DOI: 10.5061/dryad.80gb5mkw1
title: A supermatrix phylogeny of the world’s bees (Hymenoptera: Anthophila)

description: The increasing availability of large molecular phylogenies has provided
 new opportunities to study the evolution of species traits, their origins
 and diversification, and biogeography; yet there are limited attempts to
 synthesise existing phylogenetic information for major insect groups. Bees
 (Hymenoptera: Anthophila) are a large group of insect pollinators that
 have a worldwide distribution, and a wide variation in ecology,
 morphology, and life-history traits, including sociality. For these
 reasons, as well as their major economic importance as pollinators,
 numerous molecular phylogenetic studies of family and genus-level
 relationships have been published, providing an opportunity to assemble a
 bee ‘tree-of-life’. We used publicly available genetic sequence data,
 including phylogenomic data, reconciled to a taxonomic database, to
 produce a concatenated supermatrix phylogeny for the Anthophila comprising
 4,586 bee species, representing 23% of species and 82% of genera. At
 family, subfamily, and tribe levels, support for expected relationships
 was robust, but between and within some genera, relationships remain
 uncertain. Within families, sampling of genera ranged from 67–100% but
 species coverage was lower (17–41%). Our phylogeny mostly reproduces the
 relationships found in recent phylogenomic studies with a few exceptions.
 We provide a summary of these differences and the current state of
 molecular data available and its gaps. We discuss the advantages and
 limitations of this bee supermatrix phylogeny (available online at
 beetreeoflife.org), which may enable new insights into long-standing
 questions about evolutionary drivers in bees, and potentially insects more
 generally.
description: METADATA A supermatrix phylogeny of the world's bees (Hymenoptera:
 Anthophila) Patricia Henriquez-Piskulich*, Andrew F. Hugall*, Devi
 Stuart-Fox *A.F.H and P.H.-P. contributed equally to this work. File:
 Almeida75p_TV74j90c7_RAxML_bipartitions.result.pdf Description: PDF figure
 of RAxML tree of our subset 'stub' of Almeida_75p_completeness
 UCE data matrix (with bootstrap support values). File: BEE_mat7_520BT.zip
 Description: Full 4,591 species 44,780 site supermatrix in phylip format
 (compressed). Includes outgroups. Note species labels also include
 information on number of nuclear and mitochondrial genes (n#m#), and
 family. Information on the data and partitions is in BEE_Supp_file3. File:
 BEE_mat7_fulltree.nwk Description: All 4,591 species tree with ultrafast
 bootstrap node support values. Assembled from IQTree analyses of the three
 family subsets. Includes outgroups. Note species labels include gene
 numbers (n#m#) and family. File: BEE_mat7_fulltree_tplo35_sf20lp.nwk
 Description: All 4,586 bee species tree converted to dated chronogram with
 treePL, including ufbs node support values. Outgroups removed. File:
 BEE_MAT7_GENE_ALIGNS.zip Description: Folder with the 13 individual
 'gene' alignments for all taxa in our database, prior to
 trimming of sites (compressed). FASTA format with consensus first
 sequence. File: BEE_mat7_IQTufbs_tplo_1001bin.zip Description: The all
 4,586 bee species chronogram tree plus 1,000 bootstrap samples treePL
 transformed. First tree in the file is the maximum likelihood version.
 Outgroups removed. Labels only show species_genus. This tree set is also
 available online at beetreeoflife.org. File:
 BEE_mat7gen_IQTufbs_tplo_med.tre Description: TreeAnnotator MCC summary
 tree of treePL transformed genus representative tree bootstrap samples.
 Outgroups removed. File: BEE_mat7gen_p8pmAa_fst.nwk Description: The 428
 bee genus representative tree, with ufbs node support values. Includes
 outgroups. Bee taxa labels show genus_species~~family~~subfamily~tribe.
 File: BEE_script_v9.sh Description: Assorted Bash and R scripts used to
 assist in supermatrix construction and checking. File: BEE_Supp_file1.xlsx
 Description: Taxonomic database to reconcile nomenclature of molecular
 data. Column headers sheet taxonomy_database: * previous_binom: previous
 recognised species name * final_binom: current species name * ref_comment:
 reference for nomenclature decision * Column headers sheet systematics: *
 Family: family taxonomic rank * Subfamily: subfamily taxonomic rank *
 Tribe: tribe taxonomic rank * Genus: genus taxonomic rank File:
 BEE_Supp_file3.xlsx Description: Supermatrix data summary. Column headers:
 * BEE_mat7_520BT: species cumulative count * label: working label in
 trees, showing nuclear/mito genes, and family * final-taxonomy: final
 species taxonomy * family: family of the species * subfamily: subfamily of
 the species * genus: genus of the species * genes: number of data elements
 ("genes") * bases: total number of aligned nucleotide base
 characters (IUPAC code) * sites: total length of th aligned supermatrix *
 p-sites: proportion of site with bases * ex-stub: proportion of site with
 bases, ignoring the PG stub DATA SOURCE-&gt;: columns to the right
 indicate data source * Phylogenomic stub: source data of the phylogenomic
 stub * UCE STUB: source data of the UCE stub * ArgK: accession number ArgK
 gene * CAD: accession number CAD gene * NaK: accession number NaK gene *
 Pol II: accession number Pol II gene * Wnt-1: accession number Wnt-1 gene
 * LW Rh: accession number LW Rh gene * EF-1a: accession number EF-1a gene
 * 28S rDNA: accession number 28S rDNA gene * 16S rDNA: accession number
 16S rDNA gene * COI: accession number COI gene * CYTB: accession number
 CYTB gene BASES-&gt;: columns to the right indicate number of aligned
 nucleotide base characters (IUPAC code) per source * PG stub: number of
 aligned nucleotide base characters (IUPAC code) of the phylogenomic stub *
 UCE STUB: number of aligned nucleotide base characters (IUPAC code) of the
 UCE stub * ArgK: number of aligned nucleotide base characters (IUPAC code)
 of the ArgK gene * CAD: number of aligned nucleotide base characters
 (IUPAC code) of the CAD gene * NaK: number of aligned nucleotide base
 characters (IUPAC code) of the NaK gene * Pol II: number of aligned
 nucleotide base characters (IUPAC code) of the Pol II gene * Wnt-1: number
 of aligned nucleotide base characters (IUPAC code) of the Wnt-1 gene * LW
 Rh: number of aligned nucleotide base characters (IUPAC code) of the LW Rh
 gene * EF-1a: number of aligned nucleotide base characters (IUPAC code) of
 the EF-1a gene * 28S rDNA: number of aligned nucleotide base characters
 (IUPAC code) of the 28S rDNA gene * 16S rDNA: number of aligned nucleotide
 base characters (IUPAC code) of the 16S rDNA gene * COI: number of aligned
 nucleotide base characters (IUPAC code) of the COI gene * CYTB: number of
 aligned nucleotide base characters (IUPAC code) of the CYTB gene * NOTES:
 notes regarding column headers BEE_mat7 gene site table: gene site summary
 of file BEE_mat7 gene site table * part: section of the file * sites:
 total length of the aligned supermatrix * start: where the section starts
 * end: where the section ends * gene: gene or stub belonging to the
 section File: BSFPPsu94_TV74c7v2_nn.treefile.pdf Description: PDF figure
 of IQ-Tree tree of our composite UCE stub, with bootstrap support. Labels
 denote taxa from the five original datasets.