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

Citation

Morales-Hojas, Ramiro et al. (2020), Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes, Dryad, Dataset, https://doi.org/10.5061/dryad.k0p2ngf5x

Abstract

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 sampled in 12 populations of England obtained using FreeBayes (in vcf format).

England_samples_vcf_filtered.zip: SNPs from S. avenae after filtering the file England_samples_vcf.zip using vcftools (max-missing 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file was used in all population genetic analyses of the English populations in the paper, transforming the vcf to the corresponding formats.

England_samples_SNPs.fas: fasta file of phased SNPs.

England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in the phylogenetic reconstruction of S. avenae haplotypes using RAxML. This file is the same as England_samples_SNPs.fas after removing sites which were not polymorphic (e.g. a site that contains N and T in different samples is not considered polymorphic for RAxML and has to be removed)

England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with England_samples_SNPs_polymorphic.fas.

Funding

Biotechnology and Biological Sciences Research Council, Award: BBS/OS/NW/000004

Biotechnology and Biological Sciences Research Council, Award: BBS/E/C/000J0200

Biotechnology and Biological Sciences Research Council, Award: BBS/OS/CP/000001

National Key R & D Plan of China, Award: 2017YFD0201700

China Agricultural Science and Technology Innovation Programme, Award: ASTIP no. CAAS-XTCX201820

National Key R & D Plan of China, Award: 2017YFD0201700