Genomic diversity under the influence of environmental factors highlights the future vulnerability of rare conifers: the case of the southernmost Pilgerodendron uviferum (Cupressaceae)

Landscape genomics applied to tree species provides crucial insights into their ecological, economic, and evolutionary roles, as well as their adaptive capacity under climate change, forming a basis for effective conservation. This is particularly relevant for rare conifers in the Cupressaceae family that play essential ecological functions in threatened Patagonian forests, especially on the driest slopes of the Andes in Argentina. We study ­Pilgerodendron uviferum, a monotypic genus listed as vulnerable by the IUCN and included in CITES Appendix 1. We aim to evaluate genomic diversity and structure, and their association with environmental factors in extreme climatic conditions. A total of 67 adaptive single nucleotide polymorphisms (SNPs) were identified in 90 individuals, showing greater genetic diversity than the 5682 neutral SNPs, which exhibited higher levels of admixture. Six adaptive SNPs aligned with transcripts related to abiotic stress tolerance and plant development. Genotype–environment association analyses showed significant latitudinal associations with climate and soil variables. Ecological niche model predictions indicate a future reduction in the distribution of Pilgerodendron, particularly in northern populations, while also identifying areas of persistence and potential southwards movement. Our findings highlight climate-driven pressures on genetic diversity and underscores the importance of conservation efforts to maintain gene flow and ensure long-term species persistence.