Welcome to the repository for the Interspecific hybridization in insects in times of climate change book chapter

by

Rosa Ana Sánchez-Guillén, Luis Rodrigo Arce-Valdés, Andrea Viviana Ballén-Guapacha, Jesús Ordaz-Morales & Miguel Stand-Pérez

In this repository you will find raw literature search results, raw data and scripts for bioinformatic analyses for this book chapter. To have a quick view of supporting tables including all hybrid and barriers species pairs take a look at RawData_Summaries.xlsx.

Repository structure

Here is the structure of the directory of the book chapter, several folders of intermediary files have been gitignored. Within each folder bin includes the scripts that make up our general pipeline. Scripts in the bins folders are written either in bash or in R.

+-RawData_Summaries.xlsx					#This excel file contains summarized tables including all the species pairs and references we used in our chapter.
+---Linux									#Linux directory contains all scripts and results for figures and statistical testing.
|   +---01_Consensus						#Contains scripts to download and make a COI consensus sequence
|   |   +---bin
|   |   +---data
|   |   \---results
|   +---02_Genetic_Distances				#Contains scripts for the first set of figures included in the book chapter.
|   |   +---bin
|   |   \---figures
|   +---03_Additional_Species_Distances		#We needed to estimate genetic distances in some additional species. We did this directory for that.
|   |   +---bin
|   |   +---data
|   |   \---results
|   +---04_Barriers_vs_Distance				#In this directory we make analysis between reproductive isolation and genetic distance.
|   |   +---bin
|   |   +---data
|   |   \---results
|   +---05_Barriers_Calculation				#Now in this directory we plotted results from the previous directory.
|   |   +---bin								
|   |   \---figures
|   +---06_COIs_Meta						#We used this directory to create a list of all COI sequences access numbers we downoladed and used from BOLD and Genbank.
|   |   +---bin
|   |   +---data
|   |   \---results
|   +---07_Consequences						#Directory for consequences of hybridization plots.
|   |   +---bin
|   |   \---figures
|   \---08_Publication_BIAS					#Directory for figures for publication bias.
|       +---bin
|       +---data
|       \---figures
\---Windows									#In the windows directory we saved information on literature seraches, our results and filtering and raw data.
    +---Busquedas							#Our directory containing literature searches.
    |   +---Barriers						#This directory contains our results and data colection on reproductive barriers. 
    |   |   +---Diptera
    |   |   +---Hymenoptera
    |   |   +---Lepidoptera
    |   |   +---Odonata
    |   |   |   +---bin
    |   |   |   +---data
    |   |   |   \---results
    |   |   +---Odonata2
    |   |   \---Orthoptera
    |   +---Consequences					#This directory contains our results and data colection on hybridization consquences.
    |   +---Hybrid							#This directory contains our results and data colection on hybridization reports.
    |   |   +---Diptera
    |   |   +---Hymenoptera
    |   |   +---Lepidoptera
    |   |   +---Odonata
    |   |   +---Odonata2
    |   |   \---Orthoptera
    |   \---R								#This directory contains additional r scripts we used for analyse windows data.

Need help?

If you are seeing this repository and need to do something similar as in our book chapter feel free to email Luis Rodrigo.