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 neutral processes. This study provides a unique population genetics perspective of Buchnera-aphid host coevolution on a microevolutionary scale.

Methods
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.