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

Abstract

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.

Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence

“…We do not know if it is the case in M. ines , or Lepidoptera in general. We note that male biased mutation rates have been observed in many organisms including D. melanogaster (Wang et al 2023).…”

Highly resolved genomes as a tool for studying speciation history of two closely related louse lineages with different host specificities

“…Boostrap replicates (20 for each lineage) are plotted in lighter lines. Coalescence rates were rescaled using the mutation rate of Drosophila according to Wang et al (2023) (3.3 × 10–9) and generation time was estimated as 12 generations per year.…”

The divergence of mutation rates and spectra across the Tree of Life

“…Thus, with the expectation that both mutators and anti‐mutators are recurrently introduced into all populations (Denamur & Matic, 2006; Lynch, 2008, 2011; Raynes & Sniegowski, 2014), virtually all natural populations likely harbor polymorphisms for the mutation rate. This supposition is corroborated by several‐fold ranges of variation for observed for natural isolates of species ranging from Chlamydomonas (López‐Cortegano et al , 2021) to Saccharomyces (Gou et al , 2019; Jiang et al , 2021) to Drosophila (Schrider et al , 2013; Wang et al , 2023) to mice (Sasani et al , 2022) to humans (Rahbari et al , 2016; Kessler et al , 2020).…”