Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans

Genome Research · 7 authors, 3 centres

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It found significant variation in these rates between populations and species, and that paternal-derived mutations were more frequent than maternal ones.

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Eighty-nine flies from 18 families of D. melanogaster (West African and European populations) and D. simulans (European population) were sequenced. Key findings include a lower mutation and transposition rate but higher recombination rate in the West African D. melanogaster population compared to the European population. European D. simulans had a similar mutation rate to European D. melanogaster but a higher recombination rate and a lower, non-significant, transposition rate. The study also found that paternal-derived mutations were more frequent than maternal ones in both species. Limitations include the focus on mutations in low-complexity regions and the use of a specific bioinformatics pipeline. These direct estimates from wild genomes provide fundamental parameters for evolutionary models.

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preclinical research

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ORIGINAL PAPER

PMC10234296

Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans

Genome Research

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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 as Drosophila melanogaster and Drosophila 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 of D. melanogaster and a European population of D. simulans . Across 89 flies, we observe 58 single-nucleotide mutations, 286 crossovers, and 89 transposable element (TE) insertions. Compared to the European D. melanogaster , we find the West African population has a lower mutation rate (1.67 × 10 −9 site −1 gen −1 vs. 4.86 × 10 −9 site −1 gen −1 ) and a lower transposition rate (8.99 × 10 −5 copy −1 gen −1 vs. 23.36 × 10 −5 copy −1 gen −1 ), but a higher recombination rate (3.44 cM/Mb 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. Our study quantifies the variation in rates of mutation, recombination, and transposition among different populations and sexes, and our direct estimates of these parameters in D. melanogaster and D. simulans will benefit future studies in population and evolutionary genetics.

CITATION EXPORT

Yiguan Wang, Paul McNeil, Rashidatu Abdulazeez et al.. Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans. Genome Research. (2023). https://doi.org/10.1101/gr.277383.122

AUTHORS

7 · 3 CENTRES

Yiguan Wang, Paul McNeil, Rashidatu Abdulazeez, Marta Pascual, Susan E. Johnston, Peter D. Keightley, Darren J. Obbard

1Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
2Department of Zoology, Ahmadu Bello University, 810107 Zaria, Nigeria;
3Departament de Genètica, Microbiologia i Estadística and IRBio, Universitat de Barcelona, 08028 Barcelona, Spain