Fig. 4

Population genomic analyses of 112 spinach accessions including 81 representative S. oleracea (including two hybrids), 11 S. tetrandra, and 20 S. turkestanica varieties. a The proposed origin and evolutionary route of S. oleracea varieties. After origination from the Middle East area, S. oleracea dispersed to nine geographical regions with two branches: Asia (Afghanistan, Syria, Georgia, India, China, and Japan), and Europe and North-America (Macedonia, Belgium, and the USA). b Heterozygosity rates. c Population structure analysis clustered 112 accessions into four subgroups (K = 4) and divided S. oleracea into nine subgroups. d Phylogenetic relationships among 112 accessions discovered using nuclear genome SNPs and whole chloroplast genomes, revealing a conflict between phylogenies based on the nuclear and chloroplastic genomes of S. oleracea and wild species. e Historical effective population sizes (N_e) for the domesticated S. oleracea, compared to wild S. turkestanica and S. tetrandra, estimated using the nucleotide substitution rate μ = 6e−9 and generation time gt = 1. The S. oleracea population has undergone one recent N_e bottleneck ~10.87 Kya, reached its minimum value at ~6.5 Kya, and recovered well ~4.8 Kya, although the two wild populations did not experience this bottleneck. The S. turkestanica population has undergone two periods of ancient geologic upheaval during late Tarantian Age at 148–177 Kya and Holocene at 18.97–26.51 Kya. The S. tetrandra population experienced one Ne decline from the Chibanian to Calabrian ages at 1.035–1.321 Mya. The estimates are the medians (one thick line) from 200 bootstrap replicates with 2.5%, 12.5%, 87.5% and 97.5% confidence intervals (four thin lines)