DOI: 10.5061/dryad.qv9s4mwtj
title: Data from: Phylogenomics and biogeography of the cleptoparasitic bee genus <em>Triepeolus</em> Robertson (Hymenoptera: Apidae), with a revised subgeneric classification of <em>Triepeolus</em> and its sister genus, <em>Epeolus</em> Latreille

description: Triepeolus Robertson (Hymenoptera: Apidae: Nomadinae) is the
 second-largest genus of cleptoparasitic apid bees in the world, but its
 evolutionary diversification through space and time has not been
 previously investigated. We present a dated phylogeny based on
 ultraconserved elements that includes 64 Triepeolus and 21 representative
 species of all seven other genera in the tribe Epeolini and propose a
 subgeneric classification for Triepeolus and its sister genus, Epeolus
 Latreille.
description: See the associated publication for additional details on
 methodology.
description: # Phylogenomics and biogeography of the cleptoparasitic bee genus
 *Triepeolus* Robertson (Hymenoptera: Apidae), with a revised subgeneric
 classification of *Triepeolus* and its sister genus, *Epeolus* Latreille
 **Assembled_contigs.zip:** Contigs generated for 84 epeoline bees and one
 brachynomadine bee through the genome assembly algorithm SPAdes
 implemented in the package phyluce (v1.7.3) (85 FASTA files in total).
 Summary statistics are provided in Table S1 of the associated publication.
 **BEAST_2_analysis_files.zip:** 100_percent_taxon_matrix_for_BEAST_2.nex:
 the concatenated matrix of 150 UCE loci (those with sequence data
 available for all specimens sampled for phylogenomic analysis) used to
 generate the input file (in BEAUti 2) for BEAST 2 analysis.
 BEAST_2_analysis.log: the resulting log file from analysis of
 BEAST_2_input_file.xml, which was imported into Tracer (v1.7.2) to assess
 convergence. BEAST_2_input_file.xml: the input file for BEAST 2 analysis
 through which the divergence times presented in the associated publication
 were estimated. **Files_for_BioGeoBEARS_analysis.zip:**
 BEAST_2_tree_for_BioGeoBEARS.newick: the version of the tree obtained from
 divergence dating analysis in BEAST 2 (in Newick format) that was read
 into R for biogeographic analysis with the package BioGeoBEARS.
 Geography_file.data: the file read into R for biogeographic analysis with
 the package BioGeoBEARS that indicates the known areas of occurrence for
 each terminal in the phylogeny presented in Figure 2 of the associated
 publication, with 0 indicating absence from an area and 1 indicating
 presence within an area. The four areas considered are Afroeurasia, the
 Antilles, North America (NAm), and South America (SAm).
 **SWSC-EN-partitioned_80_percent_taxon_matrix_after_Spruceup.zip:** The
 files generated using the Sliding-Window Site Characteristics method based
 on site entropies (SWSC-EN) implemented in the CURE pipeline and used to
 construct the final IQ-TREE 2 phylogeny presented in Figure 1 of the
 associated publication. **Tree_files.zip:**
 80_percent_taxon_matrix_after_Spruceup_coalescent_tree.tre: phylogeny of
 *Triepeolus* and other epeoline genera summarized from gene trees
 generated for 2,100 UCE alignments via ASTRAL-MP. This tree is presented
 in Figure S1 of the associated publication.
 80_percent_taxon_matrix_after_Spruceup_partitioned_by_UCE_region.treefile:
 phylogeny of *Triepeolus* and other epeoline genera based on 2,101 UCE
 loci (those with sequences available for at least 80% of the sampled taxa)
 partitioned using SWSC-EN and estimated via IQ-TREE 2. This tree is
 presented in Figure 1 of the associated publication, albeit without
 *Brachynomada* (the root) to greatly reduce the width of the figure.\
 80_percent_taxon_matrix_original_unpartitioned.treefile: preliminary
 phylogeny of *Triepeolus* and other epeoline genera based on 2,101 UCE
 loci (those with sequences available for at least 80% of the sampled taxa)
 considering each UCE as a different partition and estimated via IQ-TREE 2
 using the substitution model GTR+I+G. **Unpartitioned_matrices.zip:**
 80_percent_taxon_matrix_after_Spruceup.phylip: an unpartitioned
 concatenated matrix of 2,101 UCE loci (those with sequences available for
 at least 80% of the sampled taxa) generated through phyluce (v1.7.3) after
 additional trimming with Spruceup.
 80_percent_taxon_matrix_original.phylip: an unpartitioned concatenated
 matrix of 2,101 UCE loci (those with sequences available for at least 80%
 of the sampled taxa) generated through phyluce (v1.7.3).