Phylogeography and conservation genetics of the Amazonian freshwater stingray Paratrygon aiereba Müller & Henle, 1841 (Chondrichthyes: Potamotrygonidae)

Fingerprinting based on spectral reflectance and chemometrics - An analytical approach aimed at combating the illegal trade of stingray meat in the Amazon

The survival of Amazon stingrays is threatened due to excessive fishing and habitat degradation. To address this issue, this study developed a groundbreaking method to authenticate and differentiate Amazon stingray meats using a portable spectrophotometer and chemometrics. Samples were collected from various species, including an endangered one with a commercialization ban and no population reduction records. Principal Component Analysis (PCA), identified natural groupings based on the meat's commercial origin, while Partial Least Squares-Discriminant Analysis (PLS-DA), accurately discriminated the commercial and geographic origins with 100 % accuracy. Moreover, Data-Driven Soft Independent Modeling of Class Analogy (DD-SIMCA), effectively distinguished Amazon stingray meat from other marketable species. This approach offers a rapid, precise, and non-destructive means for monitoring and controlling the illegal trade of these species, thereby supporting decision-making in the field and promoting the conservation and sustainability of freshwater stingrays in the Amazon region.

Signatures of positive selection in the mitochondrial genome of neotropical freshwater stingrays provide clues about the transition from saltwater to freshwater environment

Neotropical freshwater stingrays (subfamily Potamotrygoninae) are carnivorous bottom feeder batoids widely distributed in most river basins of South America. They represent the unique extant group of elasmobranchs that evolved to live exclusively in freshwater environments. These species are exploited either by commercial fisheries (e.g., for food or ornamental industry) or by indigenous communities allocated along with their natural range. Restrictive life history characteristics coupled with habitat degradation make Potamotrygoninae species highly vulnerable to human impacts and highlight the necessity of studies to inform basic biological aspects, from ecology to genetics, to guide their conservation and clarify the molecular basis of adaptation to the freshwater environment. We used available and newly assembled Potamotrygon spp. mitogenomes to perform a comparative investigation of their molecular evolution. A phylogenetic estimation using the mitogenome of Potamotrygon falkneri and other Elasmobranchii supports monophyly for Potamotrygonidae and indicates a close relationship to Dasyatidae. A synteny analysis comprising 3 Potamotrygon and other 51 batoids revealed a highly conserved mitogenomic context. We detected various amino acid sites under positive selection exclusively in Potamotrygon spp., within the sequences of ND4, ND5, ND6, and COXII genes. Positively selected mutational events in key genes of energetic metabolism may be related to the physiological adaptation of Potamotrygon spp. during the ancient incursion into freshwater. This broad comparative mitogenomic study provides novel insights into the evolutionary history of neotropical freshwater stingrays and their relatives and stands out as a valuable resource to aid in current and future research on elasmobranch molecular evolution.

Molecular phylogeny for the Neotropical freshwater stingrays (Myliobatiformes: Potamotrygoninae) reveals limitations of traditional taxonomy

The subfamily Potamotrygoninae, the only extant clade of elasmobranchs exclusive to freshwater environments, encompasses four genera and 38 species distributed across almost every major South American river basin. Despite their importance in the ornamental fish trade, the taxonomy and evolutionary relationships within potamotrygonines have not yet been resolved. Here, we present a comprehensive molecular phylogeny for the Neotropical freshwater stingrays, based on extensive species and population sampling (35 species and > 350 individuals from drainages across South America). Our phylogeny corroborates the monophyly of the genera Paratrygon and Heliotrygon and the monophyly of the Potamotrygon + Plesiotrygon clade. Within the Potamotrygon + Plesiotrygon clade, we identify a core Potamotrygon clade characterized by short branches, low nodal support and incongruence with current species-level taxonomy. In the core Potamotrygon clade, specimens of widespread species, such as Potamotrygon motoro and Potamotrygon orbignyi, do not form monophyletic lineages; instead, specimens from these species are often closely related to those of other species from the same river basins. These patterns could be caused by inaccurate taxonomy, hybridization, incomplete lineage sorting and rapid diversification. We discuss the conservation of Neotropical freshwater stingrays from a phylogenetic perspective and suggest ways to prioritize potamotrygonid conservation efforts with respect to endemism and evolutionary distinctiveness.

Two new species of freshwater stingrays of the genus Paratrygon (Chondrichthyes: Potamotrygonidae) from the Orinoco basin, with comments on the taxonomy of Paratrygon aiereba

Abstract The genus Paratrygon, currently recognized as the sole monotypic genus of the family Potamotrygonidae, has a considerably greater diversity than previously indicated, including molecular studies, which supported P. aiereba (hitherto the only recognized species in the genus) as a possible species complex. Here we describe two new species of the genus that are both endemic to and sympatric in the Orinoco basin. Paratrygon aiereba, type species of the genus, is now restricted to the Amazon basin. Both new species are identified and defined through morphological characters such as coloration, dermal denticle morphology, arrangement of thorns, distribution and morphology of ventral lateral line canals, morphology of skeletal elements, and morphometrics. An extensive comparison of these characters between the new species herein described and P. aiereba is presented. Finally, a taxonomic reappraisal of P. aiereba is provided through a revision of preserved material and its original description, plus new evidence about its type-locatity, collectors, and a reconsideration of the destination of its type-specimen.

Phylogeography, genetic diversity and population structure of the freshwater stingray, Paratrygon aiereba (Müller & Henle, 1841) (Myliobatiformes: Potamotrygonidae) in the Colombian Amazon and Orinoco basins

The freshwater stingray Paratrygon aiereba have coloration, osteological and morphometric variations that could suggest the existence of more than one species in Colombia. In order to evaluate the phylogeography, population structure and genetic diversity for P. aiereba distributed in the Amazon and Orinoco basins, we amplified Cytochrome oxidase subunit 1 (COI) partial region of mitochondrial DNA (mtDNA) in 50 samples from eight different sub-basins. Our results suggest three phylogroups and a vicariance event occurred 43 million years ago proposing how Paratrygon diverged into the basins. A high population structure (Φ_ST = 0.692; p < 0.005) and a value of (K) of 3 were defined. A high genetic diversity within phylogroups was found: Phylogroup A (h = 0.64; π% = 2.48), Phylogroup B (h = 0.552; π% = 1.67), and Phylogroup C (h = 0.49; π% = 0.73). These results should be considered in local management plans, conservation programs and reclassification in at least Amazon and Orinoco.

Paratrygon aiereba irradiated anti-mucus serum reduce edematogenic activity induced in experimental model

Accidents by freshwater stingrays are common in northern Brazil, there is no specific therapy for high morbidity and local tissue destruction. The irradiation of venoms and toxins by ionizing radiation has been used to produce appropriate immunogens for the production of antisera. We planned to study the efficacy of stinging mucus irradiation in the production of antisera, with serum neutralization assays of edematogenic activity and quantification of cytokines performed in animal models of immunization with native and irradiated mucus of Paratrygon aiereba, a large freshwater stingray. Antiserum potency and its cross-reactivity with mucus from other freshwater stingrays were detected by ELISA. Immunization models demonstrated the ability to stimulate a strong humoral response with elevated levels of serum IgG detectable by ELISA, and both native and irradiated mucus were immunogenic and capable of recognizing mucus proteins from other freshwater neotropical stingrays. Mucus P. aiereba causes cellular and humoral adaptive immune responses in cells of immunized mice producing antibodies and cytokines such as TNF-α, IL-6 and IL-17. Rabbit antisera immunized with mucus from P. aiereba irradiated at 2 kGy showed a significant reduction of mucus-induced edematogenic activity in mice. Our data suggest that the use of antisera against freshwater stingray mucus show the possibility of specific therapy for these accidents.

Ichthyofauna of sandy beaches along the Acre river, Brazil

Abstract: Despite increasing efforts in recent years to catalog the fish diversity of Amazonian rivers, many regions are still under-sampled, and sandy beach environments are particularly poorly understood. The present study focused on a 300 km stretch of the Acre river, in the southwestern Amazon basin, where we sampled 30 sandy beaches separated by a mean interval of 10 km. We collected 15,329 fish representing 80 species, 26 families, and nine orders. The Characiformes were the most abundant order, providing 88.24% of the individuals collected, followed by the Siluriformes, with 10.03%, while the Siluriformes had the highest species richness, with 37 species (45.0%), followed by the Characiformes, with 30 (37.5%). The most abundant species were the characiforms Knodus orteguasae and Creagruto barrigai. Reliable data on a region’s biota is fundamental for the evaluation of patterns of biodiversity, and the occurrence and management of threatened species. As fish are directly affected by pollutants and the degradation of aquatic environments, further research in areas that are still poorly sampled will be essential for the elaboration of effective conservation strategies.

The largest fish in the world's biggest river: Genetic connectivity and conservation of Arapaima gigas in the Amazon and Araguaia-Tocantins drainages

Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (F_ST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.

A Multilocus Approach to Understanding Historical and Contemporary Demography of the Keystone Floodplain Species Colossoma macropomum (Teleostei: Characiformes)

We studied the natural populations of a flagship fish species of the Amazon, Colossoma macropomum which in recent years has been suffering from severe exploitation. Our aim was to investigate the existence or not of genetic differentiation across the wide area of its distribution and to investigate changes in its effective population size throughout its evolutionary history. We sampled individuals from 21 locations distributed throughout the Amazon basin. We analyzed 539 individuals for mitochondrial genes (control region and ATPase gene 6/8), generating 1,561 base pairs, and genotyped 604 individuals for 13 microsatellite loci obtaining, on average, 21.4 alleles per locus. Mean H_E was 0.78 suggesting moderate levels of genetic variability. AMOVA and other tests used to detect the population structure based on both markers indicate that C. macropomum comprises a single and large panmitic population in the main channel of the Solimões-Amazonas River basin, on the other hand localities in the headwaters of the tributaries Juruá, Purus, Madeira, Tapajós, and localities of black water, showed genetic structure. The greatest genetic differentiation was observed between the Brazilian Amazon basin and the Bolivian sub-basin with restricted genetic flow between the two basins. Demographic analyzes of mitochondrial genes indicated population expansion in the Brazilian and Bolivian Amazon basins during the Pleistocene, and microsatellite data indicated a population reduction during the Holocene. This shows that the historical demography of C. macropomum is highly dynamic. Conservation and management strategies should be designed to respect the existing population structure and minimize the effects of overfishing by limiting fisheries C. macropomum populations.

Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing

Background

Mitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study we sequenced the whole mitogenome of 93 Critically Endangered Speartooth Shark Glyphis glyphis from the last three river drainages they inhabit in northern Australia.

Results

Genetic diversity was extremely low (π =0.00019) but sufficient to demonstrate the existence of barriers to gene flow among river drainages (AMOVA Φ_ST =0.28283, P <0.00001). Surprisingly, the comparison with single gene sub-datasets revealed that ND5 and 12S were the only ones carrying enough information to detect similar levels of genetic structure. The control region exhibited only one mutation, which was not sufficient to detect any structure among river drainages.

Conclusions

This study strongly supports the use of single river drainages as discrete management units for the conservation of G. glyphis. Furthermore when genetic diversity is low, as is often the case in elasmobranchs, our results demonstrate a clear advantage of using the whole mitogenome to inform population structure compared to single gene approaches. More specifically, this study questions the extensive use of the control region as the preferential marker for elasmobranch population genetic studies and whole mitogenome sequencing will probably uncover a large amount of cryptic population structure in future studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0232-x) contains supplementary material, which is available to authorized users.