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Dataset supporting Figure 3: Generalist/Specialist Analyses

dataset
posted on 2024-03-12, 21:57 authored by Dana OpulenteDana Opulente, Abigail LaBellaAbigail LaBella, Chris Todd HittingerChris Todd Hittinger, Antonis Rokas, Marie-Claire Harrison, John F. Wolters, Chao Liu, Jacek Kominek, Jacob SteenwykJacob Steenwyk, Margarida Silva, Carla GonçalvesCarla Gonçalves, Yuanning LiYuanning Li, Amanda Beth Hulfachor, Xiaofan ZhouXiaofan Zhou, Xing-Xing ShenXing-Xing Shen, Yonglin Li, Marizeth Groenewald

  

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

Funding

DIMENSIONS: Collaborative Research: The Making of Biodiversity Across the Yeast Subphylum

Directorate for Biological Sciences

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Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts

Directorate for Biological Sciences

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DIMENSIONS: Collaborative Research: The Making of Biodiversity Across the Yeast Subphylum

Directorate for Biological Sciences

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Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts

Directorate for Biological Sciences

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Great Lakes Bioenergy Research Center

Office of Biological and Environmental Research

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Hatch Project 1020204

History

Research Institution(s)

UW-Madison; Villanova; Vanderbilt; UNC Charlotte; Zhejiang U.; South China Agricultural U.; UC Berkeley; U. NOVA de Lisboa; Shandong U.; Zhejiang U.; Westerdijk Fungal Biodiversity Institute

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  • Yes

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  • Yes

Competing Interest Statement

J.L.S. is a scientific adviser for WittGen Biotechnologies and an adviser for ForensisGroup Inc. A.R. is a scientific consultant for LifeMine Therapeutics, Inc. J.K. is an employee of LifeMine Therapeutics, Inc. The other authors declare no other competing interests.