HSP90 as an Evolutionary Capacitor Drives Adaptive Eye Size Reduction via atonal

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.

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. 019).

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 2.xlsx: Genome-wide analysis of allele frequency differences in T. castaneum. 

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

《HSP90作为进化电容器通过无刚毛基因（atonal）驱动适应性小眼尺寸缩减》（HSP90 as an Evolutionary Capacitor Drives Adaptive Eye Size Reduction via atonal）的配套R Markdown文件与数据集

作者：Rascha Sayed、Özge Şahin、Mohammed Errbii、Reshma R、Tobias Prüser、Lukas Schrader、Nora K. E. Schulz及Joachim Kurtz

本仓库包含用于生成该手稿图表与统计结果的全部R Markdown文件及对应数据集（原始数据格式为XLSX）。文件排布顺序与手稿中出现的顺序一致。借助原始数据与对应R脚本，可复现所有图表与统计分析过程。

所有图表与统计分析均在R（版本2024.04.2+764）中通过RStudio完成。

### Markdown文件
每个Markdown文件均以其对应的图表编号命名，包含该图表各子图的绘图与统计分析结果。同时提供了用于生成各子图绘图及执行统计分析的配套R脚本。

### XLSX文件
XLSX文件同样以图表编号命名，内含与对应Markdown文件中引用的全部绘图及统计分析所用原始数据的工作表。

### 压缩文件夹
此类文件夹包含手稿中展示的原始照片，命名规则与对应图表编号一致。

### qPCR结果
所有qPCR结果均上传至名为"Extended Data Figure 2_qPCR_raw_data"的压缩文件中。

### Extended Data Table 3.xlsx
眼表型候选区域的拓展分析。原始XLSX表格已作为本文件（编号019）附后。

本仓库包含以下内容：
01. Figure-1_Markdown_file.html：包含以下内容的绘图、统计分析及R脚本：
- HSP90抑制后小眼表型缩减比例
- 标准化小眼面积
- 平均小眼面（ommatidia）数量
- 持续光照条件下的成年子代数量
02. Figure1_raw_data.xlsx：包含以下内容的原始数据：
- HSP90抑制后小眼表型缩减比例
- 标准化小眼面积
- 平均小眼面数量
- 持续光照条件下的成年子代数量
03. Figure 1_Original photos.zip：包含HSP90抑制后小眼表型缩减的原始照片。
04. Figure-2_Markdown_file.html：包含以下内容的绘图、统计分析及R脚本：
- 连续多代中小眼表型缩减的遗传模式
- 孟德尔遗传规律
- 持续光照条件下子代小眼表型缩减的外显率
05. Figure2_raw_data.xlsx：包含以下内容的原始数据：
- 连续多代中小眼表型缩减的遗传模式
- 孟德尔遗传规律
- 持续光照条件下子代小眼表型缩减的外显率
06. Figure 3_Original photos.zip：包含经atonal敲低后小眼表型缩减的原始照片。
07. Extended-Data-Figure-1_Markdown_file.html：包含以下内容的绘图、统计分析及R脚本：
- 经Hsp83敲低及17-DMAG处理后，包括小眼表型缩减在内的异常表型比例
08. Extended Data Figure 1_raw_data.xlsx：包含以下内容的原始数据：
- 经Hsp83敲低及17-DMAG处理后，包括小眼表型缩减在内的异常表型比例
09. Extended Data Figure 1_raw_data.zip：包含HSP90抑制后小眼表型（侧面观）的原始照片。
10. Extended-Data-Figure-2_Markdown_file.html：包含以下内容的绘图及R脚本：
- 首次在17-DMAG初始实验中观察到的小眼缩减甲虫（F1代）的相对小眼面积与体长比值
11. Extended Data Figure 2_raw_data.xlsx：包含以下内容的原始数据：
- 首次在17-DMAG初始实验中观察到的小眼缩减甲虫（F1代）的相对小眼面积与体长比值
12. Extended Data Figure 2_Original photos.zip：包含经Hsp83敲低后生殖腺的原始照片。
13. Extended Data Figure 2_ qPCR_raw_data.zip：包含用于Hsp83与Hsp68基因qPCR结果的原始数据。
14. Extended-Data-Figure-4_Markdown_file.html：包含以下内容的绘图、统计分析及R脚本：
- 标准化相对小眼面积
- 标准化头部面积
- 标准化躯体面积
- 发育速率
15. Extended Data Figure 4_raw_data.xlsx：包含以下内容的原始数据：
- 标准化相对小眼面积
- 标准化头部面积
- 标准化躯体面积
- 发育速率
16. Extended-Data-Figure-6_Markdown_file.html：包含以下内容的绘图、统计分析及R脚本：
- 经HDAC抑制剂处理后小眼表型缩减的外显率
17. Extended Data Figure 6_raw_data.xlsx：包含以下内容的原始数据：
- 经HDAC抑制剂处理后小眼表型缩减的外显率
18. Extended Data Figure 7_Original photos.zip：包含经RNA干扰（RNAi）对候选基因进行幼虫期及蛹期敲低后成虫异常表型的原始照片。
19. Extended Data Table 2.xlsx：赤拟谷盗（Tribolium castaneum）全基因组等位基因频率差异分析结果。
20. Extended Data Table 3.xlsx：眼表型候选区域的拓展分析。