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

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 <i>Mellitidia</i>by Silas Bossert &amp; 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 <i>Mellitidia australis</i>, <i>Mellitidia gressitti</i>, <i>Mellitidia tomentifera</i>, <i>Ptilonomia plumosa</i>, and the newly described <i>Mellitidia glossata</i>. The assembly files were generated with SPAdes and are in fasta format.4. UCE_assemblies.zipThis archive contains the newly generated UCE assemblies of <i>Austronomia gracilipes</i>, <i>Melittidia horvathi</i>, <i>Mellitidia</i> sp., <i>Ptilonomia micheneri</i>, <i>Reepenia bidentata</i>, and <i>Reepenia triangulifera</i> (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.