Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.

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Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma) of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary histories could have been strongly and similarly influenced by Miocene geotectonic events that modified the landscape and produced the drainage pattern of Central Africa seen today.

The distribution of astroblepids was examined using predictive niche modelling techniques to explore the physical and environmental factors responsible for determining the limits to their geographic distribution in the tropical Andes. Astroblepids occur in streams across a wide range of elevations (100-4600 m) and ecosystems from Panama to Bolivia, with most occurrences between 500 and 2000 m and associated with a narrow range of mean temperatures (17-24° C). The Maxent-predicted distribution was 83% accurate, statistically significant (AUC = 0·965), and closely matched the known distribution, with few notable exceptions. Four environmental variables contributed a cumulative 84% to the prediction, with elevation the most important, followed by temperature seasonality, isothermality and maximum temperature of the warmest month. The greatest discrepancy between the predicted and known distributions involved areas of predicted habitat suitability where there are no associated occurrence records. A jackknife test of variable contribution to the model showed that elevation contributed to the predicted distribution in ways not simply accounted for by temperature. Contrary to expectations, land cover type and vegetation characteristics contributed relatively little to the model prediction.

The Yucatán Peninsula (YP) contains one of the most spectacular and developed karstic aquifers in the world, which connects to the surface through water‐filled sinkholes locally known as cenotes. Cenotes and their associated submerged caves are home to a remarkable diversity of aquatic fauna, yet very little is known about spatial patterns of intraspecific genetic and morphological variation across the aquifer. The strong affinity to cenotes (vs. submerged caves) exhibited by most fishes inhabiting the YP aquifer raises a fundamental question about the ecology and evolutionary history of its ichthyofauna: how genetically structured and morphologically divergent are fish populations from different cenotes across the YP? To shed light on this question, we investigated phylogeographic structure in the Neotropical catfish Rhamdia guatemalensis, arguably the most ubiquitous representative of the YP aquifer ichthyofauna. Geographic patterns of genetic variation were determined through phylogeographic and population genetics analyses of mitochondrial (mt)DNA sequence data. Body shape variation was investigated using both traditional and geometric morphometrics. Dense sampling across the previously overlooked YP region, coupled with the inclusion of samples from basins unrepresented in past studies, allowed for revision of previous estimates of phylogeographic structuring across the species’ range. Our results reveal a striking spatial correspondence between major mtDNA lineages and physiographic regions defined on the basis of broad‐scale patterns of groundwater flow. Morphological variation in populations from the YP, although considerable, neither reflects the observed spatial signal of genetic differentiation nor displays any other discernible geographic pattern. The resulting range‐wide phylogeographic pattern is largely consistent with a latitudinal, isolation‐by‐distance gradient, and the expectations from catchment hydrology, while revealing an unexpectedly close relationship between YP aquifer and epigean populations (both inside and outside the YP). Although the inferred range‐wide phylogeographic history is consistent with a single aquifer colonisation event followed by multiple instances of dispersal out of the aquifer and into neighbouring epigean basins, hypotheses regarding the colonisation and exodus of the YP by R. guatemalensis require further investigation. Within the YP aquifer, regional‐scale hydrogeological differences might impose limits to underground dispersal, potentially driving genetic divergence in populations of R. guatemalensis, and possibly in other cenote‐dwelling fishes as well. Future research focused on other YP aquifer species, however, is needed to test the generality of our findings. Phylogeographic research on the stygofauna of the YP aquifer is a relatively nascent field of inquiry. Besides shedding novel light into the patterns and drivers of genetic differentiation in fish populations from across the aquifer, this study sets the stage for future research aimed at unra...

To investigate the presence of cryptic diversity in the African longfin‐tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p‐distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.

We describe a new species in the endemic Malagasy cichlid genus Ptychochromis. Ptychochromis mainty, new species, is known from four individuals, all collected in the Fort Dauphin region of southeastern Madagascar, and shares a palatine morphology (eastern-type palatine) with other eastern congeners. Ptychochromis mainty is distinguished from all congeners by a nearly uniform dark brown to black pigmentation pattern in preservation and by the presence of a relatively continuous and expansive black longitudinal midlateral blotch in life, extending from the posterior margin of the opercle to the caudal peduncle. The new species is further distinguished from other eastern Ptychochromis species by having minimal or no overlap of the first supraneural with the dorsoposterior region of the supraoccipital crest (vs. marked overlap). We present a molecular-based phylogeny for all available Ptychochromis species, which supports the hypothesis that P. mainty is a distinct taxon. The new species is recovered as the sister taxon to P. grandidieri within a clade comprising species with an eastern-type palatine morphology. We present a geometric morphometric analysis that provides additional evidence to distinguish P. mainty from congeners.