Functional trait divergence and climate-associated genomic variation in two Southeast Asian pines and their contact zone

Climate gradients are associated with functional and genomic differentiation in forest trees, but the coupling between trait variation and genomic differentiation remains poorly understood in tropical and subtropical conifers and their contact zones. We quantified 13 wood anatomical traits and two needle traits across natural populations of Pinus kesiya Royle ex Gordon , Pinus yunnanensis Franch., and their contact zone populations in Southeast Asia. Using genotyping-by-sequencing SNPs, we inferred genomic ancestry, identified climate - associated loci, and partitioned trait variation between genomic ancestry and climate. Wood and needle traits varied within and between species and were associated with climate variation Pinus kesiya had larger pit diameter and tracheid area in warmer, wetter environments, while Pinus yunnanensis exhibited higher stomatal and pit density with smaller tracheid area, representing contrasting hydraulic trait syndromes. Contact zone populations were largely intermediate with no pervasive transgressive trait. Genome scans identified a subset of loci associated with climatic variables, including a small number of annotated candidates with functions previously linked to stress responses. Variance partitioning showed that the relative associations of genomic ancestry and climate with trait variation differed between wood and needle traits. Together, these results show that functional trait variation across these pine species covaries with climatic differentiation and genomic ancestry, while the underlying genotype–phenotype relationships remain to be resolved.