Dataset supporting Figure 2: Phylogenomics

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.This item includes raw and underlying data associated with Figure # 2 in the manuscript. Input files and results from the construction of the phylogenetic tree of the Saccharomycotina subphylum.Each item contains a README.txt file that gives specific details on the analysis, file structure, and folder structure.y1000p_1403_OG_files.tar.gz - The 1403 ortho groups used to construct the phylogeny of the subphylum1154yeasts_1403OGs_ml_timetree.tree - Tree file containing the time tree calibrated phylogeny1154yeasts_1403OGs_ml_timetree_times.txt - File containing the estimated times associated with the time tree1175taxa_1403OGs_iqtree_ML_rooted.nex - Nexus tree file containing the rooted tree file used in Figure 2 and the supplemental tree file1175taxa_1403OGs_astral_length_rooted_lpp_added.tre - Tree file containing the yeast phylogeny estimated using ASTRAL1000_strip*.txt - iTOL (itol.com) files to identify the isolation environment of the strains. itol_color_strip.txt - Add colors to the tree in iTOLALL_NAMES_FILE.xlsx - The names on the tree have been adjusted to reflect the most recent naming conventions (as of November 2023). This file contains the matching names across the dataset, including earlier versions of the phylogenetic trees which were used for some analyses