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

#### Dataset Description

This dataset (Łabiszak_et_al_ME.zip) includes genomic data collected from over 1,300 individuals sampled in both allopatric populations and three naturally occurring hybrid zones. SNP data were generated using a custom Axiom PineGAP SNP array, and a diagnostic cpDNA marker (trnL-trnF) was also employed for paternal lineage identification. The dataset contains a PLINK file in .raw format with genotypes and an R genind object with cleaned genotyping data used in the study.

## File List

* **GENIND_HYBRIDS_DATA**\
R `genind` object containing processed SNP genotype data (7,390 filtered loci) for 1,323 individuals. Saved as an R native RDS file. Open in R using the ReadRDS() function.
* **hybrid_pines_clean_A.raw**\
genotype file in .raw PLINK format

## Sampling Information

* **Total individuals**: 1,345
* Hybrid zones: 1,020 individuals
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