Species discovery and delimitation in ground beetles of the subgenus Trepanedoris: matrices and trees
Data files
Mar 17, 2026 version files 5.33 MB
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Maddison_et_al._Trepanedoris_Matrices_And_Trees.v2.nex
4.89 MB
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README.md
1.46 KB
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Supplementary_Figures.pdf
117.60 KB
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Supplementary_Tables.pdf
326.13 KB
Abstract
We infer species boundaries in small ground beetles of the genus Bembidion, presenting the discoveries made by a class of students in an experiential learning course at Oregon State University. Focusing on the Bembidion connivens group of subgenus Trepanedorisoutside of California, we integrate data from external structure and male genitalia, DNA sequences of one mitochondrial gene and six nuclear genes, and geographic distribution. We analyze the DNA data using Bayesian multispecies coalescent methods to help infer reproductive communities or species; SPEEDEMON tended to split species more than what our integrated approach inferred, whereas DELINEATE tended to lump more than synthetic inference. We infer 12 species in North America outside of California, including four new species. The files in this archive include a Mesquite NEXUS file containing DNA data matrices and inferred trees, Supplementary Tables including localities of specimens and GenBank accession numbers of analyzed DNA sequences, and Supplementary Figures showing intermediate results in the DELINEATE analysis.
Dataset DOI: 10.5061/dryad.9cnp5hqx1
Description of the data and file structure
Most DNA data was collected by extracting DNA from specimens collected into 95% ethanol; the DNA was then subjected to PCR and Sanger sequencing, with the resulting chromatgrams processed using the Chromaseq package of Mesquite (http://chromaseq.mesquiteproject.org).
Most phylogenetic trees contained in the file are from maximum likelihood analyses in IQ-TREE version 2.2.2.7. One phylogenetic tree is the maximum clade credibility tree from a STACEY version 1.3.1 analysis conducted within BEAST version 2.7.6.
Files and variables
File: Supplementary_Figures.pdf
Description: Two figures showing intermediate results in the DELINEATE analysis
File: Maddison_et_al._Trepanedoris_Matrices_And_Trees.v2.nex
Description: NEXUS file containing matrices of DNA sequence data as well as phylogenetic trees.
File: Supplementary_Tables.pdf
Description: One table listing locality data for specimens sequenced, and a second table giving GenBank accession numbers for all of the sequences analyzed.
Code/software
Mesquite (http://mesquiteproject.org) version 3.81 or later is needed to view all of the components of the NEXUS file.
