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

<strong>Orthogroups and species tree</strong> Proteomes included in the analysis: proteomes.tar.gz<br> Orthogroups: Orthogroups.txt<br> Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv<br> Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt<br> Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa<br> Species tree: SpeciesTree_rooted.txt <strong>Whole genome alignment of <em>S. avenae</em>, <em>S. miscanthi,</em> <em>M. dirhodum</em> and <em>A. pisum</em></strong> Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz <strong>Haplotype divergence analysis (whole genome sequences)</strong> VCF files of HapCUT2 phased variants for <em>S. miscanthi </em>Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9):<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz VCF files of HapCUT2 phased variants for <em>S. avenae </em>JIC1<em> </em>chromosomes (Siave_v2.1 assembly scaffolds 1 to 9):<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz Haplotype resolved assemblies of <em>S. avenae</em> JIC1 and <em>S. miscanthi </em>Langfang-1 based on HapCUT2 phasing results:<br> JIC1_H1.Hapcut2.fa<br> JIC1_H2.Hapcut2.fa<br> Langfang1_H1.Hapcut2.fa<br> Langfang1_H2.Hapcut2.fa SibeliaZ whole genome alignment of <em>S. avenae </em>JIC1 and <em>S. miscanthi </em>Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf <strong>Filtered VCF files used for population genomics analysis</strong> <em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf<br> <em>S. avenae</em> and <em>S. miscanthi</em> 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<br> <em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1, Langfang1 and <em>M. dirhodum </em>WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf<br> <em>S. avenae</em> and <em>S. miscanthi </em>GBS samples + JIC1, Langfang1 and <em>M. dirhodum</em> WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf<br> <em>S. miscanthi </em>GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf<br> <em>S. miscanthi </em>GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf <strong>SNAPP phylogenetic analysis configuration file and trees</strong> SNAPP configuration file: snapp.xml<br> SNAPP log file: ut.log<br> SNAPP posterior sample of trees: ut.trees<br> SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc