Molecular identification of the fish fauna from the pantanal flood plain area in Brazil

Species boundaries of the whiptail catfish Rineloricaria (Siluriformes: Loricariidae) from the Paraíba do Sul River drainage, southeastern Brazil, with species redescriptions and description of a new species

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.

Iterative taxonomic study of Pareiorhaphis hystrix (Siluriformes, Loricariidae) suggests a single, yet phenotypically variable, species in south Brazil

Pareiorhaphis hystrix is a widely distributed species, occurring in the upper and middle Uruguay River and in the Taquari River basin, Patos Lagoon system, southern Brazil. Morphological variation has been detected throughout the distribution of P. hystrix, and this work seeks to test the conspecific nature of populations in several occurrence areas. Specimens from six areas in the Uruguay River basin and three in the Taquari River basin were compared. Variance analysis (ANOVA) was performed for the meristic data, and Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were conducted for morphometric data. Molecular analyses used coI, cytb, 12S and 16S mitochondrial genes, examining nucleotide diversity, haplotype diversity, genetic distance, and delimitation of possible multiple species through the Generalized Mixed Yule Coalescent (GMYC) method. Phylogenetic relationships of studied populations were also investigated through Bayesian inference. While PCA indicated a tendency of overlap between areas, ANOVA and LDA detected a subtle differentiation between populations from the two hydrographic basins. Yet, both latter analyses recovered the population from Pelotas River, a tributary to Uruguay River, as more similar to populations from Taquari River, which is congruent to morphological observations of anterior abdominal plates. The molecular data indicated a nucleotide diversity lower than the haplotypic diversity, suggestive of recent expansion. The concatenated haplotype network points to slight differentiation between areas, with each locality presenting unique and non-shared haplotypes, although with few mutational steps in general. The species delimitation by coalescence analysis suggested the presence of a variable number of OTUs depending on the inclusion or exclusion of an outgroup. In general, the morphological data suggest a subtle variation by river basin, while the genetic data indicates a weak population structuration by hydrographic areas, especially the Chapecó and Passo Fundo rivers. However, there is still not enough differentiation between the specimens to suggest multiple species. The iterative analyses indicate that Pareiorhaphis hystrix is composed of a single, although variable, species.

Reappraisal of the systematics of Microglanis cottoides (Siluriformes, Pseudopimelodidae), a catfish from southern Brazil

The southern region of Brazil is characterized by high species diversity and endemism of freshwater fishes distributed across geographically isolated river basins. Microglanis cottoides has a widespread range across these river basins and occurs in sympatry with other endemic species of the genus (e.g. M. cibelae, M. eurystoma, and M. malabarbai). Herein we tested the monophyly of M. cottoides and presented for the first time information about the molecular phylogeny of species in the genus. The results suggest that M. cottoides currently forms a non-monophyletic group which includes populations endemic to the Uruguay River basin that are more closely related to M. malabarbai, and excludes M. cibelae, found to be nested within M. cottoides. Based on an integrative approach using morphological and molecular data, we propose M. cibelae as a junior synonym of M. cottoides, and the populations of the Uruguay River basin previously assigned to M. cottoides in fact belong to M. malabarbai. Our molecular phylogeny shows that M. cottoides is sister to M. parahybae, which is also a coastal species, and M. malabarbai is sister of M. garavelloi, both endemic to inland river basins. The time-calibrated phylogeny indicates that the separation between inland and the coastal clades occurred in the Tertiary period, and that the species within the coastal basins diverged in the Pliocene, which overlaps with the diversification times estimated for the two inland species as well. This pattern of diversification corroborates some previous studies with other fishes from the same region.

Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex

Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes)

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

ABSTRACT DNA barcoding is a widely utilized molecular-based identification of species and taxonomic resolutions. Until recently, Rhamdia voulezi and Rhamdia branneri were considered species synonyms of Rhamdia quelen; however, morphological and cytogenetic analyses have suggested the validity of distinct species. Due to the absence of molecular taxonomy of R. voulezi and R. branneri, the objective of this study was to test its validity through traditional DNA barcoding and the GMYC (General Mixed Yule Coalescent) COI-based analyses in 19 specimens from the Iguaçu River Basin. In both methodologies, three MOTUs (Molecular Operational Taxonomic Units) were identified based on the estimated optimum threshold (OT = 0.77). The average inter-MOTU distance (NJ, K2P) between R. branneri and R. voulezi was 1.4%, and 0% intra-MOTU distance in both species. The two species identified as R. branneri and R. voulezi showed correspondence with taxonomic and morphological identifications. With regard to R. quelen, the average intra-MOTU distance was greater than OT (2.7%), indicating that this species can be formed by different MOTUs. We suggest that molecular and taxonomic studies should be employed concurrently in R. quelen, to prevent contamination of wild species by hybridizations.