DOI: 10.5061/dryad.fxpnvx0wx
title: Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates

description: 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.
description: 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
description: # Title of Dataset: Data for Dating in the Dark: Elevated Substitution
 Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts
 on Molecular Date Estimates --- 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. ``` -
 "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 - Files containing *NoNoct* are the trees
 produced after removing representatives of Nocticolidae from the
 alignment. All other files are trees estimated using all taxa. - PhyloMAd*
 files are the output files from our test of substitution model adequacy in
 PhyloMAd - roaches-v1-master-probe-list-DUPE-SCREENED.fasta.gz: Final
 deduplicated probe set (minimum identity threshold of 80% and a minimum
 coverage of 83%) cleaned from sequences with ambiguous base calls and
 GC-content above 70% or below 30%, designed for all six considered genomes
 (319,243 baits targeting 30,059 loci). This deduplicated set was obtained
 with ‘phyluce_probe_get_tiled_probes’, ‘phyluce_probe_easy_lastz’ and
 ‘phyluce_probe_remove_duplicate_hits_from_probes_using_lastz’. -
 ROA_UCE_DB_CONTRIB_1.fasta.gz: Extracted UCEs from all samples using the
 bait set provided in this study. This is contribution #1 for the Cockroach
 UCE Database. Each sample was assigned a unique identification code
 (ROA-X-UCEDB). The database is maintained at:
 https://github.com/sihellem/ROA-UCE-DB/. - ROA_UCE_DB_CONTRIB_1_ids.txt:
 unique identification codes for UCE samples (ROA-X-UCEDB) ``` For more
 information or if you just want to talk noctis please do not hesitate to
 contact me (Toby) at :)