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The correlation between form and function is influenced by biomechanical constraints, natural selection, and ecological interactions. In many species of suction-feeding fishes, jaw shape has shown to be closely associated with diet. However, these correlations have not been tested in fishes that have more complex jaw functions. For example, the neotropical loricariid catfishes possess a ventrally facing oral disk, which allows for the oral jaws to adhere to surfaces to conduct feeding. To determine if jaw shape is correlated to diet type, we assessed oral jaw shape across 36 species using CT scans. Shape was quantified with traditional and automated landmarking in 3DSlicer, and diet type correlation was calculated using the phylogenetic generalized least squares (PGLS) method. We found that traditional and automated processes captured shape effectively when all jaw components were combined. PGLS found that diet type did not correlate to jaw shape; however, there was a correlation between clades with diverse diets and fast evolutionary rates of shape. These results suggest that shape is not constrained to diet type, and that similarly shaped jaws coupled with different types of teeth could allow the fishes to feed on a wide range of materials.

Parallel adaptive radiations have arisen following the colonization of islands by lizards and lakes by fishes. In these classic examples, parallel adaptive radiation is a response to the ecological opportunities afforded by the colonization of novel ecosystems and similar adaptive landscapes that favour the evolution of similar suites of ecomorphs, despite independent evolutionary histories. Here, we demonstrate that parallel adaptive radiations of cichlid fishes arose in South American rivers. Speciation-assembled communities of pike cichlids (Crenicichla) have independently diversified into similar suites of novel ecomorphs in the Uruguay and Paraná Rivers, including crevice feeders, periphyton grazers and molluscivores. There were bursts in phenotypic evolution associated with the colonization of each river and the subsequent expansion of morphospace following the evolution of the ecomorphs. These riverine clades demonstrate that characteristics emblematic of textbook parallel adaptive radiations of island- and lake-dwelling assemblages are feasible evolutionary outcomes even in labile ecosystems such as rivers.

A pharyngeal jaw and loose pharyngeal teeth from Prairie Creek, Indiana, and loose pharyngeal teeth and two basioccipital pharyngeal processes from Bell Cave, Alabama, appear to be those of Moxostoma hubbsi (Copper Redhorse). Among suckers, only M. carinatum, M. hubbsi, M. robustum, and M. ugidatli have molariform teeth on their pharyngeal jaws, with M. hubbsi having the teeth of the largest relative size. Measurements of most of the teeth from Prairie Creek overlap with those of M. hubbsi, and the largest tooth from Bell Cave is the largest pharyngeal tooth measured. The more complete pharyngeal process of the basioccipital possesses a small condyle and stout processes along it that are indicative of M. hubbsi as well as a smaller centrum for articulation with the Weberian complex. Moxostoma hubbsi currently occupies an area around Montreal, Canada, that was glaciated at the time the fossils were laid down, and the area was later occupied by the Champlain Sea and Lampsilis Lake before becoming riverine about 6000–5000 years ago, meaning that M. hubbsi had to have arrived at its current distribution relatively recently and been extirpated from elsewhere.

Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance. Standard phylogenetic methods produce conflicting results for several parts of the tree of life. Here, a new phylogenomic method is presented, which resolves controversial relationships within the Otophysi freshwater fish and several other recalcitrant groups.

Stable isotope analyses have refined the study of trophic niche diversity within an ecosystem, yet traditional trophic partitioning methods may not be appropriate to identify variation among groups with similar dietary requirements. By building on vector‐based analyses, we introduce a baseline‐standardized isotopic vector analysis (BaSIVA) to visualize dietary variation while accounting for isotopic discrepancies between locations. To test the effectiveness of our new method, we collected muscle samples from eleven species of Loricarioidea in five assemblages in Northern Peru. Loricarioidea is a large, ecomorphologically diverse superfamily of scraping‐feeding fishes. Most feed on an indistinguishable mix of detritus and algae, but some lineages have specialized diets of wood, seeds, and macroinvertebrates, making them an excellent group to study trophic variation. Isotopic data were collected using mass spectrometric isotope analyses, and communities were standardized by calculating a mean baseline (algae and periphyton) for each location. The entire community was shifted by subtracting the baseline of 15N and 13C from the consumers at each location, which allowed for comparison between assemblages. Incremental differences of 15N and 13C from the baseline were found via vector analysis, and the azimuth and module of each consumer were calculated. Standardization resulted in a significant shift of assemblages within the isotopic biplot, and vector analysis shows three trophic groups primarily described by differences in carbon assimilation. Isotopic variation between species may account for some diversification in jaw shape within the Loricarioidea, but BaSIVA suggests several instances of trophic overlap in different jaw morphologies. Moreover, results from BaSIVA are better able to delineate trophic groups than traditional trophic positioning methods while accounting for variation in basal resources. We suggest a baseline‐standardized vector analysis should be the standard for vector‐based stable isotope analysis in riverine environments with similar baseline resources.

North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis , which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis , such as Cyprinella , Luxilus , Lythrurus , and Pteronotropis , the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius , Luxilus , and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae . Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis , elevation of the subgenus Hydrophlox , expansion of species included in Miniellus , movement of Hudsonius cummingsae to Pteronotropis , and resurrection of the genera Coccotis and Paranotropis . We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala , and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).

Background The Neotropical catfish family Loricariidae contains over 830 species that display extraordinary variation in jaw morphologies but nonetheless reveal little interspecific variation from a generalized diet of detritus and algae. To investigate this paradox, we collected δ 13 C and δ 15 N stable isotope signatures from 649 specimens representing 32 loricariid genera and 82 species from 19 local assemblages distributed across South America. We calculated vectors representing the distance and direction of each specimen relative to the δ 15 N/δ 13 C centroid for its local assemblage, and then examined the evolutionary diversification of loricariids across assemblage isotope niche space by regressing the mean vector for each genus in each assemblage onto a phylogeny reconstructed from osteological characters. Results Loricariids displayed a total range of δ 15 N assemblage centroid deviation spanning 4.9‰, which is within the tissue–diet discrimination range known for Loricariidae, indicating that they feed at a similar trophic level and that δ 15 N largely reflects differences in their dietary protein content. Total range of δ 13 C deviation spanned 7.4‰, which is less than the minimum range reported for neotropical river fish communities, suggesting that loricariids selectively assimilate a restricted subset of the full basal resource spectrum available to fishes. Phylogenetic regression of assemblage centroid-standardized vectors for δ 15 N and δ 13 C revealed that loricariid genera with allopatric distributions in disjunct river basins partition basal resources in an evolutionarily conserved manner concordant with patterns of jaw morphological specialization and with evolutionary diversification via ecological radiation. Conclusions Trophic partitioning along elemental/nutritional gradients may provide an important mechanism of dietary segregation and evolutionary diversification among loricariids and perhaps other taxonomic groups of apparently generalist detritivores and herbivores. Evolutionary patterns among the Loricariidae show a high degree of trophic niche conservatism, indicating that evolutionary lineage affiliation can be a strong predictor of how basal consumers segregate trophic niche space.

The Guiana Shield in northeastern South America contains some of the largest tracts of intact forests on the globe. Guyana alone has more than 80% forest cover. In south-central Guyana a unique biogeographic feature allows for a hydrological connection between the Guiana Shield with the Amazon basin via the Rupununi savannas and wetlands (Rupununi Portal). This corridor allows for connectivity between two of the most biodiverse, carbon rich, and intact forests in the world. The significance of this (and other) hydrological corridors for terrestrial and aquatic species is underappreciated in the scientific literature. We attempt to determine the importance of the surrounding mosaic of habitats that influence fish assemblages in the Rupununi Portal. We extensively sampled fishes in this corridor over six expeditions. Multivariate analyses revealed significant trends in fish assemblage structure and environmental conditions. We found high species richness and diversity within the Takutu (Amazon River drainage) and Rupununi rivers (Essequibo River drainage). Fish assemblages were found to be most similar within the specific river drainages with some similarity within forest and savanna sites. A second Rupununi portal was revealed in the South Rupununi, at the upper Rupununi and Takutu Rivers. Ordination analyses found water body type, vegetation and water chemistry to be significantly structuring the fish assemblages of the Rupununi. Our study reveals the interdependent nature of the various habitats in the Rupununi that facilitate high biodiversity and maintain the ecosystem. With the increase in human activity in this region, and the increased connectivity of the region with the rest of the world through better roads, this area is in danger of being modified and fragmented to a point where ecosystem services begin to fail. We recommend demarcating a protected area in the region that considers the diversity of associated habitats and the importance of the ecological portal joining two diverse river basins.

Three new species of saddled hypostomine loricariids are described. According to a recent phylogenetic analysis, these species are members of the genus Peckoltia. The species differ from all described Peckoltia except Peckoltiafurcata and Peckoltiasabaji by having the dentaries meet at an angle greater than 90°. The species also have similarities to Hemiancistrus, and can be separated from all described species by having dorsal saddles. We discuss the taxonomy of Peckoltia, Hemiancistrus, and allied genera and recognize Ancistomus as valid for Peckoltiafeldbergae, Hemiancistrusmicrommatos, Ancistrussnethlageae, Hemiancistrusspilomma, and Hemiancistrusspinosissimus. We recommend descriptions of genera for several clades of Hemiancistrus and restriction of Hemiancistrus to the type species of the genus, Hemiancistrusmedians. Chaetostomusmacrops is transferred to Pseudancistrus and recognized as a junior synonym of Pseudancistrusmegacephalus. The Hemiancistrusannectens group of species (Hemiancistrusannectens, Hemiancistrusargus, Hypostomusaspidolepis, Hemiancistrusfugleri, Hemiancistrusholostictus, Hemiancistrusmaracaiboensis, Hemiancistruspanamensis, Hemiancistruswilsoni) are recognized in Hypostomus. Multivariate analysis reveals that the newly described species differ from one another in shape space, but overlap broadly with other Peckoltia (Peckoltialujani), narrowly with other Peckoltia (Peckoltiagreedoi), or broadly with Etsaputu (Peckoltiaephippiata).

Cave-obligate aquatic organisms are difficult to monitor for conservation due to cryptic diversity, unknown subterranean hydrological connectivity, and accessibility to habitats. Conservation management practices have benefitted from evolutionary data; however, the evolutionary and biogeographic histories of most cave-obligate organisms are unknown. The modes and patterns leading to most cave-obligate organism distributions are also uncertain. The Southern Cavefish (Typhlichthys subterraneus, Amblyopsidae) is the largest ranging cavefish in the world but represents a species complex of which the distribution and relatedness within remains unclear. To explore modes of cave-adaptive evolution, we performed population genomic analyses on a dataset of single nucleotide polymorphisms harvested from ultraconserved elements. We found five to eight strongly delineated genetic clusters. Little to no genetic exchange occurred between clusters, indicating high genetic distinctiveness and low connectivity, a concerning result for the fitness and conservation of these fishes. Genetic clusters did not correspond to caves nor to other geographic boundaries examined. Unfortunately, one of the geographic units most easily communicated for conservation– caves– do not match the biological units of interest. Our results support multiple independent colonization events from a widespread surface ancestor with a small degree of cave connectivity among, but not between, clusters. We suggest whole cave system conservation.