DOI: 10.5061/dryad.xwdbrv1rg
title: Data from: Repeatable genomic outcomes along the speciation continuum: Insights from pine hybrid zones (genus Pinus)

description: 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.
description: # 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 * Allopatric reference populations: 325 individuals *
 **Sampling period**: 2021–2023 * **Tissue source**: Fresh needles * **DNA
 extraction**: Genomic Mini AX Plant kit (A&A Biotechnology, Poland) *
 **DNA quantification**: Qubit 4 Fluorometer, 40 ng/µl working
 concentration ## Genotyping * **Platform**: Axiom PineGAP SNP array
 (Thermo Fisher Scientific) * **Total SNPs genotyped**: 49,829 * **SNPs
 retained post-filtering**: 7,390 * Minor Allele Frequency (MAF) &gt; 10% *
 Linkage Disequilibrium (LD) r² &lt; 0.7 * &lt;10% missing data *
 **Software**: Axiom Analysis Suite * **Additional marker**: cpDNA
 trnL-trnF intergenic region