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Aim Complex oceanographic features have historically caused difficulty in understanding gene flow in marine taxa. Here, we evaluate the impact of potential phylogeographic barriers to gene flow and assess demography and evolutionary history of a coral reef goby species complex. Specifically, we test how the Amazon River outflow and ocean currents impact gene flow. Location Western Atlantic. Taxon The bridled goby (Coryphopterus glaucofraenum) and sand‐canyon goby (C. venezuelae) species complex. Methods We used mitochondrial DNA and 2,401 genomic SNPs to investigate evolutionary history and test hypotheses of how major barriers impact species‐level differentiation. We used clustering algorithms and pairwise FST to assess population differentiation caused by minor barriers within and among regions. Finally, we tested alternate hypotheses of demographic history via coalescent simulations to determine the most plausible spread across the Western Atlantic. Results We found two unique clades of C. glaucofraenum along the Brazilian coast and the oceanic island Atol das Rocas (AR) that are more closely related to C. venzuelae. Further genetic structure within the Caribbean and separately along the Brazilian coast led to at least two distinct populations in each Province. Coalescent simulations indicated that an ancestral population of C. venezuelae split from C. glaucofraenum in the Caribbean, dispersed to Brazil, then spread to AR. Main conclusions Species‐level genetic differentiation has resulted from the Amazon River outflow and isolation of AR. Population differentiation within the Caribbean matched previous studies indicating an east‐west pattern of divergence. Brazilian population differentiation was impacted by the cold‐water upwelling filter at Cabo Frio. Overall, this research highlights how barriers to gene flow impact speciation and genetic structure within western Atlantic gobies and provides insight into the role oceanographic features have in the speciation process of fishes.

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There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.

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