Dataset supporting Figure 3: Generalist/Specialist Analyses

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 3 in the manuscript. 

These items were used to assess the evolution and frequency of the generalist and specialist niche breadth in the budding yeasts.

Each item includes a README.txt file that includes specific information about the analysis, file structure, and folder structure. 

bayes_carb_v_class_coevolution.tar.gz  - Bayestraits outputs to compare gain and loss of carbon metabolism traits in generalist and specialist backgrounds. Includes data shown in Fig 3D
bayes_carbon_nitrogen_coevolution.tar.gz - Bayestraits outputs for the analysis that modeled co-evolution between carbon and nitrogen breadth. Data discussed in the manuscript
 carbon_breadth_reconstruction.tar.gz - Bayestraits ancestral reconstruction of carbon breadth
 CarbonNitrogen_Classifications.zip - Data file containing information about carbon and nitrogen classifications