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Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided., (© 2024 Fisheries Society of the British Isles.)

A new species of Phalloceros is described from the Tijucas, Maruim, Aririú, Cubatão do Sul, Rio da Madre, D'Una and Tubarão river basins in southern Brazil. The new species is diagnosed among congeners by the bilateral asymmetry of a hood-like structure located immediately anterior to the urogenital papilla of females. The hood is fused with the urogenital papilla on the right side, but free from the papilla on the left side. This hood is reported for the first time in the genus and is present in six of the 21 valid species of Phalloceros, but its bilateral asymmetry is an exclusive condition of the new species. These species do not constitute a monophyletic group. The new species is likely to be phylogenetically related to P. caudimaculatus, whose females have a symmetrical hood., (© 2023 Fisheries Society of the British Isles.)

A recent study based on genomic data by Roxo et al. (2019) provided a phylogeny of the Loricariidae, the largest catfish family and second largest Neotropical fish family with approximately 1,000 species. The study represents a valuable and innovative contribution for understanding higher-level relationships within the family. The phylogenetic tree inferred by Roxo et al. (2019) thoroughly corroborates the monophyly and relationships of most currently accepted subfamilies of Loricariidae, based on a fair taxon sampling (nearly 14% of the species in the family) representing most genera of each but one of the subfamilies, the Lithogeninae, the sister-group of the remaining members of the family (Pereira & Reis, 2017; Reis et al., 2017). In addition to a hypothesis of relationships, Roxo et al. (2019) also proposed a series of lower-level taxonomic changes, which are deemed premature considering that the taxonomic sampling of the study targeted higher-level clades, and go against one of the pillars of biological classification: nomenclatural stability (e.g., Heterick & Majer, 2018; Beninger & Backeljau, 2019). Here we (1) discuss implications of inadequate taxonomic sampling as a basis for changes in classification of species; (2) explain why the taxonomic sampling design of Roxo et al. (2019) is inadequate for the proposed nomenclatural changes; and (3) advocate that changes to classifications must be grounded on phylogenies with dense sampling of taxa at the relevant level.

Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America. Following previous fish barcoding studies, we also tailed our primers with M13 forward and reverse primers to facilitate the DNA sequencing process. Although this practice generates primer dimers, we obtained complete and high quality COI barcode sequences for all samples. We discuss the problem of primer dimers and suggest strategies for neutralizing their influence on data quality.

Myleus pachyodus, a new serrasalmid species, is described from the Rio Teles Pires and Rio Jamanxim, both tributaries of the Rio Tapajós in Mato Grosso and Pará states, Brazil. The new species differs from all congeners by having a remarkable ontogenetic thickening of the teeth shifting from slender incisiform in juveniles to thick bulky teeth at standard length ≥ 100 mm, whereas congeners present slender, antero-posteriorly flat teeth throughout all life stages. The new species further differs from congeners by having 18-20 branched dorsal-fin rays, by the lack of a diastema between contralateral outer series of premaxillary teeth and by the presence of 16-25 prepelvic spines, with the anteriormost spine never reaching the vertical through the pectoral-fin origin., (© 2018 The Fisheries Society of the British Isles.)

Background: The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses., Results: Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3' end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group., Conclusions: Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome.

The microhylid frogs belonging to the genus Arcovomer have been reported from lowland Atlantic Rainforest in the Brazilian states of Espírito Santo, Rio de Janeiro, and São Paulo. Here, we use DNA barcoding to assess levels of genetic divergence between apparently isolated populations in Espírito Santo and Rio de Janeiro. Our mtDNA data consisting of cytochrome oxidase subunit I (COI) nucleotide sequences reveals 13.2% uncorrected and 30.4% TIM2 + I + Γ corrected genetic divergences between these two populations. This level of divergence exceeds the suggested 10% uncorrected divergence threshold for elevating amphibian populations to candidate species using this marker, which implies that the Espírito Santo population is a species distinct from Arcovomer passarellii. Calibration of our model-corrected sequence divergence estimates suggests that the time of population divergence falls between 12 and 29 million years ago.

Characidium inirim is described from the rio das Mortes, rio Araguaia basin in Central Brazil. The new species is distinguished from its congeners by having an incomplete lateral line, a conspicuous dark longitudinal stripe and dark transverse bars not extending ventrally to the lateral line, and by lacking the adipose fin and the dark caudal blotch. A phylogenetic hypothesis based on the available data on the phylogenetic relationships of the subfamily Characidiinae is presented. Results suggest that the new species is closely related to C. bahiensis, C. interruptum, C. lagosantense, C. nupelia, C. lanei, C. laterale, C. occidentale, C. orientale, C. rachovii, C. stigmosun, C. vestigipinne and C. xavante.

Background: Freshwaters are the most threatened ecosystems on earth. Although recent assessments provide data on global priority regions for freshwater conservation, local scale priorities remain unknown. Refining the scale of global biodiversity assessments (both at terrestrial and freshwater realms) and translating these into conservation priorities on the ground remains a major challenge to biodiversity science, and depends directly on species occurrence data of high taxonomic and geographic resolution. Brazil harbors the richest freshwater ichthyofauna in the world, but knowledge on endemic areas and conservation in Brazilian rivers is still scarce., Methodology/principal Findings: Using data on environmental threats and revised species distribution data we detect and delineate 540 small watershed areas harboring 819 restricted-range fishes in Brazil. Many of these areas are already highly threatened, as 159 (29%) watersheds have lost more than 70% of their original vegetation cover, and only 141 (26%) show significant overlap with formally protected areas or indigenous lands. We detected 220 (40%) critical watersheds overlapping hydroelectric dams or showing both poor formal protection and widespread habitat loss; these sites harbor 344 endemic fish species that may face extinction if no conservation action is in place in the near future., Conclusions/significance: We provide the first analysis of site-scale conservation priorities in the richest freshwater ecosystems of the globe. Our results corroborate the hypothesis that freshwater biodiversity has been neglected in former conservation assessments. The study provides a simple and straightforward method for detecting freshwater priority areas based on endemism and threat, and represents a starting point for integrating freshwater and terrestrial conservation in representative and biogeographically consistent site-scale conservation strategies, that may be scaled-up following naturally linked drainage systems. Proper management (e. g. forestry code enforcement, landscape planning) and conservation (e. g. formal protection) of the 540 watersheds detected herein will be decisive in avoiding species extinction in the richest aquatic ecosystems on the planet.

In the 1960s, as a part of the construction of the Furnas Hydroelectric Power Dam, Minas Gerais, Brazil, the Rio Piumhi was diverted from the Rio Grande drainage to the São Francisco River basin, with the resulting introduction of species from one basin to the other. Chromosomal characteristics of various populations of Astyanax fasciatus sensu Eigenmann from the transect region were studied using cytogenetic techniques, with the goal to identify and map the dispersal of invasive species in the Rio São Francisco. Populations of the Rio Grande and Rio Piumhi are distinct from those of the São Francisco basin based on chromosome markers associated to the heterochromatin, Ag-NORs, 18S rDNA, 5S rDNA, and As-51 satellite DNA sites. Individuals with karyomorph originally present in the Piumhi drainage are now present in the São Francisco basin, downstream from the transposition channel. This expansion of the distribution corroborates a hypothesis of progressive substitution of native populations by the invasive Piumhi form.

Cytogenetic studies were performed in two syntopic species of Characidium, C. lauroi and Characidium sp. cf. C. alipioi, from Ribeirão Grande, Paraíba do Sul river basin. Both species have diploid number 2n=50 chromosomes, but differ in chromosome shape, C-banding pattern and location of nucleolar organizing regions. In Characidium sp. cf. C. alipioi a new type of ZW sex chromosome system composed of equal sized metacentric chromosomes is reported for the first time in the genus Characidium. Species of Characidium with a sex chromosome system form a monophyletic group. Variations in this system are interpreted as resulting from geographic isolation among allopatric species.

Abstract- Miniaturization, which results in the presence of numerous apparently paedomorphic characters associated with reduced size, is a common phenomenon among neotropical fishes, with over 85 miniature species distributed among the five major ordinal groups. Eleven species are recognized as miniatures within the Characidiinae, a monophyletic subunit of Characiformes. A reconstruction of characidiin phylogeny is used to analyze the history of miniaturization events. Former hypotheses of origin of miniaturization among characidiins are rejected, underscoring the need for phylogenetic frameworks in the study of ontogenetic changes associated with the phenomenon of miniaturization. The 11 instances of miniature species can be most parsimoniously attributed to three independent miniaturization events within the Characidiinae. Reductive characters comprise a large proportion of phylogenetically informative characters within the Characidiinae. In the largest group of miniatures, reductive characters represent more than half of the character state transformations affecting supraspecific relationships among Elachocharax, Klausewitzia, Odontocharacidium and Microcharacidium. An analysis of patterns of character state distributions fails to reject the null hypothesis of character independence. A distinction is made between the concepts of character independence, defined as the origination of character states from different (non-simultaneous) evolutionary events, and character correlation, defined as the association of character states in terminal taxa. Character correlation is not a sufficient criterion to reject Hennig's auxiliary principle, according to which the "presence of apomorphous characters in different species is always reason for suspecting kinship, and their origin by convergence should not be assumed a priori". High values of character correlation are the expected result of congruent patterns of character distribution.