Data for: ‘Drifting’ Buchnera genomes track the microevolutionary trajectories of their aphid hosts

This repository comprises code and scripts needed to recreate the analyses presented in the manuscript:
Thia et al. 'Drifting’ Buchnera genomes track the microevolutionary trajectories of their aphid hosts. 
This study explores the coevolution between the endosymbiont Buchnera and its aphid host in the aphid species, Myzus persicae, the green peach aphid. Evidence that Buchnera is polymorphic within aphid clones indicates that these symbionts exist as populations of different strains within a single aphid. Strong signals of genomic covariation were observed between both organisms. However, genomic variation in either organism was not associated with geography or the host plant. Further examination of protein-coding SNPs in Buchnera found that the number of non-synonymous to synonymous mutations were on average comparable (ratio ~1), with similar site frequency spectra of alleles in both mutation classes. Our results suggest that Buchnera within Myzus persicae are largely evolving under ..., This study leverages previously and newly sequenced Myzus persicae to compile a global dataset of Buchnera and aphid host genomes. Analyses include quantification of genetic diversity and differentiation, protein-coding effects, and comparisons of site frequency spectra.
More details can be found in the README., , # Data for: ‘Drifting’ *Buchnera* genomes track the microevolutionary trajectories of their aphid hosts

This repository contains the data and scripts needed to replicate the analysis in:

* Thia, Zhan, et al. (2024) ‘Drifting’ *Buchnera* genomes track the microevolutionary trajectories of their aphid hosts. *Insect Molecular Biology.* DOI: [10.1111/imb.12946](https://doi.org/10.1111/imb.12946)

This study investigates the coevolution between *Buchnera* and its aphid host among a globally distributed sample of *Myzus persicae*.

This repository is split into two ZIP files: ‘Data’ and ‘Scripts’.

‘Data’ contains two directories that set out the structure for these analyses:

* 0_Metadata/
* 1_Bioinformatics/
* 2_Popgen_analysis/

‘Scripts’ contains the scripts that should be placed into either ‘1_Bioinformatics/’ or ‘2_Popgen_analysis/’ to run the analyses for these separate pipelines.

Note that the ‘2_Popgen_analysis/’ directory is intentionally left empty. This is meant to act as a pl...