Phylogeography and niche adaptation of Brachypodium stacei based on RAD-Seq and plastome assemblies

Using extensive genomic data, including 72450 SNPs and comprehensive plastome analysis, we unraveled the phylogeographic history of 17 Brachypodium stacei populations. Nuclear SNP data revealed six distinct genetic groups, indicating a sequential divergence from the Central Mediterranean to various regions. The species showed low genetic diversity and high selfing rates. Plastome data suggested interbreeding and chloroplast capture between genetically distant populations. Overall, the phylogeography of B. stacei is influenced by recent radiations, extinctions, long-distance dispersal, occasional interbreeding, and local climate adaptation.