DOI: 10.5061/dryad.2jm63xsxz
title: Phylogenomics of the major lineages of Bembidion and related ground beetles (Coleoptera: Carabidae: Bembidiini)

description: 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 less than 30 species. Most clades are insensitive to
 variations in analyses, and hold up under different sets of taxa and loci,
 analyses at the nucleotide or amino acid levels, and different analytical
 methods (maximum likelihood, including PMSF analyses, Bayesian analyses,
 invariant-based methods, and those that consider incomplete lineage
 sorting). Despite the clarity achieved in most aspects of the phylogeny,
 there are several unresolved regions, notably the relationships of
 Desarmatocillenus, Hoquedela, and Phyla to other bembidiines. A divergence
 dating analysis suggests that crown Bembidion is about 48 million years
 old (95% confidence intervals 40–58 Ma), and that the two large
 superseries are about 38 million years old (95% confidence intervals about
 29–47 Ma).
description: 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 matrices (with all 50 taxa, with the three
 longest-branch outgroup taxa plus one ingroup with limited data removed
 (yielding 46 taxa), and with four remaining non-Bembidiini removed from
 the 46 taxa set (yielding 42 taxa)).  We also analyzed matrices of all
 loci and only those loci present in at least 66% of the taxa, and analyzed
 matrices of all nucleotides, only first and second positions, and
 translated into amino acids.  Trees were inferred of concatenated data
 using maximum likelihood, PMSF likelihood, SVD Quartets, and Bayesian
 methods, and maximum likelihood trees of all loci via ASTRAL.
description: # 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 that code does not appear in the data set name, then all loci were included. The data type is either AA (amino acid), N123 (all nucleotide positions), or N12 (nucleotides but only first and second positions).  * Eight Mesquite files containing separate matrices for every locus for eight of the data sets (and from which other data sets can be derived): * **42Taxa.N123_All_Loci.nex** * **46Taxa.N123_All_Loci.nex** * **46Taxa.Occ66.AA_All_Loci.nex** * **46Taxa.Occ66.N123_All_Loci.nex** * **50Taxa.AA_All_Loci.nex** * **50Taxa.N123_All_Loci.nex** * **50Taxa.Occ66.AA_All_Loci.nex** * **50Taxa.Occ66.N123_All_Loci.nex** * **Loci.with.Paralogy.Problems.nex**: A Mesquite file containing alignments and gene trees for the five loci that were removed after visual inspection of the gene trees and alignments suggested they contained paralogs.  * **BembidiiniPhylogenomics.Trees.nex**: A Mesquite file containing all inferred trees for concatenated data and the ASTRAL analyses, including bootstrap and ultrabootstrap trees.  * **Maximum.Likelihood.Gene.Trees.nex**:  A Mesquite file containing 10 tree blocks.  Each tree block contains between 1,390 to 1,728 trees, corresponding to the maximum likelihood tree for each locus for the 50Taxa.N123, 50Taxa.Occ66.AA, 50Taxa.Occ66.N12, 50Taxa.Occ66.N123, 46Taxa.Occ66.AA, 46Taxa.Occ66.N12, 46Taxa.Occ66.N123, 42Taxa.Occ66.AA, 42Taxa.Occ66.N12, and 42Taxa.Occ66.N123 data sets.