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Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
Genome Research ( IF 7 ) Pub Date : 2023-04-01 , DOI: 10.1101/gr.277383.122
Yiguan Wang 1 , Paul McNeil 2 , Rashidatu Abdulazeez 3 , Marta Pascual 4 , Susan E Johnston 2 , Peter D Keightley 2 , Darren J Obbard 2
Affiliation  

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.

中文翻译:

果蝇和模拟果蝇突变、重组和转座率的变化

突变、重组和转座率是进化模型的核心参数。它们影响遗传多样性、对持续选择的反应以及遗传负荷水平。然而,即使对于关键的进化模型物种,如果模拟果蝇,对这些参数的估计也很少,而且我们对个体、性别或种群之间的比率如何变化知之甚少。了解这种变异对于参数化基因组进化模型至关重要。在这里,我们提供了西非和欧洲黑腹果蝇种群以及欧洲拟果蝇种群中突变、重组和转座率及其变异的直接估计。在 89 只果蝇中,我们观察到 58 个单核苷酸突变、286 个交叉和 89 个转座元件 (TE) 插入。与欧洲黑腹果蝇相比,我们发现西非种群的突变率较低(1.67 × 10 -9位点-1 gen -1 vs. 4.86 × 10 -9位点-1 gen -1)和较低的转座率(8.99 × 10 -5 copy -1 gen -1与 23.36 × 10 -5 copy -1 gen -1),但重组率更高(3.44 cM/Mb 与 2.06 cM/Mb)。欧洲拟果蝇群体与欧洲黑腹果蝇具有相似的突变率,但重组率明显较高,转座率较低,但没有显着差异。总体而言,我们发现这两个物种中父系突变比母系突变更常见。我们的研究量化了不同种群和性别之间突变、重组和转座率的变化,我们对黑腹果蝇拟果蝇中这些参数的直接估计将有利于未来种群和进化遗传学的研究。
更新日期:2023-04-01
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