Genome-wide SNPs reveal adaptation and population structure in Syagrus romanzoffiana (Arecaceae) from southern South America

Abstract Palms play crucial ecological and economic roles, and Syagrus romanzoffiana is a widely distributed species in South America. Despite its ecological importance and economic potential, population-level genetic studies of this palm remain limited. Here, we assessed the genetic diversity and structure of S. romanzoffiana across distinct vegetation types in Brazil and Paraguay using 24,859 single nucleotide polymorphisms (SNPs) derived from genotyping-by-sequencing (GBS). We analyzed 91 individuals from eight populations, revealing high genetic diversity within populations and moderate differentiation among them. Observed heterozygosity was generally high, with some populations showing an excess of heterozygotes, consistent with outcrossing and gene flow. Pairwise F ST and AMOVA confirmed that most variation is maintained within populations, while genetic structure analyses highlighted the influence of vegetation type on differentiation, with restinga populations displaying unique signatures. Despite geographic proximity, some populations exhibited greater divergence due to local environmental conditions, supporting isolation by environment. Environmental association analyses (LFMM and RDA) further identified SNPs linked to temperature and precipitation, reinforcing the role of climate as a driver of adaptive differentiation. These findings emphasize the role of ecological factors in shaping genetic variation in S. romanzoffiana and illustrate how population genomics of widespread, non-threatened palms can provide critical baselines for conservation, restoration, and sustainable management under ongoing habitat fragmentation and climate change.