Phylogenomics of the major lineages of Bembidion and related ground beetles (Coleoptera: Carabidae: Bembidiini)

Bembidion Latreille is a genus of small ground beetles containing about 1,380 species. To test previous phylogenetic hypotheses about deeper lineages of Bembidion and near relatives, we examine over 1,800 nuclear protein-coding loci from 33 species representing the main lineages of Bembidion, 10 species of other bembidiine genera, and seven outgroups. We find that Bembidion exclusive of subgenus Phyla Motschulsky is monophyletic, and we reclassify Phyla as a separate genus. Within Bembidion we find two dominant clades, the Bembidion superseries (containing about 490 species in the subgenera Eupetedromus Netolitzky and Lindrochthus Maddison, the Philochthus Stephens complex, and the Bembidion series), and the Ocydromus Clairville superseries (containing almost all other Bembidion representing about 840 species). The only known lineages within Bembidion outside of these superseries are subgenus Hoquedela Müller-Motzfeld and the Desarmatocillenus Netolitzky complex, which combined contain ..., Transcriptomes of 39 species and low-coverage genomes for six species were sequenced using Illumina sequencers.  Combined with previously published transcriptomes and genomes, 50 species were analyzed.  After read trimming (Trimmomatic) and assembly (Trinity) of transcriptomes, a suite of 5,197 purported single-copy orthologs were found using Agalma.  These target loci were then sought using Exonerate in the low-coverage genome assemblies (trimming and assembly done in CLC Genomics Workbench).  We removed low information-content loci using MARE, removed anomalous sequences using TreeShrink, discarded loci with overly heterogenous base compositions using BaCoCa, and trimmed anomalous sequence ends.  This filtered the set down to 1,875 loci.  We then inferred maximum likelihood trees of each locus, and visually inspected each gene tree and the corresponding alignment for signs of paralogy, and discarded five loci that clearly had at least two paralogs.  We then formed three sets of matric..., , # Phylogenomics of the major lineages of Bembidion and related ground beetles (Coleoptera: Carabidae: Bembidiini)

[https://doi.org/10.5061/dryad.2jm63xsxz](https://doi.org/10.5061/dryad.2jm63xsxz)

These files contain alignments of between 1,390 and 1,728 nuclear protein-coding genes derived from transcriptomes and genomes for between 42 and 50 taxa as well as inferred phylogenetic trees for most of data sets analyzed.  

## Description of the data and file structure

All files are Mesquite files in the NEXUS file format. 

Data set names are of the following format: ... The taxon set code is either 50Taxa, 46Taxa, or 42Taxa, with 50Taxa including all ingroups and outgroups, 46Taxa including all but three of the outgroups on the longest terminal branches and one ingroups with limited data, and 42Taxa having the four remaining outgroups removed from the 46Taxa taxon set. The occupancy code is \"Occ66\", which indicates that any locus present in less than 66% of the taxa was removed; if th...