A Palearctic divide, niche conservatism and host-fungal endophyte interactions shaped the phylogeography of the grassBrachypodium sylvaticum

Brachypodium sylvaticumis a perennial woodland grass selected as model species for perenniality, which is widely distributed across the Palearctic. This plant forms a symbiosis with the endophytic fungusEpichloë sylvatica. We integrate whole-genome phylogenomics, plastome analysis, environmental niche modeling (ENM), and coevolutionary analyses to investigate the diversification ofB. sylvaticumand its fungal symbiont. Using 94 representative individuals spanning Eurasia and North Africa, we recovered two deeply divergent sister lineages (Eastern and Western Palearctic), with cytonuclear discordances suggesting historical plastid capture events in the western group. Admixture analysis revealed four genetic clusters, including signatures of secondary contact and hybridization in the Western lineage. Filtered ITS sequences ofE. sylvaticarecovered from holobiont genome skimming reads enabled phylogenetic reconstruction, revealing two fungal clades that broadly mirror their host’s evolutionary history in the West. PACo and ParaFit analyses supported partial co-divergence between hosts and endophytes. ENM projections identified climatically stable glacial refugia for bothB. sylvaticummain lineages during the Last Glacial Maximum and asymmetric postglacial expansion, with moderate niche shifts in the West and stronger turnover in the East. Evidence of niche overlap and similarity indicated niche conservatism among clades, suggesting that geographic isolation, rather than adaptive divergence, was the primary driver of lineage splitting. IBD and IBE patterns significantly influenced divergences in the Western, but not the Eastern, group, highlighting contrasting demographic and ecological dynamics. Our results provide the first evidence of coevolutionary and ecological structuring inB. sylvaticum–E. sylvaticaholobionts across their Western native range.