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

The described work was supported by a CEPAMS grant (17.03.2) awarded to S.H. and a Biotechnology and Biological Sciences Research Council (BBSRC) Future Leader Fellowship (BB/R01227X/1) awarded to T.C.M.. R.H.M.W. was funded from the BBSRC Norwich Research Park Biosciences Doctoral Training Partnership Award (BB/M011216/1). Additional support was provided by the BBSRC Institute Strategy Programs (BBS/E/J/000PR9797 and BBS/E/J/000PR9798) awarded to the John Innes Centre. The JIC is grant-aided by the John Innes Foundation. This research was supported by JIC Technology Platforms, particularly the Entomology and Insectary facilities and staff. We thank the NBI Computing Infrastructure for Science Group, which provides technical support and maintenance to the John Innes Centre's high-performance computing cluster and storage systems.