Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates

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. Ou..., , 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, # Title of Dataset: Data for Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates

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The data provided consists of the output tree files (.tre) from each of the phylogenetic analyses and the associated sequence alignments and partition files (.nex) for each of the datasets.

## Description of the Data and file structure

The datasets are labelled as:
\- \"16S\" refers to the dataset containing a 440 bp fragment of the mitochondrial gene encoding 16S rRNA (16S). Note that some internal regions have been trimmed from the original alignment.

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- \"mtPCG\" refers to the dataset containing a concatenated alignment of 13 mitochondrial protein-coding genes. Note that all codon positions are present in the alignment, but only second codon positions were used in analyses

- \"UCE60p\" refers to the dataset containing a concatenated alignment of the UCE loci included in our 60 percent completeness matrix

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