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The mysterious deep-sea shrimp Physetocaris microphthalma Chace, 1940 remains a challenge for the understanding of caridean shrimp systematics. Upon first description in 1940, the unique morphology in combination with lack of material made the allocation of P. microphthalma to any family or superfamily difficult, therefore the monotypic superfamily Physetocaridoidea and family Physetocarididae were described. The rarity of the species, only documented a few times in scientific literature, in combination with a circumglobal distribution, makes the advancement of the systematics and biology of this shrimp challenging. Current literature places Physetocaridoidea as a superfamily with a sister relationship to Pandaloidea but this relationship has never been tested using molecular data. Recent expeditions to the northern Gulf of Mexico and north-eastern Pacific Ocean provided fresh material for inclusion in phylogenetic analyses. Here, we used a molecular systematics approach to investigate the phylogenetic placement of this species within the infraorder Caridea and test for cryptic diversity across oceanic basins. We sequenced five genes (12S rRNA, 16S rRNA, H3, NaK and PEPCK) and built phylogenetic trees including specimens across Pandaloidea and other carideans (n = 75) using maximum-likelihood and Bayesian approaches. Our results strongly support the inclusion of P. microphthalma within the family Pandalidae and superfamily Pandaloidea, indicating that the superfamily Physetocaridoidea and family Physetocaridae are not valid. In addition, the inclusion of specimens from the Atlantic and Pacific Oceans does not support evidence of cryptic diversity, suggesting the global distribution of P. microphthalma. This is the first study to provide genetic data for this species, resulting in an updated classification for the infraorder Caridea and highlighting that deep-pelagic species can be rare yet still widely distributed. 

The Amazon–Orinoco plume (AOP) is the world’s largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP’s formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.