DOI: 10.5061/dryad.9kd51c5p5
title: Data for: Preliminary phylogenomic analyses reveal multiple reversions to nocturnal behavior and morphology within the primarily diurnal tribe Adesmiini (Coleoptera: Tenebrionidae)

description: The darkling beetle tribe Adesmiini (Tenebrionidae: Pimeliinae) is a
 prominent part of the African and western Palearctic desert faunas, with
 most species being day-active fast-running detritivores. Taxonomic
 diversity within the tribe is highest in the southern part of the
 Afrotropical realm (all genera present), while only the species-rich genus
 Adesmia occurs north of the Sahara. Despite containing conspicuous diurnal
 species, such as the fog-basking beetle Onymacrisunguicularis (a focal
 taxon in ecological research for decades), Adesmiini has undergone few
 modern taxonomic or phylogenetic studies. Hence, generic concepts and the
 evolution of diurnal behaviors and morphologies, rare in the primarily
 nocturnal family Tenebrionidae, remain poorly explored. To investigate
 evolutionary relationships and the origin of diurnal activity within the
 tribe, a genomic dataset of 529 protein-coding genes across 43 species
 spanning 10 of 11 Adesmiini genera was assembled and analyzed. The
 resulting phylogeny for the tribe does not support the monophyly of many
 current Adesmiini genera (i.e. Adesmia, Metriopus, Onymacris, Physadesmia,
 and Stenocara). Ancestral state reconstruction of diurnal activity, using
 eye shape as a proxy and supplemented by literature and collection
 records, supports the hypothesis that Adesmiini were primitively diurnal,
 followed by at least four shifts to nocturnal or crepuscular activity.
description: Specimens used in this study were collected by the authors in
 Namibia or South Africa (permits in acknowledgements) or contributed by
 collaborators. Identifications were made using publications of Penrith
 (1979, 1986), Koch (1944), or Reitter (1916) and comparisons to identified
 material, primarily in the Ditsong Museum of Natural History (Pretoria,
 South Africa). Voucher specimens from DNA extractions are preserved in the
 Purdue Entomological Research Collection with unique identifiers (TB#s)
 tied to sequence data in the Sequence Read Archive (NCBI-SRA). Photographs
 of selected specimens were taken using a Canon 1000D body with extension
 rings and a Canon Macro Lens EF 100 mm. Scanning microscope (SEM) images
 were obtained with a Hitachi S-3400N system in the Museum and Institute of
 Zoology, PAS (Warsaw, Poland). Resulting shots were subsequently colored
 in Adobe Photoshop (ver. 21.0.1). DNA extractions were
 performed on 43 adesmiine and 11 outgroup specimens by disarticulating the
 head from the body and, in most cases, coxa from the thorax for soft
 tissue digestion. Large specimens (&gt;15mm) also had their thoracic
 cavity scraped for additional muscle tissue. Tissue digestion and DNA
 extraction were conducted using QIAGEN DNEasy Blood and Tissue kits. An
 Invitrogen Qubit dsDNA assay was used to determine the DNA concentration
 in extractions and those with a DNA mass of over 1,000 ng were applicable
 for sequencing. Adesmiine samples, except for Stenocara gracilis Solier,
 1835 and the outgroup taxa, were then sent to Daicel Arbor Biosciences for
 library preparation, targeted enrichment using custom MyBaits probes
 designed to capture 631 genetic loci from Pimeliinae (Kanda 2017), and DNA
 sequencing on a NovaSeq 6000 system for 150 bp paired end runs. Library
 preparation and targeted enrichment were done inhouse for Stenocara
 gracilis and some outgroup species using NEBNext® Ultra™ DNA Library Prep
 Kits for Illumina and the same MyBaits custom probe kit was used to
 capture 631 loci. Inhouse libraries were sequenced at the University of
 Arizona’s Genomic and Technology Core Facility (UAGC) on an Illumina
 NextSeq 550 using 150 bp paired end runs. 
description: # Preliminary phylogenomic analyses reveal multiple reversions to
 nocturnal behavior and morphology within the primarily diurnal tribe
 Adesmiini (Coleoptera: Tenebrionidae) --- The darkling beetle tribe
 Adesmiini (Tenebrionidae: Pimeliinae) is a prominent part of African and
 western Palearctic desert faunas, with most species being day-active
 fast-running detritivores. Taxonomic diversity within the tribe is highest
 in the southern Afrotropical realm (where all genera are present); only
 one genus, the species-rich Adesmia, occurs north of the Sahara. Despite
 notable species, such as the fog-basking beetle Onymacris unguicularis (a
 focal taxon in desert ecological research), Adesmiini has undergone few
 modern taxonomic or phylogenetic studies. Hence, generic concepts and
 pronounced diurnal activity, rare in the primarily nocturnal family
 Tenebrionidae, remain poorly explored. To investigate evolutionary
 relationships and diurnal origins within the tribe, we generated a genomic
 dataset of 529 protein-coding genes across 43 species spanning 10 of 11
 Adesmiini genera. Our resulting phylogeny for the tribe rejects the
 monophyly of five currently recognized Adesmiini genera (i.e., Adesmia,
 Metriopus, Onymacris, Physadesmia, and Stenocara). Ancestral state
 reconstruction of diurnal activity using eye shape as a proxy supports the
 hypothesis that Adesmiini were primitively diurnal, followed by at least
 four shifts to nocturnal or crepuscular activity. Specimens used in this
 study were collected by the authors in Namibia or South Africa (permits in
 acknowledgements) or contributed by collaborators. Identifications were
 made using publications of Penrith (1979, 1986), Koch (1944), or Reitter
 (1916) and comparisons to identified material, primarily in the Ditsong
 Museum of Natural History (Pretoria, South Africa). Voucher specimens from
 DNA extractions are preserved in the Purdue Entomological Research
 Collection with unique identifiers (TB#s) tied to sequence data in the
 Sequence Read Archive (NCBI-SRA). Photographs of selected specimens were
 taken using a Canon 1000D body with extension rings and a Canon Macro Lens
 EF 100 mm. Scanning microscope (SEM) images were obtained with a Hitachi
 S-3400N system in the Museum and Institute of Zoology, PAS (Warsaw,
 Poland). Resulting shots were subsequently colored in Adobe Photoshop
 (ver. 21.0.1). DNA extractions were performed on 43 adesmiine and 11
 outgroup specimens by disarticulating the head from the body and, in most
 cases, coxa from the thorax for soft tissue digestion. Large specimens
 (&gt;15mm) also had their thoracic cavity scraped for additional muscle
 tissue. Tissue digestion and DNA extraction were conducted using QIAGEN
 DNEasy Blood and Tissue kits. An Invitrogen Qubit dsDNA assay was used to
 determine the DNA concentration in extractions and those with a DNA mass
 of over 1,000 ng were applicable for sequencing. Adesmiine samples, except
 for Stenocara gracilis Solier, 1835 and the outgroup taxa, were then sent
 to Daicel Arbor Biosciences for library preparation, targeted enrichment
 using custom MyBaits probes designed to capture 631 genetic loci from
 Pimeliinae (Kanda 2017), and DNA sequencing on a NovaSeq 6000 system for
 150 bp paired end runs. Library preparation and targeted enrichment were
 done inhouse for Stenocara gracilis and some outgroup species using
 NEBNext Ultra DNA Library Prep Kits for Illumina and the same MyBaits
 custom probe kit was used to capture 631 loci. Inhouse libraries were
 sequenced at the University of Arizonas Genomic and Technology Core
 Facility (UAGC) on an Illumina NextSeq 550 using 150 bp paired end runs.
 ## Description of the data and file structure This data is raw paired end
 reads from the Illumina runs. Each zipped file contains a pair of reads
 for one sample. Samples can be identified by their identification code
 (TB#) which corresponds with the identification code in the paper. ##
 Sharing/Access information This is a section for linking to other ways to
 access the data, and for linking to sources the data is derived from, if
 any. Links to other publicly accessible locations of the data: *None Data
 was derived from the following sources: *This is the raw data derived from
 paired end Illumina sequencing. ## Code/Software The following software is
 used to process this data: Trimmomatic SPAdes HybPiper (pipeline) MAFFT
 trimAl FASConCAT IQTREE2