DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring

New Technique for Identification of Ichthyoplankton and Its Application in Biomonitoring Studies, Management and Conservation of Neotropical Fish

Despite significant advancements in ichthyoplankton collection and data processing, challenges persist in the taxonomic identification of these organisms, particularly their eggs. To overcome these challenges, a novel technique has been developed to facilitate the identification of live eggs collected directly in wild. This user-friendly technique includes the collection, processing of the material, and field incubation. Sampling must be conducted using a pelagic net towed at low speed, preferably during early evening. The material processing involves pre-sorting and sorting to remove eggs and larvae. The separated eggs, kept in an aerated bowl, can be identified based on their morphological and meristic characteristics. Unidentified eggs can be placed in plastic bags with oxygen and incubated directly in the aquatic environment for 48-72 h. After this incubation period, the hatched larvae at the yolk-sac or preflexion stage, are identified to the lowest possible taxonomic level. Depending on the study's purpose, hatched larvae and field-collected larvae can be transported to research centers for further development, released back into the natural environment, or fixed to complete the collection. The application of this technique supports management and monitoring programs by identifying spawning areas through egg identification, forming broodstock, and replenishing threatened species, thereby enhancing scientific collections of ichthyoplankton. Additionally, it reduces mortality in ichthyoplankton techniques, including endangered species. Therefore, we believe that this novel taxonomic technique for identifying live ichthyoplankton represents a paradigm shift in the monitoring, management, and conservation of fish, as well as in ecological stewardship and advances in this area of research.

Integrative taxonomy reveals a new species of the glass knifefish genus Eigenmannia Jordan & Evermann, 1896 (Teleostei: Gymnotiformes: Sternopygidae) from the Rio Branco basin, Brazil

A new species of Eigenmannia is described from the Rio Branco basin, Roraima, Brazil, based on morphological and molecular datasets. It is distinguished from all congeners by the following combination of characters: lateral line stripe extending from first perforated lateral line scale to distal portion of caudal filament, presence of superior midlateral stripe with origin posterior to end of body cavity anal-fin hyaline, caudal filament corresponding to 15.2%-43.1% LEA, subterminal mouth, ii,14-16 pectoral-fin rays, 166-219 anal-fin rays, 10-13 scale rows above lateral line at vertical through posterior tip of pectoral fin, 100-128 scales on lateral line, 22-28 premaxillary teeth, 19-23 dentary teeth, 7-10 endopterygoid teeth, depth of posterodorsal expansion on infraorbitals 1 + 2 half as long as infraorbitals 1 + 2 length, basibranchial 1 unossified, 13 precaudal vertebrae, and length of coronomeckelian bone corresponding to 20% of Meckel's cartilage length. The new species has significant genetic divergence from species with accessible DNA sequences in public repositories, ranging from 10.8% to 17.7%. An osteological description of the new species, a review of Eigenmannia cytochrome c oxidase subunit I (COI) sequences available in public repositories based on voucher examination, and a hypothesis of phylogenetic relationships for the new species based on COI are provided. The critical importance of including voucher examination as one of the steps in the pipeline for using DNA sequences present in public repositories in taxonomic and phylogenetic studies is discussed.

Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)

Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.

Discovering the fish fauna of a lagoon from the southeast of the Yucatan Peninsula, Mexico, using DNA barcodes

Background

Aquatic ecosystems in the tropics are typically environments with a high species richness of fishes. These systems are also among the most vulnerable in the world, threatening the overall biodiversity of tropical regions. As a first step, it is important to enumerate the species in any ecosystem to promote its conservation. This study aims to inventory the ichthyofauna in the Chile Verde Lagoon, Quintana Roo, on the Yucatan Peninsula, a system fortunately well protected in Mexico, based on faunal surveys backed up with mtDNA barcodes.

Methods

We collected larvae, juveniles, and adults of fishes in the lagoon with a variety of sampling gear targeting various life stages. Species were identified using both morphology and DNA barcodes. The abundance of species and ichthyoplankton biomass (wet weight, suction technique) were calculated from 43 samples.

Results

We collected 197 adult and juvenile fishes and 3,722 larvae, of which 306 specimens were DNA-sequenced with a success rate of 96.7%. We identified 13 families, 24 genera, and 27 species in our inventory. The species number was estimated to comprise 75% of the potential total richness using the Chao 1 richness estimator. Clupeids and gobiids accounted for 87.9% of the total abundance of fishes, and, together with cyprinodontids, also accounted for the highest ichthyoplankton biomass.

Conclusion

Adult and juvenile fishes were identified by morphology and meristic values, however larvae required DNA barcoding to identify species. The high biomass and abundance of larvae of clupeids, gobiids and cyprinodontids suggests that the Chile Verde Lagoon may be important for reproduction of these species in the region. Microgobius microlepis, a marine goby species, is reported for the first time in an inland oligohaline system. This study provides a basis for future environmental assessment and biomonitoring of the Chile Verde Lagoon in the Yucatan Peninsula of Mexico.

DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent

The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%-87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.

The DNA barcode reveals cryptic diversity and a new record for the genus Leporinus (Characiformes, Anostomidae) in the hydrographic basins of central northern Brazil

Leporinus is one of the most speciose genera of the order Characiformes, with 81 valid species distributed throughout much of Central and South America. The considerable diversity of this genus has generated extensive debate on its classification and internal arrangement. In the present study, we investigated the species diversity of the genus Leporinus in central northern Brazil, and conclude that six valid species-Leporinus maculatus, Leporinus unitaeniatus, Leporinus affinis, Leporinus venerei, Leporinus cf. friderici, and Leporinus piau-are found in the hydrographic basins of the Brazilian states of Maranhão, Piauí, and Tocantins. We analyzed 182 sequences of the Cytochrome Oxidase subunit I gene, of which, 157 were obtained from Leporinus specimens collected from the basins of the Itapecuru, Mearim, Turiaçu, Pericumã, Periá, Preguiças, Parnaíba, and Tocantins rivers. The species delimitation analyses, based on the ABGD, ASAP, mPTP, bPTP, and GMYC methods, revealed the presence of four distinct molecular operational taxonomic units (MOTUs), identified as L. maculatus, L. unitaeniatus, L. affinis, and L. piau (from the Parnaíba River). The bPTP method restricted L. venerei to a single MOTU, and confirmed the occurrence of this species in the rivers of Maranhão for the first time. The separation of L. cf. friderici into two clades and the subsequent formation of different operational taxonomic units was consistent with polyphyly in this species, which indicates the existence of cryptic diversity. The arrangement of L. cf. friderici and L. piau in two different clades supports the conclusion that the L. piau specimens from Maranhão were misidentified, based on their morphological traits, reflecting the taxonomic inconsistencies that exist among morphologically similar species. Overall, then, the species delimitation methods employed in the present study indicated the presence of six MOTUs-L. maculatus, L. unitaenitus, L. affinis, L. cf. friderici, L. venerei, and L. piau. In the case of two other MOTUs identified in the present study, one (L. venerei) is a new record for the state of Maranhão, and we believe that the other represents a population of L. piau from the basin of the Parnaíba River.

Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding

Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.

Global trends, biases and gaps in the scientific literature about freshwater fish eggs and larvae

Syntheses of knowledge are important to reveal trends, biases and gaps in the scientific literature, indicating main data shortfalls and research needs. In this regard, the authors conducted a broad systematic review on the literature about freshwater fish eggs and larvae to investigate (a) temporal trends in the global scientific production, (b) the scope and habitat types, (c) the spatial distribution of studies, (d) the fish species contemplated and their respective conservation status and (e) the factors associated with the spatial distribution of studies. They analysed 654 studies published between 1950 and 2020. The number of studies has increased over time, but with a weak trend. Most studies investigated basic questions about biology and ecology and were carried out chiefly in rivers and lakes. These studies covered 95 freshwater ecoregions (22.3% of all ecoregions) and recorded 871 fish species (4.8% of all freshwater fish currently described). Most species were assessed by the IUCN and classified into six threat categories, but approximately 35% were not evaluated. The main drivers affecting the spatial distribution of studies were ecoregion area, road density, river volume and the number of hydroelectric plants. Results point to significant biases and gaps in the global scientific literature on fish eggs and larvae, especially associated with habitat type, spatial distribution and target species, emphasizing the need to address specific topics. Such biases and gaps indicate the existence of important data shortfalls, which compromise management and conservation planning, as information on fish eggs and larvae is basic and critical for the assessment of fish recruitment and population dynamics.

Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf

A critical factor in fisheries management is the protection of spawning sites for ecologically and economically important fish species. DNA barcoding (i.e., amplification and sequencing of the mitochondrial cytochrome c oxidase I (COI) gene) of fish eggs has emerged as a powerful technique for identifying spawning sites. However, DNA barcoding of individual fish eggs is time-consuming and expensive. In an attempt to reduce costs and effort for long-term fisheries monitoring programs, here we used DNA metabarcoding, in which DNA is extracted and amplified from a composited sample containing all the fish eggs collected at a given site, to identify fish eggs from 49 stations on the West Florida Shelf. A total of 37 taxa were recovered from 4,719 fish eggs. Egg distributions on the West Florida Shelf corresponded with the known habitat types occupied by these taxa, which included burrower, coastal pelagic, epipelagic, mesopelagic, demersal, deep demersal, commensal, and reef-associated taxa. Metabarcoding of fish eggs was faster and far less expensive than barcoding individual eggs; however, this method cannot provide absolute taxon proportions due to variable copy numbers of mitochondrial DNA in different taxa, different numbers of cells within eggs depending on developmental stage, and PCR amplification biases. In addition, some samples yielded sequences from more taxa than the number of eggs present, demonstrating the presence of contaminating DNA and requiring the application of a threshold proportion of sequences required for counting a taxon as present. Finally, we review the advantages and disadvantages of using metabarcoding vs. individual fish egg barcoding for long-term monitoring programs.

Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment

The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.

Contribution to a reference library of DNA barcodes of Colombian freshwater fishes

Background

The Barcode of Life initiative was originally motivated by the large number of species, taxonomic difficulties and the limited number of expert taxonomists. Colombia has 1,610 freshwater fish species and comprises the second largest diversity of this group in the world. As genetic information continues to be limited, we constructed a reference collection of DNA sequences of Colombian freshwater fishes deposited in the Ichthyology Collection of the University of Antioquia (CIUA), thus joining the multiple efforts that have been made in the country to contribute to the knowledge of genetic diversity in order to strengthen the inventories of biological collections and facilitate the solution of taxonomic issues in the future.

New information

This study contributes to the knowledge on the DNA barcodes and occurrence records of 96 species of Colombian freshwater fishes. Fifty-seven of the species represented in this dataset were already available in the Barcode Of Life Data System (BOLD System), while 39 correspond to new species to the BOLD System. Forty-nine specimens were collected in the Atrato River Basin and 708 in the Magdalena-Cauca asin during the period 2010-2020. Two species (Loricariichthysbrunneus (Hancock, 1828) and Poeciliasphenops Valenciennes, 1846) are considered exotic to the Atrato, Cauca and Magdalena Basins and four species (Oncorhynchusmykiss (Walbaum, 1792), Oreochromisniloticus (Linnaeus, 1758), Parachromisfriedrichsthalii (Heckel, 1840) and Xiphophorushelleri Heckel, 1848) are exotic to the Colombian hydrogeographic regions. All specimens are deposited in CIUA and have their DNA barcodes made publicly available in the BOLD online database. The geographical distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

Aegla buenoi n. sp. (Decapoda: Anomura): first record of aeglid crab from Cinzas River basin, Brazil

A new species of freshwater anomuran crab, Aegla buenoi n. sp., is described. The new taxon was collected from two streams within the Cinzas River basin, Paran state, Brazil. We used morphological and molecular data (COI mtDNA) to distinguish the new species from its congeners. Aegla buenoi n. sp. is differentiated by morphological diagnostic features of the cephalothorax, chelipeds, second abdominal epimeron, and uropods. Molecular results confirm the separation of A. buenoi n. sp. from closely related species (A. castro Schmitt, 1942, A. lata Bond-Buckup Buckup, 1994, and A. jacutinga Marl Teixeira, 2020). Hence, our study increases the known diversity of aeglids and reports the first species of Aegla from the Cinzas River basin.

Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding

The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Marañón and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Marañón was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for ~80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovía Amazónica, and should serve as a pre-impact baseline.

Temporal species-level composition of larvae resources in the lower Pearl River drainage and implications for species' reproductive cycles

Resolving the temporal community composition of a larvae population can not only further our understanding of the regional species composition but also help us to infer the reproductive times of regional fish taxa, which can have implications on the development of effective monitoring and conservation policies for the regional fish stock. Nevertheless, correctly diagnosing the fish larvae is extremely challenging due to the paucity of diagnostic morphological characters at the species level. Based on daily larval samplings during March and October in 2018, this study combined morphological features with a DNA barcode technique to determine the species composition of fish larvae in the lower Pearl River drainage (LPR) and evaluate the spawning periods of identified species. Due to an absence of reference barcodes for LPR fishes, a DNA barcode library of adult fishes in the LPR was built for 384 individuals representing 78 morphological species. Analyses demonstrated the usability of the barcode library and uncovered many undetected mitochondrial lineages in 12 species. Morphological analyses performed on 81 temporal larval samples revealed 25 morphotypes and assigned 9 morphotypes into the species level. A total of 1624 larvae from 96 temporal larval samples were selected for molecular identification, and high quality barcoding sequences were obtained from 1391 larvae. We accurately assigned 1078 larvae to 37 species using our barcode library and published database. Among the identified species, a critically endangered species, namely, Ochetobius elongatus, and several invasive species were examined, providing a new perspective to assess the stock of regional endangered and invasive species. Furthermore, this study found high species diversity occurred primarily between May and September, and clarified the spawning periods of identified species inferred from the temporal occurrences of larvae. Above all, our study highlights the applicability to fish larval ecology to assist conservation and fishery management efforts.

Use of DNA barcode in the identification of fish eggs in tributaries of the Paranapanema River basin

Fish eggs are often excluded from identification analysis since at this stage of development there are few morphological characters. The correct identification of eggs can provide important information about spawning areas of species. The current work aimed to identify fish eggs in the Tibagi and Cinzas Rivers using the DNA barcode to obtain information on richness and diversity, adding to the existing data in the area. Of the 928 sequences analyzed using the BOLD Systems database, 99.78% were able to be identified at a specific level, demonstrating a high success rate for egg identification. The samples resulted in 25 species, 11 families, and 2 orders. Of the 25 species found, more than half (60%) present reproductive migration behavior, indicating that the tributaries of the Capivara reservoir are being used as a migratory route by these species. Eggs of rare and endangered species were found, indicating these tributaries as spawning grounds for these species. The results demonstrate the importance of identifying fish eggs in reservoir-influenced environments to recognize breeding areas of native and endangered species, as well as the importance of the Tibagi and Cinzas Rivers for the maintenance of native fish species in the Paranapanema River.

DNA barcoding identifies three species of croakers (Pisces, Sciaenidae) in the ichthyoplankton of the High Paraná River

In the province of Misiones (Argentina), the filling of the Yacyretá Reservoir (Argentina-Paraguay) to its final dimensions in 2011 formed new aquatic ecosystem, e.g., Garupá Stream was converted into a subreservoir. Reports have been made in this stream of adult individuals and spawning of the Family Sciaenidae, excellent colonizers of modified environments. The larvae of this family are morphologically similar, particularly among Pachyurus and Plagioscion species, making taxonomic differentiation difficult. In the present work, sciaenidae larvae were characterized molecularly at the cytochrome c oxidase subunit I gene in order to determine which species use this environment for reproduction. Additionally, genetic distances, Barcode Index Number (BIN) and Automatic Barcode Gap Discovery method (ABGD) were estimated and phylogenetic trees were reconstructed. The results indicated the presence of Plagioscion ternetzi and Pachyurus bonariensis larvae, and for the first time in tributaries of the region, Plagioscion squamosissimus. The incorporation of P. bonariensis and P. squamosissimus to the faunistic assemblage of ichthyoplankton in the Garupá Stream supports better characterization of the species richness of this secondary watercourse modified by the Yacyretá Reservoir, and advancement in our understanding of use of this area for reproduction.

Fish fauna from the Paranapanema River basin, Brazil

Abstract: The Paranapanema River is an important, extensively explored tributary of the Upper Paraná River basin. The fish fauna of the Paranapanema River has been investigated since the 1990s; however, no study has characterized the richness of fish species throughout the basin, including the main channel of the river, marginal lagoons, its tributaries, and sub-tributaries. Thus, we performed a review with 90 independent studies conducted at the upper, middle, and lower sections of the basin. We recorded 225 species, of which 165 were native, and 60 were non-native. We found that 77% of the species within the basin are composed by Siluriformes and Characiformes. Cichliformes had a significant number of non-native species established in impoundment sections of the basin. Incidence-Based Estimators (Bootstrap and Chao 2) demonstrated that the richness of native species is still underestimated. Some native (e.g., Hypostomus ancistroides) and non-native species (e.g., Plagioscion squamosissimus) are widely distributed in the basin, while others had a more restricted distribution. Among the registered species, the family Bryconidae had the highest number of representatives with threatened conservation status. In addition, we observed that the Capivara Reservoir and its tributaries were the most sampled regions, with the majority of studies performed in the Lower Paranapanema basin. The species richness recorded in large tributaries, such as Tibagi, Cinzas, Congonhas, and Pirapó rivers is critical for maintaining the fish fauna in the Paranapanema River. Our contribution may be used to support management actions and conservation strategies, as well as to indicate regions in the basin that need to be better inventoried.

DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.

Refutation of media reports on introduction of the red bellied piranha and potential impacts on aquatic biodiversity in India

The presence of a new, potentially deadly exotic fish resembling the Red Bellied Piranha, Pygocentrus nattereri was reported in India by print media from various aquatic resources. These reports raised dramatic concerns over public health issues and threats to the aquatic biodiversity of India. Considering the potential severity of the issue and concerns raised by the media, we undertook a study to evaluate the reliability of identification reports of the suspected fish, any relationships to other species of piranha and to address any possible threats to the aquatic biodiversity of India. For this study, samples were collected from most of the major river systems and lakes in India and evaluated for taxonomic identifications of the suspect fish and phylogenetic relationships to other fish species. Our results clearly show that the suspect fish is in fact Piaractus brachypomus, a species commonly referred as "Pacu", and not the red bellied piranha, P. nattereri. Comparisons of both fish do show striking similarities that may account for the misreporting in the media. Furthermore, P. brachypomusas is still an exotic fish, and as such may still have potentially harmful impacts on the native aquatic fauna of India. Quick attention to this issue and the imposition of control measures, including market bans, should be considered to prevent further loss of biodiversity.

Species diversity of drifting fish eggs in the Yangtze River using molecular identification

The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts.

A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias

With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently "masked" within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.

Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System

Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats.

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.

How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.

Revealing Hidden Diversity of the Underestimated Neotropical Ichthyofauna: DNA Barcoding in the Recently Described Genus Megaleporinus (Characiformes: Anostomidae)

Molecular studies have improved our knowledge on the neotropical ichthyofauna. DNA barcoding has successfully been used in fish species identification and in detecting cryptic diversity. Megaleporinus (Anostomidae) is a recently described freshwater fish genus within which taxonomic uncertainties remain. Here we assessed all nominal species of this genus using a DNA barcode approach (Cytochrome Oxidase subunit I) with a broad sampling to generate a reference library, characterize new molecular lineages, and test the hypothesis that some of the nominal species represent species complexes. The analyses identified 16 (ABGD and BIN) to 18 (ABGD, GMYC, and PTP) different molecular operational taxonomic units (MOTUs) within the 10 studied nominal species, indicating cryptic biodiversity and potential candidate species. Only Megaleporinus brinco, Megaleporinus garmani, and Megaleporinus elongatus showed correspondence between nominal species and MOTUs. Within six nominal species, a subdivision in two MOTUs was found, while Megaleporinus obtusidens was divided in three MOTUs, suggesting that DNA barcode is a very useful approach to identify the molecular lineages of Megaleporinus, even in the case of recent divergence (< 0.5 Ma). Our results thus provided molecular findings that can be used along with morphological traits to better define each species, including candidate new species. This is the most complete analysis of DNA barcode in this recently described genus, and considering its economic value, a precise species identification is quite desirable and fundamental for conservation of the whole biodiversity of this fish.

DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean

The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.

First DNA Barcode Reference Library for the Identification of South American Freshwater Fish from the Lower Paraná River

Valid fish species identification is essential for biodiversity conservation and fisheries management. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I for a valid identification of 79 freshwater fish species from the Lower Paraná River. Neighbour-joining analysis based on K2P genetic distances formed non-overlapping clusters for almost all species with a ≥99% bootstrap support each. Identification was successful for 97.8% of species as the minimum genetic distance to the nearest neighbour exceeded the maximum intraspecific distance in all these cases. A barcoding gap of 2.5% was apparent for the whole data set with the exception of four cases. Within-species distances ranged from 0.00% to 7.59%, while interspecific distances varied between 4.06% and 19.98%, without considering Odontesthes species with a minimum genetic distance of 0%. Sequence library validation was performed by applying BOLDs BIN analysis tool, Poisson Tree Processes model and Automatic Barcode Gap Discovery, along with a reliable taxonomic assignment by experts. Exhaustive revision of vouchers was performed when a conflicting assignment was detected after sequence analysis and BIN discordance evaluation. Thus, the sequence library presented here can be confidently used as a benchmark for identification of half of the fish species recorded for the Lower Paraná River.

Molecular identification and phylogenetic analysis of Siluriformes from the Paraguay River basin, Brazil

The objective of this study was to identify, through the DNA barcode, fishable Siluriformes which were collected from the Paraguay River basin in Pantanal. It was analyzed for genetic distance calculation using the Kimura-two-model parameters and the dendrogram was builtusing the Neighbour-Joining algorithm. The average genetic distance within species, genus and families were 0.2%, 1.6% and 4.2%, respectively. These values were lower than those reported in studies from other continents, probably due to the recent radiation process undergone by Neotropical fish. The dendrogram revealed two possible cases of hybridization, one individual Pseudoplatystoma corruscans, it was not possible to identify whether it was a natural event or commercial production exhaust and other of Pimelodus cf. argenteus leading to the assumption that the aspects of reproductive isolation cannot be clearly defined. Besides, the populations of the species Hemisorubim platyrhynchos and e Platydora armatulus may be undergoing a substructuring process, with genetic differences 3% and 4%, respectively.

Pimelodus maculatus (Siluriformes, Pimelodidae): complete mtDNA sequence of an economically important fish from the São Francisco river basin

Pimelodus maculatus is an important commercial fish found in the São Francisco and Paraná river basins. NGS was used to sequence the mtDNA of P. maculatus. The mtDNA was annotated and aligned with that of 25 other fish species to enable phylogenetic analysis. The complete mtDNA molecule had 16,561 bp and its GC content was 43.7%; the structure was similar to that of other vertebrates: 2 rRNA, 22 tRNA, 13 protein-coding genes, and a D-loop region containing 914 bp. Phylogenetic analysis yielded a tree with a high bootstrap coefficient that was coherent with the actual phylogeny of the species.