Antiquity of obligate dim-light foraging in nomiine sweat bees (Hymenoptera: Halictidae), with the description of a new species of Mellitidia

GENERAL INFORMATIONThis repository contains supplementary files associated with the research articleAntiquity of obligate dim-light foraging in nomiine sweat bees (Halictidae: Nomiinae), with the description of a new species of Mellitidiaby Silas Bossert & Simon M. TierneyFor questions on the data of this paper contact silas.bossert [at] wsu.eduThis repository consists of nine (9) files.###1. BEAST2_chronogram.pdfThis is the maximum clade credibility tree (MCC) of the Bayesian divergence time estimation using BEAST2. The dates are in millions of years (Ma). The file is a print out of the chronogram; the nexus file with the MCC output can be found in the Supplementary_Chronograms.zip archive.###2. 80p_ML_phylogeny_with_branchlengths.pdfThis is the phylogeny that was inferred through IQ-Tree2 and the 80% completeness matrix (see article for details). This is a Pdf printout of the the phylogeny; the newick string can be found under in the Supplementary_phylogenies.zip archive. Support values show Shimodaira-Hasegawa-like approximate likelihood ratio tests and ultrafast bootstraph replicates (SH-aLRT / UFBoot2).###3. WGS_assemblies.zipThis archive contains whole genome sequence data of the five sampled species of Nomiinae, namely Mellitidia australis, Mellitidia gressitti, Mellitidia tomentifera, Ptilonomia plumosa, and the newly described Mellitidia glossata. The assembly files were generated with SPAdes and are in fasta format.4. UCE_assemblies.zipThis archive contains the newly generated UCE assemblies of Austronomia gracilipes, Melittidia horvathi, Mellitidia sp., Ptilonomia micheneri, Reepenia bidentata, and Reepenia triangulifera (cf). The assemblies were generated with SPAdes and are in fasta format.###5. Concatenated_sequence_matrices_and_partitions.zipThis archive contains the six concatenated DNA sequence matrices used for phylogenetic estimates and for the dating analyses. Specifically, it contains the 80%, 90%, and 95% completeness matrices, as well as the three subsets of each 100 random loci which were used for divergence times estimates. For all alignments, we provide partition files.###6. Barcode_COI_alignment.fastaThis COI barcode alignment that was generated in the present study. Detail on the specific processing can be found in the main manuscript. The file format is fasta.###7. Supplementary_phylogenies.zipThis archive contains the newick strings for the final ML trees calculated from the 80%, 90%, and 95% completeness matrices. Support values show Shimodaira-Hasegawa-like approximate likelihood ratio tests and ultrafast bootstraph replicates (SH-aLRT / UFBoot2).###8. Supplementary_Chronograms.zipThis archive contains the nexus files for the seven separate dating analyses.###9. Beastrun_100_random_loci.xmlThis file is the XML input file for the BEAST2 analyses that were carried out in the article. The file was generated with BEAUTi.