jahanisrat / WolpertHypothesis

Code to support data analysis for manuscript (doi.org/10.1101/2024.05.12.593719)

Testing the coordination hypothesis: incompatibilities in experimentally evolved asocial amoeba in the absence of a single-cell bottleneck

Author Information

1. Name: Israt Jahan Institution: Washington University in St. Louis Email: [e-mail]
2. Name: Trey J. Scott Institution: Washington University in St. Louis Email: [e-mail]
3. Name: Joan E. Strassmann Institution: Washington University in St. Louis Email: [e-mail]
4. Name: David C. Queller Institution: Washington University in St. Louis Email: [e-mail]

README last updated on 22 June 2024

GENERAL INFORMATION

Date of data collection: 2022-2023

Geographic location of data collection: Washington University in St. Louis, USA

Information about funding sources that supported the collection of the data:

NSF DEB-1753743 and DEB-2237266 
I. J. was additionally supported by a Ph.D. fellowship from the
McDonnell International Scholars Academy, WUSTL.

DATA & FILE OVERVIEW

To recreate all the plots in the manuscript, just run the reproduce.R file located at the project root.

Folder List: data/ All the excel sheets contained data from the images reside here.

scripts/ This is where all the scripts for the project are. They should be run in the order listed. For example, 1_setup.R should be run before running 2_theme.R

figs/ All plots in the manuscript (Figures 4 through 8) are in this folder. They were generated with the script figs.R in the folder above.

Raw Images: Raw images from which the excel sheets were generated in the data folder above are compressed and uploaded on Zenodo(10.5281/zenodo.12460200). The folder contains two zip files:

1. PairwiseMixtures.zip has raw and processed images from the first experiment with 10 Clones.
2. ComplexMixtures.zip has raw and processed images from the second experiment with 3 Clones.

These are huge files so unzip in a directory with at least 5GB space!

Relationship between files, if important:

All scripts read in the appropriate files from data folder. Running the script reproduce.R at the project root will source all other scripts in the necessary order, and recreate all the figures in the folder figs.

Additional related data collected that was not included in the current data package: NONE

DATA-SPECIFIC INFORMATION:

Pairwise Mixtures: a. Number of Treatments: 3 b. Number of QS Clones: 10 c. Number of experimental lines per clone: 7 d. Number of plates/rows: 210

Complex Mixtures: a. Number of Treatments: 2 b. Number of QS Clones: 3 c. Number of plates/rows: 90

Links/relationships to ancillary data sets:

Ancestral clones and experimentally evolved lines were obtained the following paper:

Larsen, T. J., Jahan, I., Brock, D. A., Strassmann, J. E., & Queller, D. C. (2023).
Reduced social function in experimentally evolved Dictyostelium discoideum implies selection for social conflict in nature.
Proceedings of the Royal Society B, 290(2013), 20231722

Recommended citation for this dataset: zenodo link will be updated here.

METHODOLOGICAL INFORMATION

Instrument or software-specific information needed to process and interpret the data:

Plate photographs were taken with a Canon EOS 5D Mark III camera using the Adobe Lightroom software and analyzed using the ImageJ software.

Data analyis was originally done in R (version 4.2.1 (R Core Team, 2022) in the IDE RStudio (2018). Following a security issues with R in 2024. R version was updated to v4.4 and all installed packages were upgraded accordingly. The repository has an associated renv that allows packages and other environment specific information to be isolated and reproducible.

SHARING/ACCESS INFORMATION

Licenses/restrictions placed on the data: NONE

Links to publications that cite or use the data: forthcoming

Links to publicly accessible locations of the data: https://github.com/jahanisrat/WolpertHypothesis/

Are there multiple versions of the dataset? Yes/No A. If yes, name of file(s) that was updated: i. Why was the file updated? ii. When was the file updated?

Note that the title of the manuscript has changed from the first version of this manuscript which was submitted to bioRxiv in May 2024.

Non-selected incompatibilities and their effects on aggregative multicellularity in the social amoeba Dictyostelium discoideum.
 Israt Jahan, Trey J. Scott, Joan E. Strassmann, David C. Queller bioRxiv 2024.05.12.593719; doi: https://doi.org/10.1101/2024.05.12.593719

NOTE: This README.md file was first generated on 2024-05-02 by Israt Jahan (modified from Trey J. Scott)