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 datamatrix (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 trees 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 trees 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. Out groups removed. Labels only show species\_genus. This treeset 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\_v8.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.