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We performed an analysis of the descriptions of new species of Neotropical Siluriformes (catfishes) to estimate the number of new species that remain to be described for a complete knowledge on biodiversity of this order, to verify the effectiveness of taxonomic support, and to identify trends and present relevant information for future policies. We conducted a literature review of species descriptions between January 1990 and August 2014. The following metadata were recorded from each article: year of publication, number of species, journal and impact factor, family(s) of the described species, number of authors, age of the authors and coauthors, country of the first author's institution and ecoregion of the type-locality. From accumulation of descriptions, we built an estimate model for number of species remaining to be described. We found 595 described species in 402 articles. The data demonstrated that there has been an increased understanding of the diversity of Siluriformes over the last 25 years in the Neotropical region, although 35% of the species still remain to be described. The model estimated that with the current trends and incentives, the biodiversity will be known in almost seven decades. We have reinforced the idea that greater joint efforts should be made by society and the scientific community to obtain this knowledge in a shorter period of time through enhanced programs for promoting science, training and the advancement of professionals before undiscovered species become extinct. The model built in this study can be used for similar estimates of other groups of animals.

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 1288 ultraconserved element loci 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 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 2150 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.

Despite the current recognition of and as two separate valid species of China, neither species have been revised based on examination of their types and/or topotypical materials, nor have they genetically analyzed. In this study, examination of the holotype of showed that it has a serrated anterior edge of the pectoral spine, a slightly emarginate caudal fin, and longer maxillary barbels extending beyond the base of the pectoral spine, the characters shared with specimens currently identified as . Morphological comparisons and molecular analysis showed that specimens from mainland China, which are characterized by the three mentioned morphological features, represent a single species. According to the nomenclatural rule of priority, is a senior subjective synonym of . Within this concept, is widely distributed in the lower reaches of Yangtze River and coastal rivers in Zhejiang and Fujian Province and closely related to , which is endemic to Japan. The morphological differences and species-level genetic distance between and provide additional support for synonymization of and . The paper also describes ontogenetic color changes and coloration polymorphism in this species. Phylogeny of the group, to which belongs, is also discussed.

We analyzed one Bunocephalus coracoideus population from the Negro River basin using cytogenetic techniques. The results showed a diploid number of 42 chromosomes in both sexes, with the karyotypic formula 4m + 14sm + 24a and fundamental number (FN) = 60 for females and the formula 5m + 14sm + 23a and FN = 61 for males, constituting an X sub(1)X sub(1)X sub(2)X sub(2)/X sub(1)Y sub(1)X sub(2)Y sub(2) multiple sex chromosome system. The constitutive heterochromatin is distributed in the pericentromeric regions of most of the chromosomes, except for the sex chromosomes, of which the X sub(1), X sub(2), and Y sub(1) chromosomes were euchromatic and the Y sub(2) chromosome was partially heterochromatic. 18S rDNA mapping confirmed the presence of nucleolar organizer regions on the short arms of the fifth chromosomal pair for both sexes. The 5S rDNA is present in the terminal regions of the short arms on the 2nd, 10th, and 12th pairs and on the X sub(2) chromosome of both sexes; however, we observed variations in the presence of these ribosomal cistrons on the Y sub(1) chromosome, on which the cistrons are pericentromeric, and on the Y sub(2) chromosome, on which these cistrons are present in the terminal portions of the short and long arms. Telomeric sequences are located in the terminal regions of all of the chromosomes, particularly conspicuous blocks on the 10th and 12th pairs and internal telomeric sequences in the centromeric regions of the 1st, 6th, and 9th pairs for both sexes. This work describes an new sex chromosomes system for the Siluriformes and increases our genetic knowledge of the Aspredinidae family.

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.

The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in South and Central America with eight subfamilies, 41 genera and more than 300 valid species. Its members are widely distributed throughout South America, reaching Costa Rica in Central America and are recognized by extraordinary anatomical specializations and trophic diversity. In order to assess the phylogenetic relationships of Trichomycteridae, we collected sequence data from ultraconserved elements (UCEs) of the genome from 141 specimens of Trichomycteridae and 12 outgroup species. We used a concatenated matrix to assess the phylogenetic relationships by Bayesian inference (BI) and maximum likelihood (ML) searches and a coalescent analysis of species trees. The results show a highly resolved phylogeny with broad agreement among the three distinct analyses, providing overwhelming support for the monophyletic status of subfamily Trichomycterinae including Ituglanis and Scleronema . Previous relationship hypotheses among subfamilies are strongly corroborated, such as the sister relationship between Copionodontinae and Trichogeninae forming a sister clade to the remaining trichomycterids and the intrafamilial clade TSVSG (Tridentinae-Stegophilinae-Vandelliinae-Sarcoglanidinae-Glanapteryginae). Monophyly of Glanapteryginae and Sarcoglanidinae was not supported and the enigmatic Potamoglanis is placed outside Tridentinae.

Pterygoplichthys pardalis is an endemic as well as economically important fish species in the Amazon basin. Thirty P. pardalis specimens were purchased at assorted fairs in the city of Manaus. Fish were necropsied, and then, had their organs investigated for parasites. The identified parasites were observed under Light bright field microscopy and that of Scanning Electron Microscopy (SEM). Through the analyses it was observed 219 metazoan parasite specimens, belonging to four taxonomic groups: Monogenoidea, Digenea, Acanthocephala, and Copepoda. Six metazoan parasitic species were identified: Monogenoidea Unilatus unilatus Mizelle and Kritsky, 1967 and Copepoda Therodamas elongatus (Thatcher, 1986) from the gills, Digenea Austrodiplostomum compactum (Lutz, 1928), Megacoelium spinicavum Szidat, 1954 and Diplostomum sp. from the eyes, stomach, and gonads, respectively, and Acanthocephala Gorytocephalus elongorchis Thatcher, 1979 from the intestine. Gorytocephalus elongorchis was the one presenting the highest prevalence value, followed by digeneans M. spinicavum, Diplostomum sp., and A. compactum. The present study has come to provide the very first SEM M. spinicavum, G. elongorchis, and T. elongatus images, thus improving on the up to now available data addressing P. pardalis parasitic fauna, which has been found to be infecting, the fish species presently being marketed in Manaus. Moreover, the current survey has demonstrated the identified parasite species pose no public health concern at all.

The Neotropical region hosts 4225 freshwater fish species, ranking first among the world’s most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a largescale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications.

Abstract The sand catfish or painted catfish (Hypostomus affinis) is a species native to Brazil and has some peculiar characteristics: a flattened body covered by bony plates and fins with spikes for fixing on rocks. Molecular studies have been carried out to better understand this and other species of fish. In this study, a comparison was made between DNA extraction methodologies to define the best extraction protocol for this species. For the study, approximately two grams of the caudal fin of twenty adult specimens of Hypostomus affinis were used for DNA extraction. For this, three extraction protocols were performed. The quantification of the genetic material was carried out in a NanoDrop 2000c Spectrophotometer, thus obtaining the DNA concentration in ng/µL and purity of each sample (A260/A280 and 230/260 ratio). Protocol I, based on Barrero, was the one that presented the best result of DNA concentration of 2846.28 ng/µL. Showing no difference from the III NaCL, which showed 2385.69 ng/µL of DNA. It is concluded that the protocol I presented the best results in terms of quantity and purity. Resumo O bagre-da-areia ou bagre-pintado (Hypostomus affinis) é uma espécie nativa do Brasil e possui algumas características peculiares: corpo achatado coberto por placas ósseas e nadadeiras com espinhos para fixação nas rochas. Estudos moleculares têm sido realizados para melhor compreender esta e outras espécies de peixes. Neste estudo foi feita uma comparação entre metodologias de extração de DNA, para definir o melhor protocolo de extração para esta espécie. Para o estudo, foram utilizados aproximadamente dois gramas da nadadeira caudal de vinte espécimes adultos de Hypostomus affinis para extração de DNA. Para isso, foram realizados três protocolos de extração. A quantificação do material genético foi realizada em Espectrofotômetro NanoDrop 2000c, obtendo-se assim a concentração de DNA em ng/µL e a pureza de cada amostra (relação A260/A280 e 230/260). O protocolo I baseado em Barrero, foi o que apresentou melhor resultado de concentração de DNA 2846,28 ng/µL. Não apresentando diferença em relação ao III NaCL, que apresentou 2385,69 ng/µL de DNA. Conclui-se que o protocolo I apresentou os melhores resultados em termos de quantidade e pureza.