Nathan R. Lovejoy

Functional variation in rhodopsin, the dim-light-specialized visual pigment, frequently occurs in species inhabiting light-limited environments. Variation in visual function can arise through two processes: relaxation of selection or adaptive evolution improving photon detection in a given environment. Here, we investigate the molecular evolution of rhodopsin in Gymnotiformes, an order of mostly nocturnal South American fishes that evolved sophisticated electrosensory capabilities. Our initial sequencing revealed a mutation associated with visual disease in humans. As these fishes are thought to have poor vision, this would be consistent with a possible sensory trade-off between the visual system and a novel electrosensory system. To investigate this, we surveyed rhodopsin from 147 gymnotiform species, spanning the order, and analysed patterns of molecular evolution. In contrast with our expectation, we detected strong selective constraint in gymnotiform rhodopsin, with rates of non-synonymous to synonymous substitutions lower in gymnotiforms than in other vertebrate lineages. In addition, we found evidence for positive selection on the branch leading to gymnotiforms and on a branch leading to a clade of deep-channel specialized gymnotiform species. We also found evidence that deleterious effects of a human disease-associated substitution are likely to be masked by epistatic substitutions at nearby sites. Our results suggest that rhodopsin remains an important component of the gymnotiform sensory system alongside electrolocation, and that photosensitivity of rhodopsin is well adapted for vision in dim-light environments.

Aim: The Guiana Shield region exhibits extraordinary topography that includes sheer, flat‐topped mountains (tepuis) atop an upland platform. Rivers of the eastern Pakaraima Mountains descend to Atlantic coastal lowlands, often traversing spectacular rapids and waterfalls. For fish species distributed in both uplands and lowlands, it is unclear whether these rapids and waterfalls present population or biogeographical boundaries. We sought to test this using the geographically widespread banded‐electric knifefish (Gymnotus carapo) as a model.Location: The Guiana Shield region of South America.Methods: We sampled 60 Gymnotus carapo specimens from the Guiana Shield region, and 75 G. carapo and closely related species from other parts of South America. We sequenced the mitochondrial cytochrome b gene and an intron from the nuclear S7 ribosomal protein gene, and used maximum likelihood and Bayesian tree‐building approaches to generate phylogenetic trees of haplotypes.Results: Haplotype sharing is minimal between populations separated by elevational barriers. We found evidence for two main haplotype clades in the Guiana Shield: one distributed in Atlantic coastal regions that includes most lowland samples, and one inland that includes most upland samples. Inland Guiana samples are more closely related to samples from the Amazon basin than to those of Atlantic coastal regions. A single sample from Tafelberg tepui in Suriname was most closely related to the Atlantic coastal lineages.Main conclusions: Riverine barriers that result from steep elevational gradients in the Guiana Shield inhibit gene flow between uplands and lowlands, even for a widely distributed species. Biogeographical relationships of Guiana Shield G. carapo are complex, with most upland lineages showing affinities to the Amazon basin, rather than to nearby lowland drainages of the Atlantic coast.

Flyingfishes are large enough to eat zooplankton, small enough to be consumed by top predators, and therefore form a central mid-trophic component of tropical epipelagic marine food webs. Characterizing patterns of flyingfish abundance, distribution, and habitat preference has important implications for understanding both localized and generalized functions of marine ecosystems. The eastern tropical Pacific Ocean (ETP) supports many flyingfish species and their predators, yet no studies to date have identified oceanographic factors that define flyingfish habitats or estimate species richness and diversity at broad taxonomic and geographic scales. In this study, we analyzed 11,125 flyingfish representing 25 species and all seven named genera, collected from the ETP over a 21-year period. We applied spatially explicit analysis methods (ARCGIS, DIVA-GIS, MAXENT) and compared specimen locality data to remotely sensed oceanographic data and previously described oceanographic partitions. Our results show that Exocoetus is the most abundant genus (49%) and E. monocirrhus the most abundant species (32%) of flyingfishes in the ETP. Mean sea surface temperature was most important for defining flyingfish habitats (19.2–41.7%) and species richness (highest in the North Equatorial Current). Additionally, flyingfish species diversity was found to be highest in coastal regions of the study area (Shannon indices > 1.5). Together, these results provide unprecedented characterizations of a mid-trophic epipelagic community in an economically valuable region during a time when sea surface temperatures are predicted to increase as a result of global climate change.

Two‐wing flyingfish (Exocoetus spp.) are widely distributed, epipelagic, mid‐trophic organisms that feed on zooplankton and are preyed upon by numerous predators (e.g., tunas, dolphinfish, tropical seabirds), yet an understanding of their speciation and systematics is lacking. As a model of epipelagic fish speciation and to investigate mechanisms that increase biodiversity, we studied the phylogeny and biogeography of Exocoetus, a highly abundant holoepipelagic fish taxon of the tropical open ocean. Morphological and molecular data were used to evaluate the phylogenetic relationships, species boundaries, and biogeographic patterns of the five putative Exocoetus species. We show that the most widespread species (E. volitans) is sister to all other species, and we find no evidence for cryptic species in this taxon. Sister relationship between E. monocirrhus (Indo‐Pacific) and E. obtusirostris (Atlantic) indicates the Isthmus of Panama and/or Benguela Barrier may have played a role in their divergence via allopatric speciation. The sister species E. peruvianus and E. gibbosus are found in different regions of the Pacific Ocean; however, our molecular results do not show a clear distinction between these species, indicating recent divergence or ongoing gene flow. Overall, our phylogeny reveals that the most spatially restricted species are more recently derived, suggesting that allopatric barriers may drive speciation, but subsequent dispersal and range expansion may affect the distributions of species.

Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps) from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266). AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (Φ_ST = 0.035, pST = 0.026, pE. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic range of the species.

The bluntnose knifefish genus Brachyhypopomus^{Mago-Leccia, 1994}, is diagnosed from other Rhamphichthyoidea (Rhamphichthyidae + Hypopomidae) by the presence of a disk-like ossification in the anterior portion of the palatoquadrate, and by the following external characters: short snout, 18.7-32.6% of head length (vs. 33.3-68.6% in Hypopomus, Gymnorhamphichthys, Iracema, and Rhamphichthys), absence of a paired accessory electric organ in the mental or humeral region (vs. presence in Hypopygus and Steatogenys), presence of 3-4 pectoral proximal radials (vs. 5 in Akawaio), presence of the antorbital + infraorbital, and the preopercular cephalic lateral line canal bones (vs. absence in Racenisia). Brachyhypopomus cannot be diagnosed unambiguously from Microsternarchus or from Procerusternarchus on the basis of external characters alone. Brachyhypopomus comprises 28 species. Here we describe 15 new species, and provide redescriptions of all 13 previously described species, based on meristic, morphometric, and other morphological characters. We include notes on ecology and natural history for each species, and provide regional dichotomous keys and distribution maps, based on the examination of 12,279 specimens from 2,787 museum lots. A lectotype is designated for Brachyhypopomus pinnicaudatus (^{Hopkins, Comfort, Bastian & Bass, 1990}). Brachyhypopomus species are abundant in shallow lentic and slow-flowing freshwater habitats from southern Costa Rica and northern Venezuela to Uruguay and northern Argentina. Species diversity is highest in Greater Amazonia, where 20 species occur: B. alberti, new species, B. arrayae, new species, and B. cunia, new species, in the upper rio Madeira drainage; B. batesi, new species, in the central Amazon and rio Negro; B. beebei, B. brevirostris, B. regani, new species, B. sullivani, new species, and B. walteri, widespread through the Amazon and Orinoco basins and the Guianas; B. belindae, new species, in the central Amazon basin; B. benjamini, new species, and B. verdii, new species, in the upper Amazon basin; B. bennetti, in the upper, central, and lower Amazon, lower Tocantins, and upper Madeira basins; B. bullocki in the Orinoco, Negro and Essequibo drainages; B. diazi in the Orinoco Llanos; B. flavipomus, new species, and B. hamiltoni, new species, in the central and upper Amazon basin; B. hendersoni, new species, in the central Amazon, lower Negro and Essequibo basins; B. pinnicaudatus in the central and lower Amazon, lower, upper Madeira, lower Tocantins and Mearim basins, and coastal French Guiana; and B. provenzanoi, new species, in the upper Orinoco and upper Negro basins. Five species are known from the Paraná-Paraguay-Uruguay basin and adjacent southern Atlantic drainages: B. bombilla in the lower Paraná, upper, central, and lower Paraguay, Uruguay and Patos-Mirim drainages; B. brevirostris in the upper Paraguay basin; B. draco in the lower Paraná, lower Paraguay, Uruguay, Patos-Mirim, and Tramandaí basins; B. gauderio in the lower Paraná, upper, central, and lower Paraguay, Uruguay, Patos-Mirim and Tramandaí basins; and B. walteri in the lower Paraná and upper Paraguay basins. Two species occur in small Atlantic drainages of southern Brazil: B. janeiroensis in the São João, Paraíba and small intervening drainages; and B. jureiae in the Ribeira de Iguape and Una do Prelado. One species occurs in the middle and upper São Francisco basin: B. menezesi, new species. Three species occur in trans-Andean drainages: B. diazi in Caribbean drainages of northern Venezuela; B. occidentalis in Atlantic and Pacific drainages of southern Costa Rica and Panama to Darién, and the Maracaibo, Magdalena, Sinú and Atrato drainages; and B. palenque, new species, in Pacific drainages of Ecuador.

Three complete mitochondrial genomes of South American electric fishes (Gymnotiformes), derived from high-throughput RNA sequencing (RNA-Seq), are reported herein. We report the complete mitochondrial genome of the bluntnose knifefish Brachyhypopomus n.sp.VERD, determined from newly sequenced data. We also provide the complete mitochondrial genomes for Sternopygus arenatus and the electric eel Electrophorus electricus, assembled from previously published transcriptome data. The mitochondrial genomes of Brachyhypopomus n. sp. VERD, Sternopygus arenatus and Electrophorus electricus have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs and 22 transfer RNAs, and are 16,547, 16,667 and 16,906 bp in length, respectively. Phylogenetic analysis of the eight available mitochondrial genomes of gymnotiform fishes shows Apteronotus to be the sister lineage of other gymnotiformes, contradicting the "Sinusoidea'' hypothesis that Apteronotidae and Sternopygidae are sister taxa.

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.