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 (>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