DOI: 10.5281/zenodo.7108778
title: Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids

description: <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
description: 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.