Néstor Ríos

Based on an integrative approach (genetic, morphology and biogeography), two new species of Acantholebias are described from Laguna de Rocha and middle Cebollatí River basins respectively (Laguna dos Patos ecoregion). The new species from Laguna de Rocha is diagnosed by a chromatic character and cytochrome b mutations; the new species from middle Cebollatí is diagnosed by a combination of chromatic and squamation patterns. Both species are allopatrically distributed relative to the other species of the genus and to each other. This study also indicates that Acantholebias quirogai presents high chromatic polymorphism that could be related to drainage rearrangements between the Lower Uruguay and Laguna dos Patos ecoregions.

Rhamdia quelen is a catfish widely distributed throughout South America, characterized by a complex taxonomic history. This species is a valuable resource for both fisheries and aquaculture. Due to its cultural and economic importance, it has been prioritized for conservation in the Neotropical region. Population genomics studies supported two main lineages latitudinally distributed (North and South) in the Neotropical basins Río de la Plata and Laguna Merín based on current genetic isolation and signals of local adaptation. In this study, we characterized the R. quelen transcriptome in brain, head kidney, liver, skeletal muscle, testis, and ovary by RNAseq to target genes and associated markers involved in key adaptive traits. After filtering, a comprehensive catalog of 24,433 transcripts was annotated, providing insights into the immune function of head kidney and liver, the association of brain with the endocrine system, and the metabolic function of liver. Skeletal muscle and brain expressed genes associated with growth were also identified. Transcriptomic differences suggestive of adaptation to temperature and salinity were revealed between North and South genomic lineages. A total of 100,045 SNPs loci were identified within transcripts, most of them (78.8%) showing low genetic differentiation between lineages (F_ST ≤ 0.100). However, 2504 loci (2.5%) showed high differentiation (F_ST ≥ 0.800), some of them located within genes associated with putative adaptation of genomic lineages to environmental factors such as temperature and salinity. These SNPs represent useful gene markers for future functional and population genomic studies for sustainable management of wild populations and their application in breeding programs.

Spirometra Faust, Campbell et Kellogg, 1929 is a genus of cestodes belonging to the family Diphyllobothriidae. To date, amphibians, reptiles, and mammals are known second intermediate hosts of these parasites; humans can also be infected (the zoonotic disease is known as sparganosis or spirometrosis). Although the number of phylogenetic studies on Spirometra spp. has increased worldwide in recent years, there are few in South America. Specifically in Uruguay, molecular studies have shown that tapeworms of S. decipiens (Diesing, 1850) complexes 1 and 2 are present in this country. In this study, we characterised the larvae of Spirometra present in the annual fish Austrolebias charrua Costa et Cheffe. Phylogenetic analysis of the cytochrome c oxidase subunit I (COI) sequences of these larvae showed that they belong to S. decipiens complex 1. This is the first report of teleost fishes serving as a second intermediate host for tapeworms of the genus Spirometra in nature.

Annual killifishes inhabit seasonal ponds and wetlands that dry out completely during the dry season, and tend to present very restricted distributions, meaning that local extinctions can lead to the disappearance of entire populations. Using morphological and genetic approaches the present study identifies a new population of Austrolebias charrua in an isolated area of the lower basin of Maldonado stream (Atlantic Ocean coastal basin) in Uruguay. The new population extends the previous area of occurrence by 20 km², 100 km to the south of previous records, and shows some genetic and morphological characteristics that indicate it is isolated from other populations in the previously known range. This species has been catalogued as a priority for conservation by the National System of Protected Areas of Uruguay; the new record does not significantly affect the size of the area of occupation of the species. The new site, located in the Alameda de San Carlos, is a small area that suffers human threats that may lead to environmental impacts and thus jeopardize the conservation of this population.

Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.

The genus Austrolebias (Cyprinodontiformes: Rivulidae) represents a specious group of taxa following annual life cycles in the neotropical ichthyofauna. They live in temporary ponds and each generation must be completed in a few months, depending on environmental stochasticity. Annual fish survive the dry season through diapausing eggs buried in the substrate of these ponds. A hypothesized bimodal hybrid zone between two taxa of the genus, A. charrua and A. reicherti from Dos Patos Merin lagoon system, was recently proposed based on genetics and morphological analyses. However, hundreds of additional nuclear molecular markers should be used to strongly support this hypothesized bimodal pattern. In the present paper, we conducted RNA-seq-based sequencing of the transcriptomes from pools of individuals of A. charrua, A. reicherti and their putative natural hybrids from the previously characterized hybrid zone. As a result, we identified a set of 111,725 SNP (single nucleotide polymorphism) markers, representing presumably fixed allelic differences among the two species. The present study provided the first panel of 106 SNP markers as a single diagnostic multiplex assay and validated their capacity to reconstruct the patterns of the hybrid zone between both taxa. These nuclear markers combined with Cytb gene and morphological analyses detected a population structure in which some groups among the hybrid swarms showed different level of introgression towards one or the other parental species according to their geographic distribution. High-quality transcriptomes and a large set of gene-linked SNPs should greatly facilitate functional and population genomics studies in the hybrid zone of these endangered species.

The objective of the present paper was to characterize the morphological and genetic patterns of variability in four taxa of the Austrolebias robustus species group distributed in two of the major southernmost river basins in South America. We compared results from the two approaches followed in this study to access hypotheses of species limits using an integrative taxonomic framework and patterns of population differentiation. Mitochondrial Cytb gene genealogy and networks analyses detected four major clades which do not fully correspond to currently known species of the A. robustus species group. Although the clade including A. robustus and A. nonoiuliensis received well support, the clade of A. cinereus also contains individuals of A. vazferreirai. BEAST analysis suggested that these taxa may have emerged from independent vicariant allopatric events. While high level of overlap was detected in all morphological analyses, in which species were distinguished only by small changes in body and head shape, the patterns of morphological variation detected among taxa were generally congruent with the different hypotheses of differentiation emerging from genetic population analyses. Based on all present results and following the principle of priority, we propose that A. vazferreirai is a junior synonym of A. cinereus. The subtle morphological discrimination among these taxa, representing local adaptations, reinforces the need to implement urgent actions in order to preserve the A. cinereus population, only reported since its description for the type locality in the PLPUB region. Our results are relevant and informative, supporting the implementation of biodiversity conservation programmes in these endangered endemic allopatric killifish populations, from the major southernmost unsampled areas of the Neotropical basins.