--- # filename in this repository: description mixed.esm.KNWV.SF01_peanut_core_v14.xlsx: The main descriptive information about the genotyped accessions, including information about replicate similarity; phylogenetic clades, geographic origin, and phenotype; and summaries of phenotypic and country information relative to clade assignments. mixed.esm.KNWV.SF02_SNPs_whole_Axiom_Arachis2.txt: The original genotype calls for the Axiom array (for poly-high resolution SNPs). mixed.esm.KNWV.SF03_SNPs_whole_Axiom_Arachis2.vcf: The Axiom array genotype calls, in VCF format. mixed.esm.KNWV.SF04_SNPs_w_4_genomes.tsv: The predominant DNA variants at each SNP location, for all accessions, including variants inferred from four available genome assemblies - A. duranensis and A. ipaensis together, and A. hypogaea accessions Tifrunner, Shitouqi, and Fuhuasheng. The format is in a simple tab-separated table, with 14431 columns (SNP positions). mixed.esm.KNWV.SF05_SNPs_w_4_gnm_mrgd.fas: The same SNP as in S4 above, but in fasta format. SNP locations without DNA assignments for A. duranensis and A. ipaensis have been removed, giving an alignment of 10278 bases. mixed.esm.KNWV.SF06_chip_and_genome_samples_v05.xlsx: DNA base-calls for 16 selected, diverse accessions, with comparisons to the variants observed in the A. duranensis and A. ipaensis genomes, and inferences regarding the likely progenitor for the DNA, i.e. A-genome (A. duranensis) or B-genome (A. ipaensis). mixed.esm.KNWV.SF07_SNPs_w_4_gnm_mrgd_cen98.fas: Reduced fasta alignments (relative to the complete alignment file, S5). File S7 has the centroid representatives at 98% identity, and S8 has centroid representatives at 99% identity. These files have 518 and 680 sequences, respectively. mixed.esm.KNWV.SF08_SNPs_w_4_gnm_mrgd_cen99.fas: Reduced fasta alignments (relative to the complete alignment file, S5). File S7 has the centroid representatives at 98% identity, and S8 has centroid representatives at 99% identity. These files have 518 and 680 sequences, respectively. mixed.esm.KNWV.SF09_SNPs_w_4_gnm_mrgd_rt3_nh.txt: Phylogenetic tree (Newick format) calculated from the alignent in S5, and corresponding with the phylogenetic tree shown in Figure 1. mixed.esm.KNWV.SF10_K5_membership.pdf: The proportion of accessions assigned to clusters 1-5 in a Structure analysis (Figure 3), for K=5 clusters. mixed.esm.KNWV.SF11_K5_cluster_assignment.xlsx: The proportional assignments of each cluster to all accessions (relative to the Structure diagram shown in Figure 3). mixed.esm.KNWV.SF12_pca_34.pdf: Principal Component Analysis of 1120 samples based on 2063 unlinked SNP markers. The X-axis represents PC 3 and the Y-axis represents PC 4. Samples are colored and grouped according to A. clade membership as defined in the phylogenetic and network analyses, B. botanical varieties, C. market type, D. growth Habit, E. pod shape, and F. collection type mixed.esm.KNWV.SF13_chip_and_genome_GFFs.xlsx: Inferred subgenome origins of SNPs relative to the A-genome and B-genome progenitors (A. duranensis and A. ipaensis). This data is in GFF format, derived from S6, and used as the basis for the plots in Figure 7 (showing regions of possible subgenome invasions). mixed.esm.KNWV.SF14_PI497426_pods.jpg: Pods from accession PI 497426 (clade 4), illustrating the distinctive reticulation pattern seen in some accessions in this clade. mixed.esm.KNWV.SF15_Sipan_neclkace_Donnan_Einstein.jpg: Picture of necklace of peanuts, sculpted in gold and silver, from the Moche-era tomb at Sipán (c.AD 250) in coastal Peru. Photograph by Susan Einstein, courtesy of Christopher Donnan.