DOI: 10.5281/zenodo.14982418
title: HSP90 mediates evolutionary capacitance of eye size via atonal in Tribolium

description: R Markdown files and Data sets for Manuscript: "Evolutionary Capacitor HSP90 mediates Adaptive Eye Size Reduction via atonal"

Authors: Rascha Sayed, Özge Şahin, Mohammed Errbii, Reshma R, Tobias Prüser, Lukas Schrader, Nora K. E. Schulz and Joachim Kurtz

The repository includes all R Markdown files and corresponding datasets (raw data in XLSX format) used to generate the manuscript's figures and statistical results. The files are organized in the same order as they appear in the manuscript. Each plot and statistical analysis can be reproduced using the raw data and the corresponding R script.

All Figuers and statistical analyses were performed in R (version 2024.04.2+764) using RStudio.



Markdown files:  


Each Markdown file is named according to its corresponding figure number and includes plots and statistical analysis results for each panel within that figure. The associated R scripts needed to generate the plots and perform the statistical analyses for each panel are also provided.



XLSX files: 


 The XLSX files are also named by figure number and contain sheets with all the raw data sets used for plotting and statistical analysis, as referenced in the corresponding Markdown file.



Compressed folders: 


These folders include the original photos displayed in the manuscript, named according to their corresponding figure numbers.



qPCR results: 


All qPCR results are uploaded in a compressed file titled "Extended Data Figure 2_qPCR_raw_data".



Extended Data Table 3.xlsx: Expansion of candidate region for eye phenotype. The original table in xlsx is attached here (file Nr. 19).


 

The repository contains the following items:

01. Figure-1_Markdown_file.html: contains plots, statistical analysis and R scripts for:



Percentage of reduced-eye phenotype after HSP90 inhibition,

Normalized eye area,

Average number of ommatidia, and

Number of adult offspring under continuous light.


02. Figure1_raw_data.xlsx: contains raw data used for:



Percentage of reduced-eye phenotype after HSP90 inhibition,

Normalized eye area,

Average number of ommatidia, and

Number of adult offspring under continuous light.


03. Figure 1_Original photos.zip: contains the original photos for reduced-eye phenotype after HSP90 inhibition.

04. Figure-2_Markdown_file.html: contains plots, statistical analysis and R scripts for:



Inheritance of the reduced-eye trait across successive generations,

Mendelian inheritance, and

Penetrance of the reduced-eye phenotype in offspring under continuous light.


05. Figure2_raw_data.xlsx: contains raw data used for: 



Inheritance of the reduced-eye trait across successive generations,

Mendelian inheritance, and

Penetrance of the reduced-eye phenotype in offspring under continuous light.


06. Figure 3_Original photos.zip: contains the original photos for reduced-eye phenotype after atonal knockdown.

07. Extended-Data-Figure-1_Markdown_file.html: contains plots, statistical analysis and R scripts for:



Percentage of abnormal phenotypes including reduced-eye phenotype after Hsp83 knockdown and 17-DMAG.


08. Extended Data Figure 1_raw_data.xlsx: contains raw data used for: 



Percentage of abnormal phenotypes including reduced-eye phenotype after Hsp83 knockdown and 17-DMAG.


09. Extended Data Figure 1_raw_data.zip: contains the original photos for reduced-eye phenotype after HSP90 inhibition_lateral view.

010. Extended-Data-Figure-2_Markdown_file.html: contains plots and R scripts for:



Relative eye size to body length in reduced-eye beetles (F1) first observed in the initial 17-DMAG experiment.


011. Extended Data Figure 2_raw_data.xlsx: contains raw data used for:



Relative eye size to body length in reduced-eye beetles (F1) first observed in the initial 17-DMAG experiment.


012. Extended Data Figure 2_Original photos.zip: contains the original photos for gonads after Hsp83 knockdown.

013. Extended Data Figure 2_ qPCR_raw_data.zip: contains raw data used for qPCR results_Hsp83 and Hsp68 genes.

014. Extended-Data-Figure-4_Markdown_file.html: contains plots, statistical analysis and R scripts for:



Normalized relative eye size,

Normalized Head area,

Normalized Body area, and

Developmental speed.


015. Extended Data Figure 4_raw_data.xlsx: contains raw data used for:



Normalized relative eye size,

Normalized Head area,

Normalized Body area, and

Developmental speed.


016. Extended-Data-Figure-6_Markdown_file.html: contains plots, statistical analysis and R scripts for:



Penetrance of reduced-eye phenotype following HDAC inhibitor treatment.


017. Extended Data Figure 6_raw_data.xlsx: contains raw data used for: 



Penetrance of reduced-eye phenotype following HDAC inhibitor treatment.


018. Extended Data Figure 7_Original photos.zip: contains the original photos for: Abnormal phenotypes in adults after larval and pupal knockdown for candidate genes using RNAi.

019. Extended Data Table 3.xlsx: Expansion of candidate region for eye phenotype.