Extended Data Fig. 9: Relationships within H. bulbosum.

(a) Neighbor-joining tree constructed from a genome-wide SNP matrix (variant calling by deepvariant long reads pipeline) of 32 H. bulbosum haplotypes and one H. vulgare genome. Geographic origins and ploidy are color-coded. (b) Neighbor-joining tree constructed from graph pangenome similarity from ODGI (c) Maximum likelihood (ML) tree constructed from the whole chloroplast genomes of 32 H. bulbosum individuals and one H. vulgare individual. The wheat chloroplast genome was included as an outgroup. (d) Population trajectory as inferred by PSMC of the Libyan diploid PI365428, diploids from other countries, autotetraploids, and synthetic heterozygotes between the Libyan diploid and other diploid and tetraploid haplotypes. (e) Genetic distance of PI365428 to other populations. (f) Heatmap showing the identity-by-state (IBS) distance matrix between 270 H. bulbosum and 3 H. vulgare genotypes. (g) Genetic distance of the Greek tetraploid populations. The central line represents the median; the lower and upper edges of the box correspond to the first (Q1) and third quartiles (Q3), respectively. The interquartile range (IQR) is defined as Q3 − Q1. Whiskers extend to the most extreme data points within 1.5 × IQR from the quartiles. Data points beyond this range are plotted individually as outliers. (h) The diagram of the hypothesis of at least two origins. The base map was created using tiles provided by Stadia Maps, styled by Stamen Design, and incorporating geographic data from OpenStreetMap contributors via OpenMapTiles. Map data © OpenStreetMap contributors, licensed under the Open Database License; visual design © Stamen Design, licensed under CC BY 3.0; map tiles © Stadia Maps, licensed under CC BY 4.0.