DOI: 10.5061/dryad.sj3tx967w
title: Data from: Phylogenomics and biogeography of North American Trechine cave beetles (Coleoptera: Carabidae)

description: Cave trechines beetles (Coleoptera: Carabidae: Trechini) are members of
 cave communities globally and important models for understanding the
 colonization of caves, adaptation to cave life, and the diversification of
 cave-adapted lineages. In eastern North America, cave trechines are the
 most species-rich group of terrestrial troglobionts, hypothesized to
 comprise over 150 taxa in six genera with no extant surface members.
 Previous studies have hypothesized that the Pleistocene climate change was
 a major driver of cave colonization and diversification in the temperate
 terrestrial cave fauna in this region. However, our time-calibrated
 molecular phylogeny resulting from the analysis of 16,794 bases from 68
 Ultraconserved Elements (UCEs) loci for 45 species of the clade supports
 an alternative hypothesis whereby cave colonization of the surface
 ancestor of eastern North American cave trechines likely began in the
 early Miocene in the Appalachians Ridge and Valley (APP) and dispersed
 into the Interior Low Plateau (ILP) in an east to west manner beginning
 17.0 Mya. The APP served as a cradle for diversification and as a bridge
 linking the southern Appalachians and Interior Low Plateau enabling the
 dispersal and subsequent diversification of this cave beetles. Major
 clades in our time-calibrated phylogeny attained their present-day
 geographic distributions by the early Miocene followed by multiple
 additional episodes of cave colonization and diversification occurring
 throughout the Pliocene and Pleistocene. The genera Neaphanops,
 Darlingtonea, Nelsonites, and Ameroduvalius were nested within speciose
 genus Pseudanophthalmus supporting the hypothesis that these taxa are
 derived Pseudanophthalmus. Moreover, while several morphologically-defined
 species groups of Pseudanophthalmus were recovered as monophyletic, others
 were not warranting future taxonomic and systematic research. The
 molecular systematics and biogeography of these unique trechine cave
 beetles offer a model for other comparative evolutionary and ecological
 studies of troglobionts to further our understanding of factors driving
 speciation and biogeographic patterns.
description: # Data from: Phylogenomics and Biogeography of North American Trechine
 Cave Beetles (Coleoptera: Carabidae)
 [https://doi.org/10.5061/dryad.sj3tx967w](https://doi.org/10.5061/dryad.sj3tx967w) ## Description of the data and file structure We collected specimens of 45 cave trechine taxa from caves in the APP, ILP, and OZK, including 41 species of *Pseudanophthalmus* from 20 of the 26 species groups defined by Barr (2004), as well as *Ameroduvalius jeanneli*, *Darlingtonea kentuckensis*, *Neaphaenops tellkampfi*, and *Nelsonites jonesi*. We were not able to obtain specimens of *Nelsonites walteri* nor both species of *Xenotrechus*. Beetles were collected from terrestrial and riparian cave habitats, such as mud banks, the splash zones of active drips, near streams and rimstone pools, underneath rocks and coarse woody debris, or within cobble and gravel. Two species of the genus *Trechus — T. obtusus* and *T. humbolti —* and *Trechoblemus westcotti* were included as outgroups. To generate a reduced representation genomic dataset of Ultraconserved Element (UCE) loci of cave trechines, we employed UCE phylogenomics (Faircloth et al. 2012; Branstetter et al. 2017), an approach that combines the targeted enrichment of thousands of nuclear UCE loci with multiplexed next-generation sequencing. Enrichment was performed using a published bait set that targets loci shared across all Coleoptera (‘Coleoptera 1.1Kv1’; Faircloth 2017). It includes 13,674 unique baits targeting 1,172 UCE loci. Whole genomic DNA was extracted from muscle, meso-metathorax, and leg of the cave trechine specimens following the DNA extraction method from Maddison et al. 1999. Further UCE molecular work was performed following the UCE methodology described in (Branstetter et al. 2017), including library preparation, UCE enrichment, sample pooling, and sequencing on an Illumina HiSeq 4000 (PE150 v4) at the Arbor Biosciences (Ann Arbor, Michigan, USA). ### Files and variables #### File: MrBayes\_bayesian\_phylogeny\_cave\_beetles\_75\_UCE.tre **Description:** Bayesian phylogeny of cave trechine beetles from eastern North America inferred from 75% complete concatenated UCE matrix #### File: RAxML\_maximum-likelihood\_phylogeny\_cave\_beetles\_75\_UCE.tre **Description:** Maximum-likelihood phylogeny of cave trechine beetles from eastern North America inferred from 75% complete concatenated UCE matrix #### File: ASTRAL\_68\_coalescent\_species\_trees.tre **Description:** ASTRAL coalescent species tree, with input trees derived from multi-partitioned IQTree analyses of individual gene trees #### File: BEAST\_time-calibrated\_maximum\_clade\_credibility\_tree\_75\_UCE.tree **Description:** Time-calibrated maximum clade credibility tree inferred from 75% concatenated UCE matrix. Branches are proportional to time in millions of years #### File: BioGeoBEARS\_DEC\_J\_Cave\_beetles\_karst\_region\_stochastic\_map.pdf **Description:** Ancestral karst region estimation for cave trechine beetles from eastern North America based on the preferred DEC+J model. Ancestral areas were estimated across the time-calibrated phylogeny inferred from 75% complete concatenated UCE matrix #### File: RAxML\_maximum-likelihood\_phylogeny\_cave\_beetles\_50\_UCE.tre **Description:** Maximum-likelihood phylogeny of cave trechine beetles from eastern North America inferred from 50% complete concatenated UCE matrix #### File: MrBayes\_bayesian\_phylogeny\_cave\_beetles\_50\_UCE.tre **Description:** Bayesian phylogeny of cave trechine beetles from eastern North America inferred from 50% complete concatenated UCE matrix #### File: BioGeoBEARS\_DEC\_J\_cave\_beetles\_karst\_subregion\_stochastic\_map.pdf **Description:** Ancestral karst sub region estimation for cave trechine beetles from eastern North America based on the preferred DEC+J model. Ancestral areas were estimated across the time-calibrated phylogeny inferred from 75% complete concatenated UCE matrix #### File: SVDQuartets\_coalescent\_species\_trees.nexus **Description:** Phylogenetic relationships among the cave trechine beetles based on SVDQuartets coalescent species trees with 50% majority rule consensus for SVDQuartets #### File: Cave\_beetle\_aligned\_data\_matrices\_75\_UCE.nex **Description:** 75% complete concatenated and aligned UCE data matrix of cave trechine beetles from eastern North America #### File: Cave\_beetle\_aligned\_data\_matrices\_50\_UCE.nex **Description:** 50% complete concatenated and aligned UCE data matrix of cave trechine beetles from eastern North America ## Code/software FigTree (Rambaut 2010) Adobe Acrobat Reader Textedit/Notepad ## Access information Other publicly accessible locations of the data: * The sample voucher numbers, related meta-data, and raw Illumina sequencing reads are openly available at the NCBI Short-Read Archive (BioProject PRJNA894729; [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA894729](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA894729))