DOI: 10.5281/zenodo.16104778
title: HSP90 as an Evolutionary Capacitor Drives Adaptive Eye Size Reduction via Atonal

description: R Markdown files and Data sets for Manuscript: "HSP90 as an Evolutionary Capacitor Drives 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.





The repository contains the following items:



 

00. READ ME: For detailed descriptions of the raw data, original photos, tables, figures, and analysis items included in the repository, please refer to the accompanying "READ ME" Word file; these items are also listed below.

Figure-1:

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.

Figure-2:

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.


Figure 3:

06. Fig. 3_RNe_RRe_DNe_DRe.covFiltered.edited.fet: contains raw data used for the gentic analysis

07. Fig. 3_R_script: contains R scripts used for the gentic analysis

08. Fig 3_code: contains codes used for the gentic analysis

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

10. Fig.3f_qPCR_ato in diff lines: contains raw data used for qPCR results

11. Fig.3g_qPCR_ato after Hsp83kd: contains raw data used for qPCR results

Extended-Data-Figure-1:

12. 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.


13. 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.


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

Extended-Data-Figure-2:

15. 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.


16. 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.


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

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

Extended-Data-Figure-4:

19. 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.


20. 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.


 Extended-Data-Figure-6:

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



Penetrance of reduced-eye phenotype following HDAC inhibitor treatment.


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



Penetrance of reduced-eye phenotype following HDAC inhibitor treatment.


Extended Data Figure 7:

23. 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.

24. Extended Data Figure 8.pdf: IGV visualization of alignment files from the four pooled samples analyzed in this study.

25. Extended Data Figure 9.pdf: Genome browser view of the 100 kb candidate region showing transcription factor binding motifs identified by MEME.

26. Extended Data Table 2.xlsx: Genome-wide analysis of allele frequency differences in T. castaneum. 

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