Abstract

The rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia magna, an ecological and evolutionary model system. We report extremely high base substitution mutation rates (µ-n,bs = 8.96 × 10⁻⁹/bp/generation [95% CI: 6.66–11.97 × 10⁻⁹/bp/generation] in the nuclear genome and µ-m,bs = 8.7 × 10⁻⁷/bp/generation [95% CI: 4.40–15.12 × 10⁻⁷/bp/generation] in the mtDNA), the highest of any eukaryote examined using this approach. Levels of intraspecific variation based on the range of estimates from the nine genotypes collected from three populations (Finland, Germany, and Israel) span 1 and 3 orders of magnitude, respectively, resulting in up to a ∼300-fold difference in rates among genomic partitions within the same lineage. In contrast, mutation spectra exhibit very consistent patterns across genotypes and populations, suggesting the mechanisms underlying the mutational process may be similar, even when the rates at which they occur differ. We discuss the implications of high levels of intraspecific variation in rates, the importance of estimating gene conversion rates using a mutation–accumulation approach, and the interacting factors influencing the evolution of mutation parameters. Our findings deepen our knowledge about mutation and provide both challenges to and support for current theories aimed at explaining the evolution of the mutation rate, as a trait, across taxa.

中文翻译：

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水蚤的自发突变率很高且变化很大。

摘要

自发突变的频率和范围是基础生物学和应用生物学的关键参数，因为它们决定了引入种群的遗传变异的速度和特征，这是进化的先决条件。我们使用突变累积方法从全基因组序列数据中估算变异参数，该数据来自生态和进化模型系统Daphnia magna多个种群的多种基因型。我们报告了核基因组和µ-m中极高的碱基取代突变率（µ-n，bs = 8.96×10 ^-9 / bp /代[95％CI：6.66-11.97×10 ^-9 / bp /代] bs = 8.7×10 ^-7 / bp /代[95％CI：4.40–15.12×10 ^-7[/ bp / generation]），是使用这种方法检查的所有真核生物中最高的。种内变异的水平基于从三个种群（芬兰，德国和以色列）收集的9个基因型的估计范围，分别跨越1和3个数量级，导致基因组之间的差异高达300倍左右同一谱系中的分区。相反，突变谱在基因型和种群之间表现出非常一致的模式，这表明突变过程的潜在机制可能是相似的，即使它们发生的速率不同。我们讨论了种内比率高水平变异的含义，使用突变积累方法估算基因转化率的重要性，以及影响突变参数演变的相互作用因素。我们的发现加深了我们对突变的认识，并为当前的理论提供了挑战和支持，这些理论旨在解释整个类群中突变率（作为特征）的演变。