Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the Black Mangrove (Avicennia germinans). Fifty-seven trees were sampled in seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation genetic differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought-tolerance or plant response to drought. Moreover, our results suggest the occurrence of rapid evolution of a population, likely in response to sudden and persistent limitation in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcripts expression levels associated with increased drought-tolerance, through accumulation of osmoprotectants and antioxidants, biosynthesis of plant cuticle, protection against stress-induced proteins degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree. 

Here, we provide the SNP genotype dataset used for all population genetics analyses performed in our study. Our genotype dataset is available in *.raw format, along with its complementary text file, containing all samples identification. Additionally, we provide an R script describing all the criteria we used to assemble this *.raw genotype dataset from the original *.vcf file received from the SNPsaurus sequencing facility, which has performed the next-RAD sequencing of Avicennia germinans samples from the North-Northeast Brazilian coastline. Moreover, this R script contains the command lines used to perform genetic structure analyses and to export the SNP genotype dataset to different formats required to run all the analyses described in our study.