Updated checklist and DNA barcode-based species delimitations reveal taxonomic uncertainties among freshwater fishes from the mid-north-eastern Caatinga ecoregion, north-eastern Brazil

Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding

The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.

DNA barcoding identification of Greek freshwater fishes

Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.

Review of the armoured catfish genus Hypostomus (Siluriformes: Loricariidae) from the Parnaíba River basin, Northeastern Brazil, with description of a new species

Abstract The species of Hypostomus from the Parnaíba River basin were reviewed through molecular and morphological analysis. Five species were found in the basin, including a new species herein described. The distribution of H. pusarum was expanded to this basin, and a closely related species was recorded (H. aff. pusarum), also the presence of H. johnii and H. vaillanti was confirmed. The new species is distinguished from most congeners by its large number of premaxillary and dentary teeth, a wide dental angle of 115° to 135°, presence of a rounded dark spots on a lighter background and anteromedial region of the abdomen depleted of plaques (vs. anteromedial region of the abdomen covered by platelets and odontodes in H. johnii, H. pusarum, H. aff. pusarum and H. vaillanti). Furthermore, an identification key of the species from the Maranhão-Piauí ecoregion and maps with the geographic distribution of these species are presented. The species of Hypostomus in the Parnaíba River basin have different geographic distributions, suggesting different niches or geographical barriers, providing an opportunity for ecological and evolutionary studies.

First record of Moenkhausia costae (Steindachner 1907) in the Paraíba do Norte basin after the São Francisco River diversion

Abstract: Construction of water diversions in drylands is boosted by increasing demands for freshwater often due to prolonged droughts. Even though these mega-enterprises result in benefits to society, it also poses a threat to freshwater biodiversity. In Northeastern Brazil, for instance, the São Francisco River Integration Project already supplies water for millions of people, but over time it will also favor the introductions of multiple aquatic species in the river basins of the Northeastern Caatinga and Coastal Drainages ecoregion. These introductions can cause unprecedented impacts in the native ichthyofauna, such as homogenization of freshwater faunas, transmission of pathogens and loss of native species. This study compares the composition and relative frequency of fish species from Poções reservoir using data obtained by gillnetting and trawling before and after the São Francisco diversion in the dry and rainy seasons, and reports the first detection of Moenkhausia costae introduction in the Paraíba do Norte basin, through the São Francisco River channel. Our results show some evidences that M. costae may become dominant and invasive in Poções reservoir. The introduction of M. costae adds a new component of disruption for these freshwaters and may pose a serious threat to the endemic ichthyofauna in lentic and lotic systems from the Paraíba do Norte basin.

Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.)

Graylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe’s colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient.

Geographic distribution and conservation of seasonal killifishes (Cyprinodontiformes, Rivulidae) from the Mid-Northeastern Caatinga ecoregion, northeastern Brazil

The Rivulidae fish family, which includes Neotropical seasonal killifishes, is one of the most diverse taxonomic groups in the aquatic systems of Caatinga in Brazil. Cynolebias and Hypsolebias genera, with 20 and 35 endemic species, respectively, concentrate the greatest diversity of rivulid species in the semiarid. Sixty-eight years after the first records of annual killifishes in the Mid-Northeastern Caatinga ecoregion (MNCE), only four valid species have been sampled in this area. Here we combined bibliographic surveys and recent samplings to investigate the distribution of seasonal rivulids in MNCE. Twenty-one records were obtained, nine of which are new localities, expanding the distribution of three species: Hypsolebias martinsi, H. antenori and Cynolebias microphthalmus. Hypsolebias longignatus is still only known from its type locality in Ceará, near the Environmental Protection Area in Pacoti River, and has not been sampled ever since its description in 2008. Among the four species present in MNCE, H. antenori is the only species occurring within the limits of a conservation unit in the Furna Feia National Park. Anthropogenic impacts were observed in most temporary habitats visited, which ranged from river channel to small ponds in cave entrances. All records are found in coastal basins that discharge in the northern coast of the MNCE, in Ceará and Rio Grande do Norte states, which are crucial for the conservation of the Caatinga’s killifishes. The results also evidenced the importance of karstic habitats in the Jandaíra Formation as potential biotopes for seasonal fish in MNCE. This information must be used to update the conservation status of these species and highlight the importance of strategies for preserving the Caatinga’s temporary aquatic habitats, which should be considered for environmental licensing purposes.

Freshwater fish richness baseline from the São Francisco Interbasin Water Transfer Project in the Brazilian Semiarid

Abstract Among Neotropical freshwater ecoregions, the Mid-Northeastern Caatinga (MNCE) is a fish knowledge gap. Its temporary drainages are receptors of the São Francisco interbasin water transfer project (SFR-IWT) in the Brazilian semiarid. We provide a comprehensive baseline of fish richness of the five SFR-IWT basins. Species richness, shared, endemic, threatened and non-native species were obtained using sampling, ichthyologic collections, literature and online repositories (306 localities). In total 121, species were recorded, 111 of them native, and 16 (14.41%) listed for all basins. Higher richness of native species (78, 70.27%) was recorded in the São Francisco lower-middle stretch (SFRE), including 23 endemic, 61 (54.95%) in MNCE basins (13 endemic), and 28 (25.23%) shared between both ecoregions. In the MNCE, 50 species were recorded in Jaguaribe (JAG), 39 in Piranhas-Açu, 36 in Paraíba do Norte, and 32 in Apodi-Mossoró (APO). The number of species shared between the SFRE and each receptor basin varied from 24 (23.08%, JAG) to 20 (22.22%, APO). JAG contains 81.97% of the receptor basins’ species. Its higher richness and endemism deserve special attention regarding the ongoing hydrological changes. This study will help detect possible modifications in the ichthyofauna of the main MNCE drainages.

Integrative systematics unveils the controversial identity of Engraulidae fishing stocks in a Neotropical estuary, northeast Brazil

ABSTRACT In Brazil, the use and diversity of the common names of fish species, coupled with taxonomic uncertainties, hinder the reliability of fishing statistical data. In this scenario, there are the so-called pilombetas of the São Francisco River, an important fishing resource in region. Despite its importance, the real diversity of species identified in the area remains obscure. In order to properly identify and delimit the species popularly known as pilombetas, an integrative approach involving traditional taxonomy, geometric morphometrics and molecular systematics was applied. Results from geometric morphometrics and molecular analyses were consistent with the results of the traditional morphological analysis, also indicating the delimitation of six taxa belonging to Engraulidae in the lower São Francisco River. In addition, species delimitation methods revealed an intrapopulation genetic divergence of 1.7% for Lycengraulis grossidens. The results revealed that the currently known richness species of Engraulidae in the studied area has been underestimated. Thus, an updated taxonomic key is herein proposed for the Engraulidae species from the lower São Francisco River and estuary. The integrative analysis approach revealed to be effective to address taxonomic questions and help the management of stocks, ensuring the maintenance of local diversity of fishes in the Neotropical region.