Perini Samuel, Johannesson Kerstin, Butlin Roger K, Westram Anja M
Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, Strömstad, Sweden.
Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom.
J Evol Biol. 2025 Feb 27;38(3):367-378. doi: 10.1093/jeb/voaf002.
Polymorphic short insertions and deletions (INDELs ≤ 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence.
多态性短插入和缺失（INDELs≤50bp）很常见，尽管不如单核苷酸多态性（SNPs）那么普遍。来自模式生物的证据表明，与SNP相比，INDELs受纯化选择的影响更大。部分由于这个原因，INDELs很少被用作群体动态过程的标记或检测分歧选择。在这里，我们比较了潮间带蜗牛滨螺（Littorina saxatilis）中的INDELs和SNPs，重点关注生态型之间的杂交带，以测试INDELs在检测分歧选择中的效用。我们使用捕获测序数据计算了INDEL和SNP位点频率谱。我们通过分析跨越栖息地边界的等位基因频率渐变来评估分歧选择的影响。我们还研究了GC偏向性基因转换的影响，因为它可能与选择特征混淆。我们发现有证据表明，短INDELs比SNPs受纯化选择的影响更大，但观察到的位点频率谱差异的一部分可归因于GC偏向性基因转换。我们没有发现短INDELs和SNPs在分歧选择影响上的差异。短INDELs和SNPs在基因组中的分布相似，因此可能以相同的方式对间接选择做出反应。INDELs揭示了一些可能受分歧选择影响的区域，而SNPs则没有。短INDELs可以作为有用的（额外的）遗传标记，有助于识别对适应和种群分化重要的基因组区域。
