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 mitochondrial genomes and UCE loci. Furthermore, 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 nine 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.

To view the tree files we recommend using FigTree: https://github.com/rambaut/figtree/releases I would open the 16S or mtPCG alignments in MEGA https://www.megasoftware.net/ or Seqotron https://github.com/4ment/seqotron/ I would avoid opening the alignment of UCEs, just let them be. Missing data code in PhyloMAd output files: NA Funding provided by: Australian Research CouncilCrossref Funder Registry ID: https://ror.org/05mmh0f86Award Number: DP220103265 Funding provided by: The Linnean Society of New South WalesCrossref Funder Registry ID: https://ror.org/021mnqw37Award Number: The Joyce W. Vickery Research Fund