Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae

GENERAL INFORMATIONThis repository contains supplementary files associated with the research articlePhylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinaeby Silas Bossert, Felipe V. Freitas, Alain Pauly, Gengping Zhu, David W. Crowder, Michael C. Orr, James B. Dorey, Elizabeth A. MurrayFor questions on the data of this paper please contact silas.bossert [at] wsu.eduThis repository consists of 6 files.###1. Shotgun_assemblies_Trinomia.zipThis archive contains the SPAdes assembly files of the newly generated whole genome sequence data for the following species: Gnathonomia aurata, Trinomia digitata, Trinomia natalensis, Trinomia tridentata, and Trinomia triodonta. Files are in 2bit format.###2. UCE_assemblies.zipThis archive contains the SPAdes assembly files of the newly generated UCE sequence data for Afronomia sjostedti and Trinomia cirrita.###3. UCE_extracts_of_shotgun_genome_data.zipThis archive contains the UCEs that were extracted from the whole genome assemblies using the Hymenoptera V2 probe set. The files are in fasta format.###4. Concatenated_sequence_matrix_and_partitions.zipThis archive contains the concatenated DNA sequence matrix of the 80% completeness matrix which was used for phylogenetic estimates, as well as the partition file as inferred by CURE and IQ-Tree2.###5. Tree_files.zipThis archive contains the phylogenies inferred through IQ-Tree2 and ExaBayes, as well as the phylogeny with divergence times estimates.###6. Occurrence_data.csvThis file contains the species occurrence data for the genus Trinomia, which was used for the occupancy modeling. As indicated in the ‘source’ column of the csv file, this data was generated through literature digitization and georeferencing of the Pauly (1999) study (‘Classification des Nomiinae africains. Le genre Trinomia Pauly (Hymenoptera Apoidea Halictidae’, Belgian Journal of Entomology, 1:101-136), the acquisition and georeferencing of new specimen data, and the extraction of records from the BeeBDC dataset (Dorey et al., 2023; ‘A globally synthesised and flagged bee occurrence dataset and cleaning workflow’, Scientific Data, 10:747).