Species with biological traits favourable to long-distance marine larval dispersal might show a phylogeographic structuring over broad regions, even when they are genetically connected within smaller scales. Here, we evaluated this hypothesis by using the widespread amphidromous shrimp Atya scabra, predicting a genetic discontinuity across biogeographical barriers throughout the Western Gulf of Mexico (WGM), Caribbean Sea (CS), south-western Atlantic (SWA) and eastern Atlantic (EA). Using cytochrome oxidase subunit 1 (COI) and 16S ribosomal unit (16S) gene fragments, we did a phylogeographic assessment and genetic characterisation with Bayesian clustering, AMOVA, haplotype networks and demographic analyses. As predicted, three discrete genetic groups, corresponding to the regions WGM, CS and EA, were uncovered by COI, as well an unpredicted SWA+CS group. The 16S fragment detected a low genetic variation, probably owing to a recent lineage differentiation, which was estimated by the COI molecular clock. We evaluated the role of the biological traits of A. scabra, as well as the consequences of Panama Isthmus closure and Pleistocene glaciation cycles in the lineage isolation of WGM and EA, as well as the genetic connectivity shown within regions and between CS and SWA. Our results highlighted that amphidromous species genetically connected over large scales should be genetically characterised in their wide distribution to provide more comprehensive systematics and to assist decision-making in biological conservation.

The Atya genus classification is mostly stabilized, comprising 13 species in the Americas and West Africa. However, nearly 40 years have passed since its last revision. Some taxonomic questions remained due to morphological uncertainty, and new ones have been raised with molecular Atyidae phylogenies. The aim of this study was to conduct the first Atya molecular systematic assessment, verifying the taxonomic status of A. gabonensis, A. innocous, A. margaritacea and A. scabra. Gene fragments (16S, COI and H3) were obtained by DNA sequencing and used for genetic distance, phylogeny and species delimitation analyses (ABGD, PTP and GMYC). Our data corroborate A. gabonensis as a species with amphi‐Atlantic distribution and suggest the use of A. innocous for specimens of the Caribbean Sea. We revalidated A. tenella Smith, 1871 for specimens from Pacific. Atya margaritacea, distributed along the Pacific coast of the Americas, was considered a valid and distinct species from A. scabra, which is distributed in the Atlantic and Pacific coasts of the Americas and West Africa; moreover, maybe this wide distribution belongs to a distinct species, being A. scabra restricted to "Gulf of Mexico lineage". We corroborated the genus as monophyletic and highlighted remaining systematic issues. Overall, our multigene‐based phylogeny and species delimitation analyses suggest that Atya comprises 14 species. This study provides data for future studies on the biodiversity, evolution and conservation of freshwater Atyidae shrimps and Neotropical fauna.

Atya gabonensis Giebel, 1875 and Atya scabra (Leach, 1816) are amphidromous shrimps. In some areas, these species populations are vulnerable due to the anthropogenic impact on their habitats and commercial exploitation. However, basic morphometric data is still lacking. This study provides morphometric data on both species in the Fluvial Island Domain of Paraíba do Sul River basin, Brazil. Sampling was performed bimonthly from January 2013 to March 2014. Individuals were analysed according to sex, weight, carapace length and width, abdomen length, second abdominal pleura height and width, length of third pereopod articles, and length and width of the male appendix interna. We sampled 42 individuals of A. gabonensis and 16 individuals of A. scabra. In both species, females showed abdomen and second abdominal pleura larger than males, while males showed third pereopod