Rapid evolution of mitochondrion-related genes in haplodiploid arthropods

Sequences and Scripts used in the paper to estimate evolutionary rates and bootstrap analysis

step0_sequences

This directory contains sequences used in the paper, including:

a. Amino acid sequences of mitochondrial genes can be found under ./step0_sequences/

b. Amino acid sequences of nuclear genes

Due to the size limit of GitHub, the two nuclear gene files (arthropoda-seqs-all.zip and arthropoda-ortho-groups.txt) can be found here: https://zenodo.org/doi/10.5281/zenodo.13831339 or can be downloaded from https://i5k.gitlab.io/ArthroFam/arthropoda.html

Download the two files above and unzip arthropoda-seqs-all.zip to ./step0_sequences/nuclear_seq/

step1_evolutionary_rate_estimation

This directory includes scripts used to estimate evolutionary rates. Detailed instructions can be found ./step1_evolutionary_rate_estimation/README.md

step2_Rscripts_for_plotting

This directory includes R scripts for plotting Figures 1 to 4 and Figures S1 to S4. Detailed instructions can be found ./step2_Rscripts_for_plotting/README.md

step3_subsampling - scripts for subsampling for gene family size

step4_SVM - r script and data for SVM model to detect gene family changes related to haplodiploid species

Citation:

Li Y, GWC Thomas, S Richards, RM Waterhouse, X Zhou, ME Pfrender, 2024, Rapid evolution of mitochondrion-related genes in haplodiploid arthropods. BMC Biology. https://doi.org/10.1186/s12915-024-02027-4