Data from: Unconstrained evolution in short introns?—An analysis of genome-wide polymorphism and divergence data from Drosophila

An unconstrained reference sequence facilitates the detection of selection. In Drosophila, sequence variation in short introns seems to be least influenced by selection and dominated by mutation and drift. Here, we test this with genome-wide sequences using an African population (Malawi) of D. melanogaster and data from the related outgroup species D. simulans, D. sechellia, D. erecta, and D. yakuba. The distribution of mutations deviates from equilibrium and the content of A and T (AT) nucleotides shows an excess of variance among introns. We explain this by a complex mutational pattern: a shift in mutational bias towards AT, leading to a slight non-equilibrium in base composition, and context-dependent mutation rates, with GC-sites mutating most frequently in AT-rich introns. By comparing the corresponding allele frequency spectra of AT-rich versus GC-rich introns, we can rule out the influence of directional selection or biased gene conversion (BGC) on the mutational pattern. Compared to neutral equilibrium expectations, polymorphism spectra show an excess of low frequency and a paucity of intermediate frequency variants, irrespective of the direction of mutation. Combining the information from different outgroups with the polymorphism data and using a generalized linear model, we find evidence for shared ancestral polymorphism between D. melanogaster and D. simulans/D. sechellia, arguing against a bottleneck in D. melanogaster. Generally, we find that short introns can be used as a neutral reference on a genome-wide level, if the spatially and temporally varying mutational pattern is accounted for.

不受约束的参考序列（unconstrained reference sequence）有助于检测选择作用。在果蝇（Drosophila）中，短内含子（short introns）的序列变异似乎受选择影响最小，主要由突变与遗传漂变主导。本研究以非洲马拉维种群的黑腹果蝇（Drosophila melanogaster）全基因组序列，以及近缘外类群物种拟果蝇（Drosophila simulans）、塞氏果蝇（Drosophila sechellia）、直立果蝇（Drosophila erecta）和雅库巴果蝇（Drosophila yakuba）的相关数据，对“短内含子序列变异受选择影响最小、主要由突变与遗传漂变主导”这一观点进行验证。研究发现，突变分布偏离平衡状态，且腺嘌呤（A）与胸腺嘧啶（T，即AT）核苷酸的含量在内含子间存在过度变异。我们通过复杂突变模式对该现象进行解释：突变偏好向AT偏移，导致碱基组成出现轻微的非平衡状态；同时突变率存在序列上下文依赖性，在富含AT的内含子中，GC位点的突变频率最高。通过对比富含AT与富含GC的内含子对应的等位基因频率频谱（allele frequency spectra），我们可以排除定向选择（directional selection）或偏向性基因转换（biased gene conversion, BGC）对突变模式的影响。与中性平衡预期相比，多态性频谱（polymorphism spectra）呈现出低频变异过量、中频变异缺失的特征，且该特征与突变方向无关。我们将不同外类群的信息与多态性数据相结合，并使用广义线性模型（generalized linear model）进行分析，发现黑腹果蝇与拟果蝇/塞氏果蝇之间存在共享的祖先多态性，这一结果不支持黑腹果蝇曾经历种群瓶颈的假说。总体而言，我们发现，若考虑到空间与时间动态变化的突变模式，短内含子可在全基因组水平上作为中性参考序列使用。