Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids

Orthogroups and species tree

Proteomes included in the analysis: proteomes.tar.gz
Orthogroups: Orthogroups.txt
Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv
Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt
Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa
Species tree: SpeciesTree_rooted.txt

Whole genome alignment of S. avenae, S. miscanthi, M. dirhodum and A. pisum

Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz

Haplotype divergence analysis (whole genome sequences)

VCF files of HapCUT2 phased variants for S. miscanthi Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9):
Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz

VCF files of HapCUT2 phased variants for S. avenae JIC1 chromosomes (Siave_v2.1 assembly scaffolds 1 to 9):
JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz

Haplotype resolved assemblies of S. avenae JIC1 and S. miscanthi Langfang-1 based on HapCUT2 phasing results:
JIC1_H1.Hapcut2.fa
JIC1_H2.Hapcut2.fa
Langfang1_H1.Hapcut2.fa
Langfang1_H2.Hapcut2.fa

SibeliaZ whole genome alignment of S. avenae JIC1 and S. miscanthi Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf

Filtered VCF files used for population genomics analysis

S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf
S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf
S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf
S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf
S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf
S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf

SNAPP phylogenetic analysis configuration file and trees

SNAPP configuration file: snapp.xml
SNAPP log file: ut.log
SNAPP posterior sample of trees: ut.trees
SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc