Data from: Repeatable genomic outcomes along the speciation continuum: Insights from pine hybrid zones (genus Pinus)

Hybridization is a widespread evolutionary process and a key source of
evolutionary novelty. However, despite intensive study, the extent to
which hybridization is deterministic and repeatable—particularly in
recurrent contact events involving the same species under varying
ecological conditions—remains unclear. Here, we investigated three
replicated contact zones between Scots pine (Pinus sylvestris) and dwarf
mountain pine (Pinus mugo) in Central Europe: two occurring in analogous
peatland habitats and one in a contrasting sandstone outcrop. Using
genome-wide SNP genotyping of over 1,300 individuals, we analyzed genomic
structure, diversity, and ancestry patterns across these zones. All sites
revealed pervasive hybridization, dominated by later-generation hybrids
and a notable scarcity of pure P. mugo. Across environments, hybrid
populations exhibited strikingly consistent genomic compositions, with
asymmetric introgression strongly biased toward P. mugo
ancestry—suggesting that hybrid genome structure may follow predictable
patterns under similar ecological conditions. Nonetheless, we also
detected site-specific differences in hybrid diversity and phenotype,
highlighting the influence of local environmental selection on shared
hybrid genomic backgrounds. We provide genomic evidence that Pinus
uliginosa—a morphologically distinct peat bog pine traditionally regarded
as a relic and endangered species—is instead an incipient hybrid taxon.
Its genome reflects partial stabilization through hybridization and
ecological filtering, yet it lacks sufficient genetic divergence to be
recognized as a distinct species. Together, these results provide evidence
for the repeatability of hybridization processes, which result in the
formation of phenotypes reflecting a species continuum subjected to strong
environmental pressures. The findings support the simplification of
taxonomic nomenclature within the Pinus mugo complex, informing adaptive
conservation strategies and the genetic management of hybrid lineages.