IntroductionMegaleporinus obtusidens, also known as "boga," is a freshwater teleost fish species widely distributed across South America with significant commercial value in Argentina and Brazil. Fishers, particularly those in the lower Paraná River, frequently classify the fish they catch as M. obtusidens. Despite various approaches, including cytogenetics, molecular data, and morphological analysis, the taxonomic classification of the boga fish remains debated among researchers, resulting in discrepancies in the literature.MethodsThis study aimed to assess the diversity of specimens captured in the La Plata River Basin, initially classified as Megaleporinus obtusidens by fishers, using DNA barcoding. The mitochondrial COI marker was employed to explore species assignment and genetic diversity in Megaleporinus, a genus with high commercial exploitation in the southern area of the La Plata Basin.ResultsOur findings indicate that some boga samples, previously identified as M. obtusidens, are actually M. piavussu. We also observed significant differences in the geographic distribution, diversity, and genetic structure between the two species.DiscussionThese results highlight the importance of studying the ecology of each species separately. Proper resource management, based on accurate species identification, is critical for the conservation of ichthyofauna in the region.

Surubim (Pseudoplatystoma corruscans, Pimelodidae) are migratory catfish native to the rivers in the La Plata and São Francisco basins. They are piscivores that attain considerable body sizes and are a valuable economic resource. Surubim exhibits extensive migrations during its life cycle that may affect the population structure at vast geographic scales. The authors examined the genetic diversity and population genetic structure of P. corruscans using microsatellite markers from a comprehensive sampling of 260 individuals from the Upper and Lower Paraná River. They identified two well-differentiated genetic clusters corresponding to a natural geographic barrier historically separating Upper and Lower Paraná regions. They also demonstrated temporal variation in population genetic structure at a site in Lower Paraná close to the confluence with the Paraguay River, most likely explained by the influx of migrant fishes at certain times of the year.

Phylogeographic research is able to identify previously unrecognized units of biodiversity. The aeglid Aegla scamosa is a species that inhabits the Desaguadero basin waterbodies in southern South America. Crabs of the family Aeglidae are especially sensitive to changes in their environment since they have restricted distributions. The aims of our study were to characterize the phylogeography of A. scamosa across its distributional range in Argentina and to identify evolutionarily significant units from these phylogeographic data. We used mitochondrial DNA, nuclear intron, and microsatellite DNA markers to study the genetic diversity, population structure, and phylogeography of the species. Our results indicate that A. scamosa populations are genetically structured in the analyzed sub-basins and that the species comprises at least two independent evolutionarily units: one corresponding to the “North” clade and another coinciding with the “South” clade. We also found a presumptive discrepancy between the information provided by nuclear and mitochondrial markers, that tell different evolutionary stories. Our results highlight the importance of carrying out this kind of study in freshwater fauna, since they may be hiding different evolutionarily significant units as in the case of A. scamosa . The evolutionary complexity of this species should not be ignored in future conservation studies.

Population genetics studies the distributions and changes in population allele frequencies in response to processes, such as mutation, natural selection, gene flow, and genetic drift. Researchers daily manage genetic, biological, and environmental data of the samples, storing them in text files or spreadsheets, which makes it difficult to maintain consistency and traceability. Here we present TEGA, a WEB-based stand-alone software developed for the easy analysis and management of population genetics data. It was designed to: 1) facilitate data management, 2) provide a way to execute the analysis procedures, and 3) supply a means to publish data, procedures, and results. TEGA is distributed under the GNU AGPL v3 license. The documentation, source code, and screenshots are available at https://github.com/darioelias/TEGA. In addition, we present Rabid Fish, the first implementation of TEGA in the Genetics Labortory of the Faculty of Humanities and Sciences at the National University of the Litoral, where research focuses on population genetics studies applied to non-model organisms.

Geographical isolation is a key element in allopatric speciation. If gene flow is interrupted for long enough by geographical barriers, populations can evolve independently and eventually form distinct species. Aegla singularis provides an ideal model to study this process due to the characteristics of the geographical area that it occupies and its limited dispersal ability. Aegla singularis inhabits streams of the Uruguay and Parana River basins in the Neotropical region of South America. The basins are separated by the Sierra Central Mountains. Here we studied the speciation of A. singularis resulting from geographical isolation by using molecular and morphometric data. Individuals of A. singularis were analysed using geometric morphometrics and genetic data (COII and EF alpha 1). We found significant differences in shape and genetics between A. singularis populations from the two basins. These differences suggest ongoing divergence due to restricted gene flow caused by the geographical barrier of the Sierra Central Mountains, indicating that the populations of the Parana and Uruguay River slopes are undergoing divergence.

Ceratium furcoides is an invasive freshwater dinoflagellate that in the last three decades has expanded its geographic distribution in South America, being recently found in Paraná River floodplain (Argentina). Despite growing concern about the presence and impacts of this invader, information regarding genetic diversity in the Southern Hemisphere is missing. This work constitutes the first phylogenetic characterization of Ceratium populations of South America, particularly, from the Paraná system. After taxonomic identification as C. furcoides based on morphological traits, two sequencing‐based approaches were applied using the ribosomal 18S gene: Sanger sequencing to isolated individuals and high‐throughput amplicon sequencing (HTS) to environmental DNA. The sequence of C. furcoides obtained shared 100% identity to Asian sequences, and formed a highly supported clade in the constructed reference phylogenetic tree. HTS helped to recover low‐frequency genetic variants suggesting the presence of different population of C. furcoides, and to alert potential invasion in its early stages.

Four valid species are currently recognized in the Neotropical migratory genus Salminus: Salminus brasiliensis, Salminus franciscanus, Salminus hilarii and Salminus affinis. However, molecular evidence strongly suggested that two different species might be contained under the taxonomic denomination Salminus brasiliensis. Therefore, the geographical distribution of each entity was evaluated in order to understand their contribution to the different stocks of major river networks in South America. 2Major river networks of the La Plata River basin were explored to characterize the geographical distribution of the two genetic lineages. To characterize further the genetic partitioning within each lineage of S. brasiliensis, a haplotype analysis was conducted. The 5 region of the mitochondrial COI gene was used as the molecular marker. In total, 45 fish samples of S. brasiliensis from 19 sites in Argentina, Brazil and Paraguay were sequenced. Additional COI sequences of S. brasiliensis, S. franciscanus and S. hilarii were gathered from public databases. 3All samples of S. brasiliensis comprised two different mitochondrial lineages. Accordingly, phylogenetic tree topologies segregated the complete set of sequences into two disparate clusters. One of these clusters was far closer phylogenetically to S. hilarii than to other S. brasiliensis. 4While one of the genetic lineages of S. brasiliensis seemed mostly restricted to the upper Parana River, the other showed a widespread distribution along major river networks of the basin. 5Fifteen unique haplotypes were identified and collapsed. Salminus hilarii and S. franciscanus have private haplotypes. In S. brasiliensis, each mitochondrial lineage also hosts a set of unshared haplotypes. 6The sympatry of two different putative species within S. brasiliensis together with their unshared haplotypes present a difficult situation for management and conservation that calls for timely solutions.

The yacare caiman (Caiman yacare) is a reptile from South America and 1 of the 2 crocodilian species present in Argentina. The degradation of their natural habitat and strong hunting pressure led to a sharp numerical decline of wild populations. Nowadays, C. yacare is included in Appendix II of CITES, and ranching practices in some areas in Argentina are helping hatching success. In this context, it is important to better understand the population structure and mating system of the species. To do this, we amplified 10 microsatellite markers (SSRs) in 148 individuals of 13 C. yacare nests. All of the markers were polymorphic with 2–12 alleles per locus, with allelic sizes ranging between 154 and 400 bp and medium levels of polymorphism (Ho = 0.152–0.551 and He = 0.221–0.621). We were able to determine the maternal genotype in 9 out of 13 nests. In 6 of them we found more than 1 paternal genotype, with a maximum of 3 fathers for a single nest. This study is the first to provide evidence of multiple paternity behavior. These findings will be useful to improve management and conservation strategies for the species.

Caiman latirostris wild populations have suffered a drastic reduction in the past, and for that reason, a management and monitoring plan was applied since 1990 in Santa Fe, Argentina in order to achieve population recovery. Although ranching system has a noteworthy success in terms of population size recovering, there is no information about the estimation of population genetic parameters. In particular, the consequence of the bottleneck underwent by these populations has not been assessed. We evaluated variability and genetic structure of C. latirostris populations from Santa Fe through time, using microsatellites and mitochondrial DNA. Population genetic parameters were compared among four sites and three different periods to assess the impact of management activities, and effective population size was estimated in order to detect bottleneck events. We observed an increase in microsatellite variability and low genetic variability in mitochondrial lineages through time. Variability estimates are similar among sites in each sampling period; and there is scarce differentiation among them. The genetic background of each sampling site has changed through time; we assume this fact may be due to entry of individuals of different origin, through management and repopulation activities. Moreover, taking into account the expected heterozygosity and effective population size values, it can be assumed that bottleneck events indeed have occurred in the recent past. Our results suggest that, in addition to increasing population size, genetic variability of the species has been maintained. However, the information is still incomplete, and regular monitoring should continue in order to arrive to solid conclusions.

The Patagonian silverside Odontesthes hatcheri is a native fish restricted to streams and lakes of Patagonia (Argentina and Chile). Stocking programs to enhance recreational fisheries in man-made reservoirs have introduced a nonnative, closely-related species (the pejerrey O. bonariensis) in Patagonia almost a century ago, and yet little is known about the invasiveness of this species. To evaluate the impact of these introductions we analyze genetic data (microsatellite markers and mitochondrial DNA) to quantify the incidence of hybridization between these two species and assess potential effects on native population structure. Phylogeographic analyses reveal weak geographic differentiation among populations of O. hatcheri, in agreement with previous studies for other freshwater fishes in Patagonia strongly influenced by Quaternary glaciations and hydrographic basin changes since the last glaciation. However, many populations have unique genetic pools. In several areas, introductions resulted in extensive hybridization, with high frequencies of F2 and backcrossed hybrids in natural populations, and in some cases O. bonariensis has completely displaced the native populations. The negative impact of these introductions on native populations is correlated to temperature, a critical parameter in the face of global warming, suggesting that invasiveness of O. bonariensis may increase in the future. Our results advise against continuing stocking programs to preserve the integrity of natural populations of the Patagonian silverside.

Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

Wild populations of Caiman latirostris are subject to sustainable use programs in Argentina, becoming a species with important impact in the regional economy, based in their skin and meat. Genetic studies are fundamental to acquire information on important parameters for conservation and management, which may be obtained from analysis of molecular markers. Some microsatellites have been previously isolated in this species, but due to some difficulties in using them, we obtained new ones using Next Generation Sequencing approach. This study reports eight new microsatellites for C. latirostris and tests their utility in a related species, Caiman yacare, with successful application in population genetics and mating systems studies. In addition, we shared data about a novel and fast bioinformatics tool to find microsatellites and to design their corresponding primers.

Aeglidae is the only freshwater family in the infraorder Anomura.Aegla uruguayanaSchmitt, 1942 is one of the most widely distributed species in southern South America and is found in different environments, which makes it an interesting object for population genetic studies. The main objective of this work was to analyse the genetic population structure ofA. uruguayanaalong a sea distance gradient for four populations that were studied in the La Plata Basin with an 1100-km range in relation to an east-west transect. The populations studied were the Río Tercero Reservoir, the Setúbal Lagoon, the Doll Stream and the Urquiza Stream. Aeglid DNA was extracted using a commercial kit that was amplified with ISSR markers. Of the 10 primers tested, we selected four that showed the best resolution and reproducible results. Our studies revealed a of 0.3479 ± 0.1383 (mean ± SD) and a global of 0.3583 (), demonstrating genetic differentiation among populations with low gene flow. The Urquiza Stream population showed a genetic structure clearly different from that of the other populations. However, the Río Tercero, Setúbal and Doll populations were well grouped with one effective connection among them. The geomorphologic history of the basin provides evidence for the isolation hypothesis. These data demonstrate the importance of geoclimatic history in the study region and the importance of using complete population distribution data where the species live. These data permit us to interpret that different populations have independent histories that are delineated by the geomorphological events that occurred on earth.

Prochilodus lineatus is a highly migratory fish species that sustains the most important commercial fishery of Paraná-Paraguay basin. Migratory patterns are poorly known and only few population genetic studies are available for this species in the Upper Paraná. To assess genetic population structure, we genotyped a sample of 93 individuals from the Lower Uruguay River close to Gualeguaychú city (Entre Ríos, Argentina) at three different times, July 2008 (Winter), September 2008 (Spring) and May 2009 (Fall). All individuals were genotyped for 12 microsatellite loci previously found to be informative to assess populations of P. lineatus. Our results show seasonal variation of the genetic sub-structuring at this locality that may be related to the presence of different migratory stocks throughout the year. The Fall sample includes an additional genetic cluster of individuals not detected in Winter and Spring, suggesting that this species should be considered a mixed stock fishery.

Over the last 8 years, a group of 18 former crocodile hunters, known as “caimaneros” at Cispatá Bay, Colombia have turned conservationists, joining a project to save the critically endangered American crocodile (Crocodylus acutus). The project includes recovery programs, population monitoring, biological studies on sustainable use, education and communication and it was created a capacity-building program since 2004, in order to promote local livelihoods and give the reptiles a fighting chance. Crocodile eggs are hatched in incubators and reared until they are large enough to release into the wild. As the project is based on sustainable use of the population it will need ongoing monitoring and research that will help form a sound management plan. The project is supported by the Environmental Regional Authority CVS and is part of the integrated management plan for local mangroves on which many people depend for livelihoods. Preliminary Management Plan for the Conservation of Populations of Caiman Aguja (Crocodylus acutus, Cuvier 1807) at Sardinata, San Miguel, New President and Tibu Rivers, Norte de Santander, Colombia Giovanni Andrés Ulloa Delgado and Juan M. Peláez Montes croco_mangle@hotmial.com; juanmanuelpelaez@gmail.com It was discovered and scientifically documented the population of crocodiles or “caiman aguja or caiman of Magdalena” (Crocodylus acutus) most important of Colombia, for its abundance and because population structure corresponds to an acceptable condition of conservation. In the 132 studied kilometres of Sardinata, San Miguel, new President and Tibú Rivers, the census showed 196 established crocodiles with total density of 1.48 crocodiles per km at Sardinata River basin, and an estimate of several thousands of animals. Also the research concluded that deforestation in gallery forest formations was identified as the most significant alteration of the ecological context in the four rivers, with direct influence on the habitat of the crocodiles. In addition to the own research results, the study allowed to structure a line of continuity spanning all possible strategies, which are touted at the global level, to ensure the conservation of biodiversity and in the case of crocodiles in Sardinata River basin. Today we know where are and how are the populations of crocodiles for much of the Sardinata River basin. Also know wthat it should be done for immediate conservation: Research, Education, Community Participation and Declaration of Protected Areas; these are some of the main strategies proposed in the preliminary plan.

The knowledge about reproductive strategies of a species contributes to their conservation. Multiple paternity is a reproductive behavior increasing effective population size, which could increase genetic diversity particularly in populations submitted to bottlenecks events. In Argentina, wild populations of Caiman latirostris are subject of a management plan devoted to their preservation and sustainable utilization based on its commercial interest. This program started in response to the evident numeric reduction of the populations, as a consequence of hunting pressure and habitat modification; it had a remarkable success in population recovery allowing the commercial use of C. latirostris. Data on reproductive behavior of C. latirostris are limited because mating occurs in the water and the information about their genetic diversity is scarce too. Our specific aims were to study the mating system and population genetic structure applying microsatellite markers in twelve C. latirostris families. The obtained results showed highly significant difference among populations and a lack of correspondence between geographical distance and genetic differentiation suggesting that populations of C. latirostris represent unstable metapopulations. In the paternity analysis was detected more than one father in two nests, which could be explained by capacity of storage sperm, proposed in females of a related species. The behavior of multipaternity could contribute to maintain viable populations of C. latirostris, since the maintenance of genetic variability within populations could help increase their capacity to respond to selective pressure. Further studies employing genetic and behavioral framework are needed to better understand the reproductive biology of C. latirostris.

Sometimes, commercial products obtained from wild animals are sold as if they were from domestic animals and vice versa. At this point of the productive chain, legal control of possible wildlife products is difficult. Common in the commerce of northern Argentina, skins of two wild species, the carpincho and the collared peccary, look very similar to each other and to those of the domestic pig; it is extremely difficult to differentiate them after they have been tanned. Because there was no an adequate methodology to discriminate between leather of these three species, we developed a new methodology of DNA extraction from skin and leather. This new method involves digesting a leather sample using proteinase K, followed by precipitation of proteins with 5 M NaCl, cleaning with absolute isopropanol and DNA precipitation with 70% ethanol. DNA is hydrated in Tris-EDTA buffer. This protocol provided good-quality DNA suitable for analysis with molecular markers. This new protocol has potential for use in identifying leather products of these species using molecular markers based on RAPDs.

Thirteen new polymorphic microsatellite loci were developed and tested in 57 individuals from three locations along the Paraná River. All loci were polymorphic, with 2–22 alleles per locus. Cross-species amplifications were successful for all loci in four other Prochilodus species, suggesting that these microsatellites will be useful for investigation of genetic variation and structure in Prochilodus populations.

Eight polymorphic microsatellite loci were isolated and characterized for the migratory freshwater fish Salminus brasiliensis (Characiformes) and tested on 67 individuals from nine geographically distant locations along the Paraná Basin. The number of alleles per locus ranged from four to 14, with observed heterozygosity estimates ranging from 0·15 to 0·79.