Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements

Ultraconserved elements from transcriptome and genome data provide insight into the phylogenomics of Sternorrhyncha (Insecta: Hemiptera)

Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification

In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.

Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes)

The South American characiform family Hemiodontidae comprises five genera and 34 species. The family lacks comprehensive phylogenetic hypotheses resolving its species relationships. The studies that addressed these questions exhibited a narrow taxon sampling or used single-locus markers. Herein we surveyed hundreds of ultraconserved elements (UCEs) loci to provide the first molecular phylogenetic hypothesis and divergence time estimates for hemiodontids encompassing all its genera and most species (27 of the 34 valid species). We also tracked the history of the protractile upper jaw in the genera Argonectes and Bivibranchia across the recovered phylogenies through ancestral state reconstruction. Our results corroborate the monophyly of Hemiodontidae and the genera Argonectes and Bivibranchia in all phylogenetic methods with maximum clade support. The genera Anodus and Hemiodus were not monophyletic because Anodus elongatus was sister to the monotypic Micromischodus instead of A. orinocensis, and H. immaculatus did not form a clade with its other congeners, but instead was sister to the clade including Anodus and Micromischodus. All remaining species of Hemiodus were placed together into a monophyletic group, where they were arranged into four major subclades. The relationship in the family is summarised as: (Bivibranchia, (Argonectes, ((H. immaculatus, (Anodus, Micromischodus)), Hemiodus clade))), in discordance with the morphological phylogeny that placed all genera monophyletic and resolved the family as: ((Anodus, Micromischodus), (Hemiodus, (Argonectes, Bivibranchia))). The origin of Hemiodontidae was estimated from the Late Cretaceous to the Middle Paleogene, with the mean age in the Paleocene, while the origin of most hemiodontid genera except Bivibranchia occurred in the Miocene. Unordered parsimony and likelihood reconstruction indicates that Argonectes and Bivibranchia developed their protractile upper jaw independently.

Anatomy, ecology, and behavior of a new species of Scleronema Eigenmann, 1917 (Siluriformes: Trichomycteridae) from coastal drainages in the southern Brazilian Atlantic Rainforest, with comments on the monophyly and phylogeny of the genus

A new species of Scleronema (Trichomycteridae) is described from the lowlands of three coastal river basins in the Atlantic Forest of the Santa Catarina state, Southern Brazil. Aspects of the anatomy, reproduction, diet, feeding behavior and habitat of the new species are described and discussed in comparison with related taxa. The conservation status of the new species, which currently faces several threats due to environmental impacts on its region of occurrence, is established. Based on characteristics observed in the new species, as well as in most of its congeners, the phylogenetic position and monophyly of Scleronema are discussed and traits considered synapomorphic for the subgenera Plesioscleronema and Scleronema are reviewed. The monophyly of the genus Scleronema is supported by a new synapomorphy. In addition, two new synapomorphies, one of which based on behavior, are suggested for the subgenus Scleronema, justifying the inclusion of the new species. Within the subgenus Scleronema, the new species is assigned to the S. minutum group, which currently includes the majority of species of the genus, due to the presence of synapomorphic traits related to the body shape, maxillary barbel, skin flap of the opercle, caudal and pectoral fins, as well as osteological features of the lower jaw, hyoid arch, and postcranial axial skeleton. The species herein described differs from all its congeners by a combination of characters from various morphological complexes, which are described in detail using different methodologies, including radiography, whole-specimen clearing and double-staining procedures, and tridimensional computer nanotomography (3D nano-CT).

Two new miniature translucent catfish species of the rare genus Tridens (Siluriformes: Trichomycteridae) from the Madeira River basin, northern Brazil

Two new miniature species of the trichomycterid genus Tridens are described from the Madeira River drainage, Acre and Rondônia States, Brazil. Until this work, Tridens was a monotypic genus composed solely of Tridens melanops, from the Putumayo/Içá River drainage, upper Amazonas River basin. Tridens vitreus sp.n. is known from upper and middle Madeira River drainage and differs from all other congeners by the lack of pelvic fins and girdle and by vertebra and dorsal-fin ray counts. Tridens chicomendesi sp.n. is known from Abunã River, middle Madeira River drainage and is distinguished from all other congeners by the number of vertebrae, dorsal-fin ray count and anal-fin base colouration pattern. Tr. chicomendesi sp.n. is further distinguished from T. vitreus by a combination of character states regarding the position of urogenital opening, dorsal-fin position, anal-fin position, maxillary barbel length, number of premaxillary teeth, number of dorsal-fin rays, number of anal-fin rays, number of lateral-line system pores, frontal bone anatomy, degree of ossification of maxilla, anatomy of quadrate-hyomandibular joint, size of posterodorsal process of hyomandibula, length of opercular patch of odontodes, number of interopercular odontodes, proportion of upper hypural plate cartilage relative to its area ; by the absence of a proximal, distal and ventral cartilages on ventral hypohyal; by the absence of a lateral process on basibranchial 4; by the presence of a cartilage block on the lateral process of autopalatine, the presence of a well-developed ossification on proximal margin of ventral hypohyal, the presence of hypobranchial foramen; and by the presence of an anterior cartilaginous joint between quadrate and base of posterodorsal process of hyomandibula. This work represents the first species description for the subfamily Tridentinae in more than 30 years and for the genus Tridens since its original description in 1889.

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America

Hyphessobrycon is one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Mar Chiquita Lagoon in Buenos Aires, Argentina. The majority of Hyphessobrycon diversity shows a cis-Andean distribution; only nine species are trans-Andean including H. compressus (Meek 1908). It is well established that Hyphessobrycon is not monophyletic but it has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we tested the monophyly of trans-Andean species of Hyphessobrycon and investigated the placement of H. compressus. We inferred the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly of trans-Andean Hyphessobrycon inclusive of H. compressus, strong support for three species groups, and evidence of cryptic diversity within the widespread H. compressus and H. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history of Hyphessobrycon in Middle America. Our ancestral range estimation analysis suggests a single event of cis- to trans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Chocó block) to northern Middle America (Maya block). Our work supports the recognition of the trans-Andean species as Hyphessobrycon sensu stricto and provides an evolutionary template to examine morphological characters that will allow us to better understand the diversity of Hyphessobrycon in Middle America.

Morphologic and genetic variation within a relict Andean catfish, Hatcheria macraei , and its relationship with Trichomycterus areolatus and Bullockia maldonadoi (Siluriformes: Trichomycteridae)

The South American siluriform fishes are found primarily in the Neotropical region, north and east of the Colorado River of Argentina, with a few relict species distributed southward and westward on both sides of the Andes Mountains. Three of these, the closely related trichomycterids Hatcheria macraei, Trichomycterus areolatus and Bullockia maldonadoi, have been subject to historical taxonomic and nomenclatural arrangements. Here, we amplify a 652-bp fragment of COI mtDNA from 55 H. macraei individuals and use publicly available Cytb mtDNA sequences of the three taxa to assess their relationship, genetic variation and haplotype distribution in relation to hydrographic basins. In addition, we extend a recent morphometric study on H. macraei by analyzing body shape in 447 individuals collected from 24 populations across their entire cis-Andean distribution. We identified some lineages previously assigned to T. areolatus that show a closer relationship to either B. maldonadoi or H. macraei, revealing new boundaries to their currently known trans-Andean distribution. We found a great morphologic variation among H. macraei populations and a high genetic variation in H. macraei, T. areolatus and B. maldonadoi associated with river basins. We highlight further integrative studies are needed to enhance our knowledge of the southern Andean trichomycterid diversity.

Perils of Underestimating Species Diversity: Revisiting Systematics of Psammocambeva Catfishes (Siluriformes: Trichomycteridae) from the Rio Paraíba do Sul Basin, South-Eastern Brazil †

Psammocambeva, a subgenus of Trichomycterus s.s., includes a clade endemic to south-eastern Brazil, the Psammocambeva alpha-clade (PAC), containing species with similar colour pattern and fin morphology, making difficult their identification without accurate examination. The greatest diversity of PAC species occurs in the Rio Paraíba do Sul basin area (RPSA), situated within the Atlantic Forest, one of the most important and endangered biodiversity centres in the world. Herein, we: perform a multigene phylogeny focusing on species of PAC; revise morphological characters diagnosing species of PAC from the RPSA, with special attention to those equivocally synonymised in a recent study; describe two new species, and provide a key for species identification. Molecular and morphological evidence supported the recognition of eight valid species belonging to four species complexes. Data indicated that T. auroguttatus, T. travassosi, and T. longibarbatus are valid species. Finally, we discuss the negative impacts of underestimating species diversity in regions under the intense process of natural habitat loss, concluding that integrative approaches are important tools to estimate species diversity, but they should include a range of morphological characters informative to delineate and diagnose groups and their respective species, in association with phylogenies generated by robust molecular datasets.

Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae)

Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.

Secretive fish diversity: A new species of Listrura (Siluriformes, Trichomycteridae) from a supposedly well-known river in south-eastern Brazil

The trichomycterid catfish Listrura menezesi, new species, is described from a flooded area adjacent to Rio das Panelas, Rio São João basin, Cachoeiras de Macacu municipality, Rio de Janeiro State, Brazil. It represents a most valuable remnant of Atlantic Forest biome that still resists the devastation of Brazilian coastlands. Listrura menezesi can be distinguished from its congeners, except L. boticario and L. depinnai, by the absence of a dorsal fin. It mainly differs from L. boticario and L. depinnai by a continuous midlateral dark stripe along the entire body (vs. discontinuous) and a longitudinal row of irregular dots along the dorsal limit of the abdomen extending for nearly the entire body (vs. only on the posterior half of the body in L. boticario and not forming a distinct row in L. depinnai). Although the new species shares with L. boticario and L. depinnai the absence of dorsal fin, recent phylogenetic analyses show a close relationship between L. menezesi and L. macaensis, the latter having a dorsal fin. A putative apomorphic condition for this clade is presented: the abrupt widening on the mesethmoid axis starting posteriorly on the horizontal through the middle region of the autopalatine (vs. anteriorly, on the horizontal through the anterior region of the autopalatine). Listrura menezesi comes as an addition to the ichthyofauna of the Rio São João drainage, a region extensively sampled for the past 20 years and supposedly well known. This paper also highlights the vulnerability of this species and the possibility of its disappearance in the near future.

Phylogenetic position of Trichomycterus astromycterus (Siluriformes: Trichomycteridae), an enigmatic trichomycterid from eastern Brazil, inferred from molecular data

Recently in this journal, a new trichomycterine from eastern Brazil, Trichomycterus astromycterus, was described and considered possibly related to the Chilean Bullockia maldonadoi due to morphological similarities. Subsequently, osteological data supported T. astromycterus in the subgenus Psammocambeva of Trichomycterus, from eastern Brazil. Phylogenetic analyses, performed here, using a multigene data set for a broad trichomycterine sample, corroborate T. astromycterus as a member of Psammocambeva, reinforcing the importance of molecular data for inferring trichomycterine relationships but showing that osteological data alone may infer correctly phylogenetic placements when using broad comparative databases.

Phylogenetic Position of Trichomycterus payaya and Examination of Osteological Characters Diagnosing the Neotropical Catfish Genus Ituglanis (Siluriformes: Trichomycteridae)

The Trichomycterinae is among the most diverse catfish groups in the world, with interesting ecological specializations; however, the taxonomy of Trichomycterinae is still problematic, mainly due to unclear limits and diagnoses of the eight included genera. Herein we infer the phylogenetic position and generic placement of Trichomycterus payaya, a recently described species from north-eastern Brazil, with unique morphological features among congeners. A multigene analysis including fragments of two nuclear and two mitochondrial genes (total of 2974 bp) for 53 trichomycterine taxa and three outgroups clearly supports inclusion of T. payaya in Ituglanis, a trichomycterine genus containing 29 valid species, which is corroborated by osteological characters. An examination of osteological characters used to diagnose Ituglanis in its original description indicates that a rudimentary or absent posterior cranial fontanel is synapomorphic for Ituglanis, but this is reversed in I. payaya; an anteriorly directed antero-lateral extremity of the sphenotic-prootic-pterosphenoid complex and a narrow and long lateral process of the parurohyal are synapomorphic for Ituglanis, but homoplastically occurring in other trichomycterids; and the presence of a deep medial concavity on the autopalatine is ambiguous to diagnose Ituglanis by occurring in other closely related trichomycterine taxa. Ituglanis is also distinguishable from other trichomycterines by a unique shape of the metapterygoid and by a reduced number of ribs. The analysis supports a clade, comprising I. payaya and I. paraguassuensis, that is endemic to the Chapada Diamantina, in the semiarid Caatinga of north-eastern Brazil, reinforcing the importance of this region for trichomycterid diversification. By integrating molecular analysis and comparative morphology, the present study provides a more solid basis for delimiting Ituglanis, creating a better taxonomical resolution of the Trichomycterinae, although much more research is necessary to reach a consistent generic classification for the entire subfamily.

Osteology-focused redescription and description of the blood-feeding candirus Paracanthopoma parva and Paravandellia alleynei sp.n. (Trichomycteridae: Vandelliinae)

This study resolves a significant impediment to the taxonomy of the Neotropical endemic hematophagous candirus by providing the first high-resolution, CT-based osteological descriptions of type and nontype specimens of Paracanthopoma parva, type species of the genus. We also describe the distinctive new species Paravandellia alleynei based on specimens that were previously misidentified as Parac. parva in the only taxonomic study of that species since its 1935 description. Paracanthopoma parva is distinguished from all nominal congeners by its parietosupraoccipital and caudal skeleton morphology and by various meristics, including numbers of teeth on median premaxilla, vertebrae, and procurrent and principal caudal-fin rays. Paravandellia alleynei differs from both nominal congeners (Paravandellia oxyptera and Paravandellia phaneronema) by the unique morphology of its maxilla, mesethmoid and opercular apparatus, relative position of the pelvic- and anal-fin origins, orientation of the opercular odontodes, and various meristics, including numbers of vertebrae, median premaxillary teeth, medial teeth on premaxilla, branchiostegal rays, opercular and interopercular odontodes, distal claw-like premaxillary teeth, dorsal-fin rays and dentary teeth. This is the first species of Paravandellia recognized from Guyana and the Essequibo River basin. It is currently known only from two type specimens from the lower Essequibo River basin and 43 nontype specimens from the upper Branco River basin. By providing the first skeletal observations for type specimens of the type species Parac. parva and for topotypic specimens of all three nominal species of Paravandellia, we clarify and confirm the diagnosis of Parac. parva and establish a robust foundation for ongoing taxonomic revisions of these two small-sized and species-poor, yet trans-continentally distributed genera, both of which contain considerable unrecognized diversity.

Uncertainties and risks in delimiting species of Cambeva (Siluriformes: Trichomycteridae) with single-locus methods and geographically restricted data

Abstract Cambeva contains species with complex taxonomy or poorly delimitated in terms of morphology and geopraphic distribution. We conducted an extensive review of Cambeva populations from coastal drainages of Southern to Southeastern Brazil to evaluate species geographic limits with an integrative analysis including morphological and molecular data (COI). We test if two single-locus methods, Bayesian Poisson Tree Processes (bPTP) and Generalized Mixed Yule Coalescent (GMYC), are efficient to delimit species boundaries in Cambeva by the comparison with the diagnosable morphological units. Using GMYC, we also evaluated the combination of tree and molecular clock priors to reconstruct the input phylogeny and assessed how well the implemented model fitted our empirical data. Eleven species were identified using a morphological diagnosability criterion: Cambeva balios, C. barbosae, C. botuvera, C. cubataonis, C. davisi, C. guaraquessaba, C. iheringi, C. tupinamba, and C. zonata and two treated as undescribed species. In contrast with previous knowledge, many of them have wider distribution and high intraspecific variation. Species delimitation based on single-locus demonstrated incongruences between the methods and strongly differed from the morphological delimitation. These disagreements and the violation of the GMYC model suggest that a single-locus data is insufficient to delimit Cambeva species and the failure may be attributable to events of mitochondrial introgression and incomplete lineage sorting.

A new species of Cambeva (Siluriformes, Trichomycteridae) from the Rio Iguaçu basin, Paraná State, Brazil and redescription of Cambeva stawiarski (Miranda Ribeiro 1968)

This work aimed to describe Cambeva cauim, sp. nov., endemic to the Rio Iguaçu basin, Brazil and redescribe Cambeva stawiarski using external and internal morphological data through the revision of specimens deposited in fish collections, including the type material. In this process, we have also added comments on the possible type locality of C. stawiarski. C. cauim, sp. nov. and C. stawiarski are mainly diagnosed by the anatomy and number of procurrent caudal-fin rays in addition to colouration and several meristic and morphometric characters. Both species are compared with other possibly related species and their synapomorphic characters are discussed. C. cauim, sp. nov. and C. stawiarski along with eight other congeners are endemic to the Rio Iguaçu basin, a high impacted freshwater region which could be considered as a biodiversity hotspot to the genus.

Range extension of the miniature pencil-catfish Potamoglanis wapixana (Siluriformes: Trichomycteridae) into the Essequibo River basin, Guyana

Morphological examination of Potamoglanis specimens from three localities in the Essequibo River basin, Guyana, and one location in the Branco River basin, Brazil, confirmed their identification as Potamoglanis wapixana - a species originally described from only the Branco River basin. Morphological similarity of these miniature catfishes on opposite sides of the Rupununi savannah watershed divide and new records from lentic habitat suggest that either their modern populations predate the Pliocene division of the Branco and Essequibo rivers or the species is capable of living in and/or migrating across the Rupununi Portal - a seasonally flooded hydrological connection known to facilitate the movement of mostly much larger fishes between the Branco and Essequibo basins.

Repeated colonization of caves leads to phenotypic convergence in catfishes (Siluriformes: Trichomycterus) at a small geographical scale

Across various animal groups, adaptation to the challenging conditions of cave environments has resulted in convergent evolution. We document a Neotropical cavefish system with ample potential to study questions related to convergent adaptation to cave environments at the population level. In the karstic region of the Andes of Santander, Colombia, cave-dwelling catfish in the genus Trichomycterus exhibit variable levels of reduction of eyes and body pigmentation relative to surface congeners. We tested whether cave-dwelling, eye-reduced, depigmented Trichomycterus from separate caves in Santander were the result of a single event of cave colonization and subsequent dispersal, or of multiple colonizations to caves by surface ancestors followed by phenotypic convergence. Using mitochondrial DNA sequences to reconstruct phylogenetic relationships, we found that caves in this region have been colonized independently by two separate clades. Additional events of cave colonization – and possibly recolonization of surface streams – may have occurred in one of the clades, where surface and cave-dwelling populations exhibit shallow differentiation, suggesting recent divergence or divergence with gene flow. We also identify potentially undescribed species and likely problems with the circumscription of named taxa. The system appears promising for studies on a wide range of ecological and evolutionary questions.

Comparative Osteology, Phylogeny and Classification of the Eastern South American Catfish Genus Trichomycterus (Siluriformes: Trichomycteridae)

Trichomycterus has been considered for a long time to be the most problematic genus of the diverse neotropical subfamily Trichomycterinae. Recently, Trichomycterus was restricted to a clade from eastern South America supported by molecular data, but no unique morphological character state was found to distinguish it, making it difficult to allocate new species based on morphology alone. The objectives of this study were to conduct an osteological comparative analysis comprising a large sample of valid species of Trichomycterus, to conduct a total evidence phylogenetic analysis, combining osteological characters and a multigene database, and to propose an intrageneric classification based on the results of the phylogenetic analysis. Fifty-two osteological characters were combined with a multigene molecular data set of 2974 bp for 44 species of Trichomycterus, and 21 outgroups generated a well-supported phylogenetic tree, making it possible to delimit and diagnose intrageneric lineages, of which six subgenera are recognized. The high morphological diversity of osteological structures herein first reported for Trichomycterus from eastern South America is possibly related to some ecological specializations. This study shows that osteological characters combined with molecular data may be useful to consistently delimit and distinguish between trichomycterines, shedding light on the still persistent problems in trichomycterine systematics.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

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.

Filling distribution gaps: Two new species of the catfish genus Cambeva from southern Brazilian Atlantic Forest (Siluriformes, Trichomycteridae)

The fauna and flora of the Brazilian Atlantic Forest have been intensively inventoried since the 19th century, but some components of this rich biota are still poorly known, and some areas have been poorly sampled. Recent studies on a rich collection of mountain catfishes of the genus Cambeva have revealed a high diversity of species still undescribed in the region. Here we provide formal descriptions for two of these species, found in areas inserted in a broad gap of the presently known genus distribution. The first one is endemic to small coastal river basins of Santa Catarina state, southern Brazil; it is tentatively placed in an intrageneric clade, also including C. castroi, C. davisi, C. guareiensis and C. zonata, by all sharing the presence of a flat small process on the dorsal margin of the quadrate, laterally overlapping metapterygoid and situated just posterior to the syncondrial joint between the metapterygoid and the quadrate. Phylogenetic relationships of the second new species, endemic to the Rio Itajaí-Mirim basin, are still obscure, but it shares a derived morphology of the mesethmoid with some species of the C. balios group. Although species of Cambeva have little external morphological variation when compared to other trichomycterine groups, the present study once more shows the importance of recording and using osteological characters to diagnose externally similar trichomycterine species.

Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)

The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.

Iterative taxonomy reveals a new species of Trichomycterus Valenciennes 1832 (Siluriformes, Trichomycteridae) widespread in Rio Doce basin: a pseudocryptic of T. immaculatus

This paper reports on a new species of Trichomycterus from the Rio Doce basin. Unusually for new taxa in the genus during the past few decades, the new species is not narrowly endemic but instead widely distributed in its major drainage, the Rio Doce. The species has been collected and deposited in scientific collections for some years, but has been systematically misidentified as the more abundant Trichomycterus immaculatus or, to a lesser degree, as other morphologically similar species from south-eastern Brazil such as T. nigricans and T. pradensis. A combination of several morphological characteristics, such as vertebral number, pectoral-fin ray counts, pigmentation pattern and barcoding distance, were iteratively used and unambiguously distinguish the new species from all congeners. The present case reveals a pattern of diversity-discovery in which rare and narrowly endemic morphologically conspicuous species are discovered and described before visually inconspicuous taxa, even when the latter are more abundant and widespread. The morphological similarities among south-eastern Brazilian species with a uniform dark-grey color serve as basis for a brief discussion about the concepts of cryptic and pseudo-cryptic species in Trichomycterus and their consequences for potentially hidden diversity in the genus.

A new species from subtropical Brazil and evidence of multiple pelvic fin losses in catfishes of the genus Cambeva (Siluriformes, Trichomycteridae)

A third pelvic-less species of Cambeva from river basins draining the Geral mountain range in southern Brazil is described. It is distinguished from other congeners lacking pelvic fin and girdle, C. pascuali and C. tropeiro, by having six pectoral-fin rays, 20–23 dorsal procurrent caudal-fin rays, 15–20 opercular and 25–30 interopercular odontodes and a different colour pattern consisting of flank dark brownish-grey with two irregular horizontal rows of small pale yellow grey marks. Whereas available molecular evidence indicates that C. pascuali is more closely related to C. zonata, a species with well-developed pelvic fin, and C. tropeiro is more closely related to C. balios, another species also with well-developed pelvic fin; osteological data strongly suggest that the new species herein described is more closely related to C. diatropoporos than to other congeners. Therefore, this study indicates that the pelvic fin and pelvic-fin support have been lost independently in each of these three species of Cambeva, which corresponds to 11% of all describe species. This result highly contrasts with the closely-related trichomycterine genera Trichomycterus, in which only one in 50 species lost pelvic fin and girdle (0.2%) and Scleronema with all the nine included species having well-developed pelvic fin. These data suggest a stronger tendency to losing pelvic fin in Cambeva, but factors favouring this evolutionary event are still unknown.

Diversification of Neotropical Freshwater Fishes

Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.

Ammoglanis natgeorum, a new miniature pencil catfish (Siluriformes: Trichomycteridae) from the lower Atabapo River, Amazonas, Venezuela

A new species of the sand-dwelling catfish genus Ammoglanis is described from a marginal habitat of the lower Atabapo River, a left-bank blackwater tributary of the upper Orinoco River in Amazonas, Venezuela, adjacent to the border with Colombia. Ammoglanis natgeorum is distinguished from all congeners by trunk pigmentation pattern consisting of scattered ventral chromatophores concentrated around the anal-fin base and numerous additional meristic and anatomical characteristics. A. natgeorum is the second species of Ammoglanis described from the Orinoco River basin after Ammoglanis pulex, and several shared character states (e.g., eight total dorsal-fin rays, overall coloration pattern and presence of two finger-like papillae posterior to chin) suggest that it is more closely related to Ammoglanis obliquus (from the central Amazon basin) and A. pulex than to other congeners.

Systematic revision of the Neotropical catfish genus Scleronema (Siluriformes: Trichomycteridae), with descriptions of six new species from Pampa grasslands

ABSTRACT The Neotropical genus Scleronema is revised based on the re-examination of the type specimens and 1,713 newly collected specimens. Scleronema is diagnosed from other trichomycterids by the following unambiguous derived characters: fleshy flap at the base of the maxillary barbell; skin flap in the posterior margin of the opercle; articulation between the autopalatine and the vomer ventrally located, with the medial margins of the autopalatines very close to each other; and autopalatine with an interrupted or not interrupted ossified arch-shaped process on its dorsal surface forming a canal. Scleronema minutum and S. operculatum are redescribed, S. angustirostre is considered a junior synonym of S. minutum, and six new species are described. A lectotype is designated for Trichomycterus minutus. The type localities of S. angustirostre, S. minutum, and S. operculatum are reviewed in order to correct erroneous information cited in articles and catalogs subsequent to the original descriptions. Species of Scleronema are geographically distributed in the La Plata basin and Atlantic coastal drainages from Southern Brazil, Southern Paraguay, Northeastern Argentina and Uruguay. They inhabit rivers or streams with sand- or gravel-bottoms across the Pampa grasslands. We provide evidences to recognize two putative monophyletic units within the genus, namely the S. minutum species group and the S. operculatum species group, and discuss the distribution patterns of their species.