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Abstract AimWe studied the niche evolution and diversification modes in transisthmianAlpheusshrimps by examining the interplay between environmental niche divergence and conservatism in allopatric sister species. In a broader perspective, the current study analysed the evolution of climatic niche and the role of the environment in species diversification ofAlpheustransisthmian shrimp. LocationAtlantic and Eastern‐Pacific oceans. TaxonAlpheusshrimps (Caridea: Alpheidae). MethodsWe assembled georeferenced occurrences for 33 species ofAlpheus(with 24 sister species) from a time‐calibrated molecular phylogeny. We modelled their ecological niches and assessed niche overlap through pairwise comparisons. Additionally, we performed phylogenetic reconstructions of the ancestral environmental niche, for each niche axis. ResultsOur results demonstrate that thermal tolerances, food availability and hydrodynamic forces were relevant environmental axes in evolutionary processes in transisthmian species ofAlpheus. Among the 528 paired comparisons, we found that most niches were divergent, including in 12 clades formed by pairs of sister species (in only two of these clades were the niches fully equivalent). Phylogenetic reconstructions of ancestral niches showed an initial niche conservatism in all axes, with divergences intensifying in the last 12 million years. Main ConclusionsWe found evidence that confirms the relevance of the environmental changes that occurred in the West Atlantic and East Pacific for niche evolution in transisthmianAlpheusspecies, as well as for the emergence of some lineages. Our findings provide evidence for different modes ofAlpheusspecies speciation in a period consistent with the closure of the Isthmus of Panama. 

Abstract Snapping shrimps of the genus Alpheus Fabricius, 1798 exhibit remarkable diversity, with over 300 described species. The genus is well-known for its prevalence of species complexes, necessitating the need of new tools to facilitate species discrimination. Traditional taxonomic methods in Alpheus have primarily relied on the examination of morphological traits or comparative morphometric measurements, with an emphasis on variation in the major chela and rostro-orbital region. We applied an integrated approach that combines molecular genetics and geometric morphometrics to investigate the A. gracilipesStimpson, 1860 species complex. We additionally applied geometric morphometric techniques to study the major chela and the rostrum across different species, and used three mitochondrial genes (12S, COI, and 16S) to reconstruct phylogenetic relationships of this complex. Our results demonstrate the first application of geometric morphometric techniques to Alpheus snapping shrimps, and highlight the significance of the major chela and rostrum as taxonomically informative traits. Furthermore, we use DNA barcodes and geometric morphometric techniques to the A. gracilipes species complex to reveal two previously unidentified cryptic species. We present the first phylogenetic reconstruction of this species complex, with new localities and expanded distribution ranges reported for many species.