The determination of species limits is key to biology, with practical implications for conservation policy makers, lawyers and stakeholders. However, naming species may be a difficult task as interspecific hybridization blurs species boundaries. Natural interspecific gene flow has been reported for seven distinct mangrove genera, including the iconic genus Rhizophora. Species limits within this genus have long been debated because of morphological similarity, natural variability in diagnostic traits, disjunct geographic distribution, and recent molecular data have reignited this issue. Here, we used a phylogeographical approach based on genome-wide single nucleotide polymorphism (SNP) data to test species hypotheses of R. mangle, R. racemosa and R. X harrisonii from the Atlantic East Pacific (AEP) biogeographic region and South Pacific islands. Genetic structure patterns and Approximate Bayesian Computation (ABC) analyses revealed that taxonomic identification based only on morphological traits could not predict genetic clustering alone nor the phylogenetic relationships among groups. The American continent plays an important role as a barrier to gene flow within the genus such that trees identified morphologically as R. racemosa from the Atlantic basin are more genetically similar to R. mangle from the same basin than to R. racemosa trees from the Pacific coast. Additionally, our findings supported previous studies that showed that R. samoensis is indistinguishable from R. mangle populations from the Pacific basin. Moreover, we provide novel evidence that R. X harrisonii is likely composed by two independently originated and separately maintained evolutionary lineages in both sides of the American continent. Our findings provide novel evidence of taxonomic inconsistency of current morphology-based species designations in Western hemisphere and South Pacific islands Rhizophora species.
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