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Data set contains:

=====Assembly_graphs.zip=====
Assembly graph outputs from SPades genome assembly in .gfa format. These asseembly graphs were used as input for the DNA barcode extraction using PATHRacer (see methods for paramaters).

=====Assembly_scaffolds.zip=====
Assembled genome assembly scaffolds from SPades. These draft metagenome assemblies where used for down stream phylogenetic analysis and protein preductions (see methods for paramaters).

=====Protein_predictions_of_Psilocybin_producing_taxa.zip=====
Protein predictions in GFF format for pislocybin-producing taxa. Proteins predections were perfomred on bioinformatically reduced genomes (from diploid to haploid) using Redundands. Profiles were generated using the Program Augustus (see methods for paramaters).

=====Raw_phylogenetic_trees.zip=====

==Mega11_calibration_tests==
Time divergence trees and mega analysis environments(see methods for paramaters)

=LSU tree=
Divergence analysis for LSU species tree

Multiple sequence alignment (mafft_alignment.fasta), gene tree output from iqtree (.tre), Mega11 tree output (.nwk), and full Mega11 sesion file (.MTSX).

=Psilocybe top100 tree=
Divergence analysis for the Psilocybe species tree

Multiple sequence alignment (mafft_alignment.fasta), gene tree output from iqtree (.tre), Mega11 tree output (.nwk), and full Mega11 sesion file (.MTSX).

==Phylogenomic_trees==
Unaltered phylogenetic trees for each analysis, main and supplementary (see methods for paramaters)

=Figure_2=
raw tree file output from iqtree for only the psilocybe species used in figure 2.

=Figure_3=
mafft sequence alignment and raw tree file output from iqtree for samples used in PsiD analysis in figure 3. Also Includes PDF files with full PsiD contig infromation, and with clean labels that only include sample name.

=constraint4=
Raw tree output from iqtree for psilocybe that was used as the constraint tree for all public barcode data found in supplementary figures.

==Psilocybin_cluster_gene_trees==

Mafft alignments used for each individual Psi cluster gene tree (see methods for paramaters).

Raw tree output from iqtree or each individual Psi cluster gene tree (see methods for paramaters).

PDF file with tip labels only presenting sample names.

==Supplementary figure phylogenetic trees==
=Alignments=
Mafft alignments used for each public barcode gene tree (see methods for paramaters).

=Trees=
Raw tree output for all supplementary figures (see methods for paramaters).

=====ASR.zip=====
Input and output data used for ansectral state reconstruction (ASR) (see methods for paramaters). Includes the input tree and states, as well as the alter output file to remove outgroups from the phylogenetic tree. Also includes the ASR outputs altered to be compatible with Tracer.

=====Supplementary_tables.zip=====
This directory contains supplementary tables 1-r

Supplementary Table 1: Voucher table of Specimens

Voucher table of all specimens sequenced and analyzed. Table include relevant voucher information, current name designation, and SRA and BioSample accession numbers.

Supplementary Table 2: Genome assembly and BUSCO stats for each specimen

Genome assembly statistics, and BUSCO complete gene recovery from the Agaricales_db10 database.

Tab 1: Psilocybe
Includes Psilocybe s.s. taxa from this study

Tab2: Non-Psilocybe
Taxa found to not be Psilocybe s.s. from this study

Supplementary Table 3: RBB gene numbers, contigs, clustering results, and RBB method comparison to Exonerate
Gene and cluster recovery comparison of Reciprocal Best Blast and Exonerate methodology.

Tab1: Augustus gene prediction
Results for Psi cluster gene prediction using Augustus and RBB (reverse best blast) approach.

Tab2: Exonerate protein alignment
Results for Psi cluster gene prediction using Exonerates protein2genome function

Tab3: Augustus-Exonerate comparison
Comparison of Augustus and Exonerate output for gene prediction and contig placement.

Supplementary Table 4: Toplogy constraint testing: Individual model results
Individual model results model results and +/- symbols to indicate significance.

=====Supplementary_Information_and_Figures.zip=====

====Figures_full_resolution.zip====
High resolution copies of Figures 1-3 in both PDF and PNG format.
PDF file including all supplementary results and discussion along with supplementary table and figue legends.
PDF file Including all supplementary figures.

=====MSA_stats.zip=====
Multiple sequece alignment statistics generatned for the Psilocybe only data set used for Summary coalescent and concatened phylogenetic analysis. Stats files were generated using AMAS.py (see methods for paramaters).

=====PsiD_topology_test.zip=====
Toplogy constraint testing for HGT in Panaeolus and Pholiotina(see methods for paramaters).

==Constrained_tree==
Full IQtree directory output for PsiD Constrained tree analysis

==Unconstrained_tree==
Full IQtree directory output for PsiD unconstrained tree analysis

==Combined==
Full IQtree directory output for combined PsiD unconstrained toplogy constraint testing analysis