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 analysed 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 thirteen 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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黑暗中的约会：洞穴蟑螂（蜚蠊目：夜蛾科）的替代率升高对分子日期估计产生负面影响


整个生命之树的核苷酸取代率差异很大，对系统发育和进化分析可能产生混杂的影响。主要栖息在地下环境的蟑螂科夜蛾科的线粒体替代率大幅加速。为了评估谱系间比率异质性对系统发育关系和进化时间尺度估计的影响，我们分析了夜光蟑螂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，夜光类蟑螂谱系的替代率显着升高，尤其是线粒体蛋白编码基因的替代率。这种进化速率的差异可能导致不同的进化关系，并得到线粒体基因组和 UCE 位点的系统发育分析的支持。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 UCE 的系统发育分析是第一个涵盖所有 13 个主要蟑螂科的基因组规模研究，将 Corydiidae 和 Nocticolidae 统一起来，并将 Anaplectidae 视为其他蜚蠊总科的姐妹谱系。我们发现夜蛾科的遗传差异程度非常高，其中包括两个高度不同的进化枝，它们在大约 1.15 亿年前就分开了，尽管它们都含有夜蛾属的代表。我们的研究结果强调了谱系间高变异率对系统发育关系和进化时间尺度估计的潜在影响。