B chromosomes are supernumerary genetic elements rich in repetitive DNA. Many species within the fish genus Psalidodon possess a large metacentric B chromosome that exhibits signs of recent retrotransposon activity, resulting in truncated pseudogenic copies of standard A chromosomes genes, specifically sbno2 and simc1. We aimed to characterize the structure of the B chromosome pseudogenes sbno2-B and simc1-B and their evolutionary history in four B chromosome variants of three Psalidodon species, as well as their expression patterns in Psalidodon paranae individuals with a single B chromosome (1B). Our findings suggest that the retrotransposition process of each gene occurred in an ancestral B chromosome, which later diverged into distinct trajectories within each species following speciation. In the high-copy B chromosomes, the sbno2-B pseudogene shows dozens of interspersed copies, while the simc1-B pseudogene usually shows three copies arranged in tandem. In Psalidodon paranae 1B individuals, underexpression of the sbno2 and simc1 genes in ovaries indicates that the pseudogenic B copies probably influence gene expression through non-coding RNA interference mechanisms. This shows that the retrotransposon activity on B chromosomes generates genomic diversity and neofunctionalization, impacting gene regulatory networks, and possibly contributing to the persistence of B chromosome in populations.

We describe Rineloricaria harenaesp. nov., a sand-dwelling armoured catfish from the Itapocú River, Jaraguá do Sul, Santa Catarina, Brazil. The new species is diagnosed by a distinctive combination of characters: (1) four lateral plate series, with the mid-dorsal series absent; (2) abdomen only partially covered by central plates that do not reach the pectoral-fin insertion; (3) plates of the central abdominal complex arranged in an approximately triangular pattern; (4) cleithral (scapular) region entirely naked or bearing a few small, isolated plates; and (5) presence of five dark transverse bars on the dorsal surface of the body. Mitochondrial COI data corroborate species distinctiveness, and phylogenetic inference under the GTR model recovers R. harenae as a well-supported lineage. The species is currently known only from the type locality, a shallow (< 1 m), sandy reach showing early siltation, suggesting potential vulnerability. Although it exhibits canonical traits of sand-dwelling groups (four lateral plate series, broad naked snout, filamentous upper caudal ray), it differs from sand-dwelling congeners by displaying an abdominal plating pattern typical of rock-dwelling groups. This raises hypotheses about the origin and functional role of ventral plates in Rineloricaria and highlights conservation needs for low-order sandy habitats.

Accurate species delimitation within electric rays of the genus Narcine has been hindered by overlapping morphological characters and limited molecular resolution in previous single-locus studies. This study aims to evaluate phylogenetic relationships and species boundaries within the Narcine species complex across the Western Atlantic using complete mitochondrial genomes. Seven complete mitogenomes were newly assembled from individuals representing distinct morphotypes sampled across geographically widespread Western Atlantic localities and analyzed together with publicly available reference sequences. Mitochondrial protein-coding genes (PCGs) were examined using concatenated nucleotide and amino acid datasets under partitioned maximum-likelihood frameworks. Both approaches recovered highly congruent topologies, consistently supporting a single, well-defined western Atlantic mitochondrial lineage with low internal divergence (0.04–2.13

The integration of morphological and molecular data for Imparfinis species from Amazonian drainages of the Brazilian Shield revealed the presence of three previously undescribed species, which are formally described herein. These species are readily distinguished from their congeners by characters related to coloration: I. melanopterus, from the middle Araguaia River, has a distinctly darker lower caudal-fin lobe; I. nigropunctatus, from the upper Araguaia River, possesses conspicuous black spots on the body; and I. tessellatus, from the upper Tapajós River, is characterized by dark blocks of chromatophores on the body, forming a variegated color pattern. Additionally, our species-delimitation analysis recovered these three morphotypes as independent genetic lineages, exhibiting high levels of genetic divergence. A discussion of distributional patterns of Imparfinis within the Amazon River basin is provided.

The deep sea hosts approximately 15% of all fish species, but the difficulty of sampling limits our knowledge, causing large gaps in geographic distribution, and many deep-sea fish groups still require taxonomic revisions. Herein, the deep-sea fishes collected in the southern Brazil, western South Atlantic, are studied through DNA barcoding resulting in a better understanding of the biodiversity and genetic diversity of the region. The samples were obtained during oceanographic cruises aboard the Brazilian R/V Alpha Crucis, focusing on the continental slope off southern Brazil at depths of 200-1,500 meters. A total of 170 sequences of actinopterygian fishes from 102 different species of 49 families and 19 orders were generated. The DNA barcoding identified 84 sequences at the species level, with the remaining being identified at least to the genus level. A high level of genetic divergence between species was observed, ranging from 3.9% to 36.7%. We provided the first COI sequences for 13 species that, to date, were not represented in databases. Among the species already represented in online databases with COI sequences, we expanded the geographic coverage of existing data. As a result, we increased representation for 16 species in the Atlantic, 26 species in the South Atlantic, and 28 species in the western South Atlantic. Our efforts revealed a diverse deep-sea fish fauna in the region, highlighting new occurrences and demonstrating a high genetic divergence between some taxa.

Coryphaenoides Gunnerus, 1765 comprises 66 valid species of deep-sea fishes commonly known as grenadiers, with 6 previously reported from Brazilian waters. Here, we make the first records for Coryphaenoides striaturus and Coryphaenoides subserrulatus on the Brazilian continental slope. Both species are distributed in the subtropical regions of the Southern Hemisphere, and the former is being reported for the first time in the Southwest Atlantic, and the latter has its distribution range extended northward. The identifications were confirmed by a unique combination of morphological characters and DNA barcoding using the cytochrome oxidase subunit 1 (COI) gene.

Genetic diversity is critical to long-term survival of species but can be eroded by population declines driven by human pressures. Temporal genetic monitoring of threatened species can reveal changes in genetic diversity over time, providing key data for conservation. Specimens from natural history collections were used to assess changes in genetic diversity in the Critically Endangered largetooth sawfish (Pristis pristis). Historically, P. pristis had a circumtropical range, but following massive declines it is now primarily found in Australia, with limited depleted populations elsewhere. Genetic data (815-bp of the mitochondrial control region) from 87 specimens from across its historical range revealed significant population structure, with the Indo-West Pacific and the Atlantic/Eastern Pacific comprising distinct lineages. Comparisons between historical (approx. 1878-2000) and contemporary populations (2001-2014) revealed genetic diversity loss, with only six of 35 historical haplotypes represented in contemporary populations. Most of the lost haplotypes were from the Atlantic/Eastern Pacific, which is at risk of further genetic erosion. Genetic diversity in Australia appears stable since the 1960s, while Brazil showed a marked loss, despite contemporary estimates similar to those in Australia. These findings highlight the need to conserve remaining genetic diversity in P. pristis, emphasizing the importance of securing a stronghold in the Atlantic/Eastern Pacific.

Understanding shark reproductive modes is crucial for conservation, as these K-strategist species are vulnerable to overexploitation. The spiny dogfish (Squalus acanthias), a small shark listed as 'vulnerable' by the IUCN, has a 22-month gestation period and a reproductive output ranging from 1 to 21 pups per litter. This study aimed to investigate multiple paternity in S. acanthias using Single Nucleotide Polymorphism (SNP) markers. Samples from six litters, comprising 40 individuals collected in Argentina, were analyzed using a ddRADseq library. SNP markers were screened with the STACKS pipeline, and kinship and paternity were analyzed using COANCESTRY and COLONY software. Results revealed 1,021 to 1,620 SNPs per litter, with multiple paternity detected in all litters. The number of sires per litter ranged from 2 to 4. No correlation was found between litter size and multiple paternity, suggesting this behavior may enhance genetic diversity. The species' size and sex segregation, coupled with females in shallower waters, increase their vulnerability to fishing pressure. Overfishing and bycatch exacerbate the reduction in sexually mature individuals, threatening population recovery. This study highlights the need for management policies that incorporate reproductive strategies, especially for species like S. acanthias with complex life histories and low recovery rates.

Abstract Pterobunocephalus currently comprises two valid species: P. depressus described from the Guaporé River basin and P. dolichurus from the Trombetas River at its confluence with the Amazon River. A third nominal species, Bunocephalus albofasciatus, described from the upper Mamoré River basin, is presently considered a junior synonym of P. depressus. Based on a morphological approach, we describe here a new species of Pterobunocephalus from the upper Amazon basin (Napo, Pastaza, and Putumayo rivers) in Ecuador. The new species is distinguished from its congeners by the following combination of characters: (1) large eyes; (2) anterior margin of the mesethmoid relatively wide, shallowly concave, and sunken between anterior margins of premaxillae; (3) total number of anal-fin rays 10–11; and (4) in dorsal view, parapophysis of the fifth vertebra shaped like the blade of a shepherd’s axe with distal portion conspicuously and abruptly expanded.

Heroini encompasses Central and South American cichlids. Despite intergeneric relationships within the tribe being well-resolved, species-level relationships within several genera or groups of species remain poorly understood, as well as some genera have never had their monophyly tested through phylogenetic analyses. Here we recover the Mesonauta phylogeny using molecular data from two mitochondrial genes, COX1 and 16S, analyzed under Maximum Likelihood (ML) and Bayesian Inference (BI). Results of ML and BI phylogenies corroborates the monophyly of the genus, comprising six monophyletic groups: Clade (A) comprises Mesonauta karipuna from Amapá Grande River basin as sister to a clade comprising Mesonauta festivus from Guaporé River basin as sister to Mesonauta sp. “Pantanal” from Paraguay River basin, both as sisters to M. acora from Tocantins–Araguaia and Xingu River basins. Clade (B), sister to Clade (A), comprises Mesonauta insignis from Orinoco and Upper Negro River basins and M. egregius from the Orinoco River basin, both as sister to M. mirificus widely distributed in the Amazon River basin and M. guyanae from Amazon/Suriname River basins. However, BI analysis revealed a slightly different topology, which was consistent with the previous species delimitation investigation. Although this previous study of Mesonauta suggested that M. insignis specimens should be grouped with M. egregius, while M. mirificus should be grouped with M. guyanae, we decided to retain the validity of these species, which require further investigation. This first attempt at studying the molecular phylogeny of Mesonauta discusses the advances and difficulties to be overcome, and highlights the intrageneric relationships using molecular data. It also provides data for future studies on the evolution of the group.

Abstract Brachyglaniini is a recently described tribe of Heptapterinae, composed of four genera: Brachyglanis, Gladioglanis, Leptorhamdia, and Myoglanis. Expeditions to the Aripuanã and Tapajós River basins revealed an undescribed species of Brachyglaniini, characterized by a conspicuous light-colored band posterior to the head. Our phylogenetic results provide strong evidence that this new Brachyglaniini species belongs to the genus Leptorhamdia and is closely related to L. marmorata and L. aspredinoides. In addition to the color pattern, the new species can be distinguished from its congeners by having 19-22 anal-fin rays and 47 vertebrae.

This review synthesizes the most significant advances and innovations in the cytogenetic study of Neotropical fishes, with emphasis on recurrent chromosomal patterns, evolutionary mechanisms, and the integration of modern genomic tools. The Neotropical region, which harbors more than 12,000 fish species, exhibits not only extraordinary taxonomic richness but also remarkable chromosomal diversity. Chromosomal rearrangements have been associated with speciation and ecological adaptation in both freshwater and marine lineages. Modern techniques, including fluorescence in situ hybridization, chromosome painting, and comparative genomic hybridization (CGH), have substantially improved our ability to resolve morphologically indistinguishable species and clarify their evolutionary relationships. When integrated with phylogenetic and genomic approaches, cytogenetics becomes a robust framework for exploring biodiversity and chromosomal evolution within the complex Neotropical fauna. Despite these advances, substantial challenges remain, particularly the scarcity of cytogenetic data for many taxa and regions. Future research, driven by high-throughput genomic technologies, is expected to deepen our understanding of chromosomal evolution and to support conservation efforts for this rich but increasingly threatened fish fauna.

Pyrrhulina australis Eigenmann & Kennedy, 1903, is widely distributed across the main hydrographic basins of South America. The taxonomic integrity of this species is nevertheless challenged by the lack of clear diagnostic characters, its marked geographic variation and the morphological overlap with its congeners. In this context, the present study investigated the genetic diversity of the P. australis group (P. australis, Pyrrhulina marilynae and Pyrrhulina vittata), using sequences of the mitochondrial Cytochrome Oxidase I gene to delimit evolutionary lineages and provide insights into biogeographic patterns and divergence times. The molecular delimitation analyses (Automatic Barcode Gap Discovery [ABGD], Assemble Species by Automatic Partitioning [ASAP], Bayesian Poisson Tree Processes (bPTP), multi-rate Poisson Tree Processes [mPTP], General Mixed Yule Coalescent [GMYC] and Poisson Tree Processes [PTP]) revealed 12 consensual MOTUs, which represent a complex of cryptic species revealed under the nominal name P. australis, with widely distributed lineages. Divergence time estimates indicate a recent evolutionary history for the group, occurring between the late Pliocene and the Pleistocene. The results reveal a surprising level of diversity within P. australis and provide unprecedented discussions on the biogeographic patterns of the group.

Pseudacanthicus nyktos is a recently described loricariid catfish previously considered restricted to the lower Xingu River basin in the eastern Brazilian Amazon. Herein, we report new records from the Turiaçu River basin, Maranhão State, northeastern Brazil, supported by morphological and molecular evidence. Additional records were obtained through the reanalysis of COI sequences available in public databases and the examination of museum specimens previously identified as Pseudacanthicus sp. Molecular analyses revealed low genetic divergence (K2P = 0.47

Accurate species identification is a challenge in megadiverse regions, where morphology alone can lead to overestimation or underestimation of biodiversity. In this context, the incorporation of molecular approaches, such as DNA barcoding, has been useful in accurately estimating regional biodiversity, revealing cryptic diversity, and enabling identification by non-specialists. This study generated a molecular database of fishes for Parque Nacional dos Lençóis Maranhenses and adjacent areas, based on sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Haplotype analyses were conducted using Maximum likelihood (ML), and the delimitation of Operational Taxonomic Units (OTUs) combined the following methods: Kimura 2-parameter model (K2P), Assemble Species by Automatic Partitioning (ASAP) and Poisson Tree Processes (PTP) methods, using K2P ≥ 2

A new species of Hyphessobrycon is described from a tributary of Rio Jatuarana, lower Rio Aripuanã basin, Rio Madeira basin, Apuí, Amazonas. The new species is part of the Hyphessobrycon agulha lineage, with the typical midlateral narrow black stripe immediately followed dorsally by an iridescent stripe. Its phylogenetic position is corroborated by the DNA barcoding methodology, which also indicates the new species as closely related to Hyphessobrycon ericae and Hyphessobrycon ribeiroi, with both possessing very distinct colour patterns. The new species can be distinguished from all species of Hyphessobrycon by the association of a well-defined and horizontally elongated humeral blotch with a ventral diffuse expansion, a conspicuous caudal peduncle blotch restricted to the ventral half of the caudal peduncle and proximal half of mid rays of caudal fin, the presence of a red midlateral stripe dorsal to the iridescent stripe and lateral-line scale counts.

A new species of Characidium is described from tributaries of the Orinoco River in Colombia and Venezuela. The new species can be distinguished from congeners by a combination of characters, including presence of a conspicuous blotch on the caudal peduncle, presence of secondary vertical bars in addition to primary bars, a complete lateral line with 31-34 perforated scales, 14 circumpeduncular scales, absence of hooks on the pelvic-fin rays of mature males and absence of sexual dichromatism. Molecular species-delimitation analyses consistently supported the monophyly of C. oblivium and recognized it as an independent lineage. Molecular divergence between this lineage and other closely related species was substantially higher than the minimal variation observed within it, providing strong evidence for its status as a distinct species. This study highlights the often overlooked role of museum collections in harboring hidden biodiversity.

Abstract The Araguaia-Tocantins basin is a hotspot of ichthyofaunal endemism within the Amazon biome but is increasingly threatened by habitat fragmentation and environmental degradation, mainly driven by hydroelectric development and waterways. These impacts pose severe risks to lotic habitats, such as rapids, which sustain specialized and range-restricted taxa. We conducted the first population genomic assessment of three rheophilic species of Baryancistrus (B. longipinnis, B. niveatus, and Baryancistrus sp. “Araguaia”) using thousands of genome-wide SNPs obtained through ddRADseq. Overall, analyses revealed weak neutral population structure across species, with limited genetic differentiation. However, subtle isolation by distance was detected in B. niveatus, along with short-distance relatedness in B. niveatus and B. longipinnis. Landscape genetic models (MLPE) indicated that environmental gradients, particularly turbidity, slope, and riparian condition, significantly shaped genetic patterns, especially in B. niveatus. Remarkably, B. longipinnis exhibited low genetic diversity (HO = 0.31 (0.28–0.35); HE = 0.356 (0.36–0.37)), elevated inbreeding (F = 0.12 (0.03–0.20)), and signs of genetic erosion. Tajima’s D values suggested population contraction across all species, likely associated with habitat loss. These findings highlight the vulnerability of rheophilic taxa and identify the Pedral do Lourenço rapids as a key refuge for B. longipinnis, supporting its immediate protection.

Assessing genetic structure across ocean basins is essential to understand connectivity and guide conservation in data-deficient open-water sharks. In this study, we examined the population genomics of Squalus cf. mitsukurii by analyzing tissue samples collected from two distant regions: California, USA (Pacific Ocean) and Pernambuco, Brazil (Southwestern Atlantic Ocean). Using double-digest restriction site-associated DNA sequencing (ddRADseq), we generated 33 480 939 raw reads across 28 individuals and retained 1118 high-quality single nucleotide polymorphisms (SNPs) after stringent filtering. Genetic diversity was moderate (He = 0.211-0.244), with low inbreeding levels (Fis = -0.005-0.106). DAPC and pairwise Fst analyses revealed moderate genetic structure, indicating limited gene flow between the sampled populations. This study provides the first genomic evidence of population differentiation in S. cf. mitsukurii across these regions. Our findings underscore the importance of genome-wide data and informing regionally conservation strategies, especially for exploited species commonly misidentified in commercial landings and lacking population management.