variation in genome-wide recombination rates in natural populations of outbred individuals, and wild populations may differ systematically from populations that have been strongly selected by adaptation to the laboratory (Aggarwal, et al 2021).…”

Section: Introductionmentioning

confidence: 99%

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Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

Wang

McNeil

Abdulazeez

et al. 2022

Preprint

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Mutation, recombination, and transposition occurring during meiosis provide the variation on which natural selection can act and the rates at which they occur are important parameters in models of evolution. The de novo mutation rate determines levels of genetic diversity, responses to ongoing selection, and levels of genetic load. Recombination breaks up haplotypes and reduces the effects of linkage, helping to spread beneficial alleles and purge deleterious ones. Transposable elements (TE) selfishly replicate themselves through the genome, imposing fitness costs on the host and introducing complex mutations that can affect gene expression and give rise to new genes. However, even for key evolutionary models such as Drosophila melanogaster and D. simulans few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, populations, or species. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogaster and a European population of D. simulans. Across 89 flies, we observe 58 single nucleotide mutations, 286 crossovers, and 89 TE insertions. Compared to the European D. melanogaster, we find the West African population has a lower mutation rate (1.67 vs. 4.86 * 10-9 site-1 gen-1) and transposition rate (8.99 vs. 23.36 * 10-5 copy-1 gen-1), but a higher recombination rate (3.44 vs. 2.06 cM/Mb). The European D. simulans population has a similar mutation rate to European D. melanogaster but a significantly higher recombination rate and a lower but not significantly different transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

Wang

McNeil

Abdulazeez

et al. 2022

Preprint

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show abstract

“…Genome-wide estimates of recombination rate are available for several Drosophila species, (Stocker et al 2012), D. pseudoobscura of 3.3 -4.6 cM/Mb, D. miranda of 4.9 -6.1 cM/Mb (Heil et al 2015), D. persimilis of 4.1 cM/Mb for autosomes and 5.0 cM/Mb for X Chromosome (Stevison and Noor 2010), D. virilis of 4.6 cM/Mb (Hemmer et al 2020) and D. melanogaster of 2.5 cM/Mb (Comeron et al 2012). However, experimental studies of Drosophila have rarely looked at variation in genome-wide recombination rates in natural populations of outbred individuals, and wild populations may differ systematically from populations that have been strongly selected by adaptation to the laboratory (Aggarwal et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

et al. 2023

View full text Add to dashboard Cite

The rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses to ongoing selection, and levels of genetic load. However, even for key evolutionary model species such asDrosophila melanogasterandD. simulans, few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, or populations. Knowledge of this variation is fundamental for parameterizing models of genome evolution. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population ofD. melanogasterand a European population ofD. simulans. Across 89 flies, we observe 58 single nucleotide mutations, 286 crossovers, and 89 transposable elements (TE) insertions. Compared to the EuropeanD. melanogaster, we find the West African population has a lower mutation rate (1.67 vs. 4.86 × 10-9 site-1 gen-1) and a lower transposition rate (8.99 vs. 23.36 × 10-5 copy-1 gen-1), but a higher recombination rate (3.44 vs. 2.06 cM/Mb). The EuropeanD. simulanspopulation has a similar mutation rate to EuropeanD. melanogaster, but a significantly higher recombination rate and a lower, but not significantly different, transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species. Our study quantifies the variation in rates of mutation, recombination, and transposition among different populations and sexes, and our direct estimate of these parameters inD. melanogasterandD. simulanswill benefit future studies in population and evolutionary genetics.

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“…Thus, the resulting "gamma-sprinkled" (GS) model assumes a mixture of gamma distributions with v>1 and v=1 (cases of positive COI and no COI) with proportions 1-p and p, respectively, and appeared to be more consistent with empirical data [32]. Yet, cases of possible negative COI were also reported on different organisms (Neurospora, yeast, Drosophila, Arabidopsis, maize, barley, wheat), and the possible presence of CO clustering effect (negative COI) was reported [1,2,33,35,38,3,4,7,8,11,[14][15][16] When applied to such cases, the GS-model gives biased estimates of both parameters, p, and v, due to the presence of three components (with v>1, v=1, and v<1). Therefore, to take account of possible negative interference, we extend the GS model by fitting a mixture of the corresponding three distributions.…”

Section: Introductionmentioning

confidence: 75%

Statistical analysis and simulation allowing simultaneously positive, negative, and no crossover interference in multilocus recombination data

Sapielkin

Frenkel

Privman

et al. 2022

Preprint

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Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can be quantified by the classical coefficient of coincidence (CoC) `but this characteristic is highly variable and specific to the pair of chromosomal intervals considered. Several models were proposed to characterize COI on a chromosome-wise level. In the gamma model, the strength of interference is characterized by a shape parameter ν, while the gamma-sprinkled two-pathway model (GS) accounts for both interference-dependent and independent crossover (CO) events by fitting a mixture of gamma distributions with v>1 and v=1, correspondingly, and mixture proportions 1-p and p. In reality, COI can vary along chromosomes resulting in low compliance of the fitted model to real data. Additional inconsistency can be caused by common neglecting of possible negative COI in the model, earlier reported for several organisms. In this work, we propose an extension of the GS-model to take possible negative COI into account. We propose a way for data simulation and parameter estimation for such situations.

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Seasonal changes in recombination characteristics in a natural population of Drosophila melanogaster

Cited by 8 publications

References 92 publications

Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

Statistical analysis and simulation allowing simultaneously positive, negative, and no crossover interference in multilocus recombination data

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