Trait data for the evolution of plasticity in pairwise competitive and mutualistic community of brewer's yeast
Data files
Sep 10, 2024 version files 520.04 KB
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README.md
1.68 KB
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YeastPP_Data.xlsx
518.37 KB
Abstract
Phenotypic plasticity allows organisms to change their phenotypes in response to changing local conditions quickly in order to better function. Plasticity in response to abitoic factors such as temperature, light, and salinity for example have been well documented. What is less clear is how species interactions can influence the evolution of phenotypic plasticitiy as species adapt and interact with one another. To study this question we used a synthetic mutualism based on genetically modified brewer's yeast (Saccharomyces cerevisiae) that overproduce a certain resource but cannot produce one needed by its partner strain. In this study system, we paired one yeast strain that overproduces adenine, but cannot produce lysine, and another strain that overproduces lysine but cannot produce adenine. When placed together in media they can cross feed one another and form a mutualism. We also paired strains that just had a knockout for adenine or lysine under competition. The goal of the study was to examine how phenotypic plasticity in growth rate and resource use efficiency changed after four weeks of evolution in continuous culture.
We compared changes in growth rate, resource use efficiency and their plasticity for strains grown alone or with a mutualistic or competitive partner. Strains grown with a competitor had changes in growth rate, while those grown with a mutualist had changes in resource use efficiency. Plasticity for these traits changed very little, suggesting that there was not strong selection on plasticity evolution. This dataset and R code used to analyze the evolution of growth rate and yield and their plasticities from pairwise communities of brewer's year evolved with a competitor or mutualist partner strain.
README: Trait data for the evolution of plasticity in pairwise competitive and mutualistic community of brewer's yeast
https://doi.org/10.5061/dryad.5qfttdzgf
Description of the data and file structure
Strains of genetically engineered brewer's yeast we evolved alone, with a competitor strain, or with a mutualist strain for four weeks. Strains were then phenotyped for growth rate, yield and plasiticity in these traits.
Files and variables
File: YeastPP_Data.xlsx
Description: Data used in statistical comparisons
Variables
- strain-- strain identification number
- adelyse-- does strain make adenine or lysine
- wo-- OP is overproduction and WT is wildtype production
- marker-- null alleles for histine or leucine to use in selective plating
- plateN-- which deepwell plate was strain evolved in
- location-- row and column information for well in deepwell plate
- genotype--which strains were growing in well
- treatment-- growth in 0.1X or 0.6X media, -F media type were not used in publication
- date
- week-- week since starting evolution experiment
- ancestral-- ancestral or evolved version of strain
- block-- measurement block
- b_location-- row and column location for deepwell
- growthenv-- type of media grow in for pheonotyping
- cultureID-- unique identifier for replicate of a strain
- growth--number of hours of growth before measurement
- spec-- reading from spectrophotometer * 100
- dilution-- dilution factor
- od-- reading from spectrophotometer
- note-- additional observations
- Missing data code: NA
Code/software
R statistical package and indicated libraries in R code
Methods
Yeast strains were evolved for 4 weeks either alone, or with a competitor or mutualist strain. Each strain was then phenotyped for growth rate and yield in low and high nutrient environments by assessing population via optical density. Data were entered into MS Excel and used in R statistical software to evaluate the amount of change in traits and their plasticity.