Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes

Single Nucleotide Polymorphisms files and phylogonetic trees of S. miscanthi samples collected in China and S. avenae from the UK used to study the population genetics analyses of these species. These are:

China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10 populations of China obtained using FreeBayes (in vcf format).

China_samples_vcf_filtered.zip: SNPs from S. miscanthi after filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75, minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin 5000). This file was used in all population genetic analyses of the Chinese populations in the paper, transforming to the appropriate formats.

China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the phylogeny of S. miscanthi haplotypes using RAxML.

China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with China_samples_SNPs.fas.

England_samples_vcf.zip: dataset of SNPs from S. avenae samp...