Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analyzed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all 13 major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.

中文翻译：

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在黑暗中测年：洞穴蟑螂 （Blattodea： Nocticolidae） 的替代率升高对分子测年估计有负面影响


核苷酸替换的速率在生命之树中差异很大，对系统发育和进化分析有潜在的混杂影响。线粒体替代率的大幅加速发生在蟑螂科夜葞科，它主要栖息在地下环境中。为了评估这种谱系率异质性对系统发育关系和进化时间尺度估计的影响，我们分析了来自夜视科动物和其他蟑螂的核超保守元件 （UCE） 和线粒体基因组。与其他蟑螂相比，夜蟑螂谱系的替代率显着升高，尤其是在线粒体蛋白质编码基因中。进化速率的这种差异可能导致线粒体基因组和 UCE 基因座的系统发育分析支持不同的进化关系。此外，与灵活的本地时钟相比，使用松弛时钟模型的贝叶斯测年分析推断出更深的发散时间。我们对 UCEs 的系统发育分析是第一个包括所有 13 个主要蟑螂科的基因组规模研究，将 Corydiidae 和 Nocticolidae 结合在一起，并将 Anaplectidae 作为 Blattoidea 其他部分的姐妹谱系。我们发现了夜蛾科 （Nocticolidae） 中异常程度的遗传分化，包括两个高度不同的分支，它们在 ~1.15 亿年前分离，尽管它们都包含夜蛾属的代表。我们的研究结果强调了高谱系率变化对系统发育关系和进化时间尺度估计的潜在影响。