Graciela García

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.

Background: Neotropical annual killifish survive in seasonal ponds due to their ability to undergo embryonic diapauses in the dry season and grow, reproduce and die in the span of a few months during the rainy season. The Austrolebias genus group is endemic to the South American basins and shows remarkable speciation and genetic plasticity. Within this fish group Garcialebias charrua is sympatric with another annual killifish, Cynopoecilus melanotaenia, belonging to a tribe that diverged about 25 million years ago. Despite being closely related species within the Rivulidae family, both species show important differences in genome size. Here, we explore the genomic structure of these species to understand their evolution and unique adaptations. Results: We have sequenced the genomes of G. charrua and C. melanotaenia and determined that they show important structural differences between them. While C. melaotaenia has a genome size of around 1 Gb, similar to that of most characterized teleosts, G. charrua has undergone an evolutionarily recent and massive genome expansion, with a size three times larger (3 Gb). The expansion of the genome in G. charrua has occurred due to amplification of repetitive elements, most recently from the LINE class of elements. We explore and characterize in detail the contribution to genome expansion of repetitive elements at the level of superfamilies, as well as analyze the relationship between these elements and coding genes in G. charrua . We also examine the selection pressures on gene sequences and identify functions that are under positive or purifying selection, and compare these data with that derived from other species. Conclusions: Our study adds a crucial element to the understanding of annual fish evolution and life history. We show that the genetic variability and plasticity in G. charrua is accompanied by a recent genome-wide expansion with an important contribution of repetitive elements. By comparing these findings with data from other species, we show that G. charrua has undergone bursts of repetitive element expansion, with specific superfamilies of retrotransposons and DNA transposons being the most prevalent and recent. In addition, we characterize genes that are potentially implicated in adaptive traits because of their interaction with mobile elements or because they display evidence of intensified selection. These genes are candidates for functional studies aimed at unraveling the genetic basis of annualism.

The South American annual killifish of the Austrolebias sensu lato constitute an extensive species group and serve as a remarkable evolutionary model, inhabiting riparian wetlands in the La Plata River grasslands. This region contains three major areas with allopatrically distributed local and regional endemic species assemblages. At present, the IUCN Red List includes nearly 75% of the species in the Austrolebias genus group. A synapomorphic characteristic of this group is their expanded genome size. Vicariance/dispersal and secondary contact have played key roles in the diversification of most genera within this group, explaining their current distribution across endemic areas. Riparian wetlands are transitional zones that support exceptionally high levels of biodiversity and productivity. The effective conservation of biodiversity in these zones enhances connectivity between river corridors and floodplains, linking aquatic and wetland habitats where annual killifish inhabit, while ensuring the long‐term evolutionary potential of populations. Due to these unique characteristics, the annual killifish of the Austrolebias genus group could be an umbrella species, providing benefits in the conservation of riparian wetlands in the temperate regions of the La Plata River grasslands, and ensuring both biota integrity and long‐term evolutionary processes.

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.

The term Annual killifish describes a short-lived and amazing group of vertebrates inhabiting temporary ponds exposed to an extremely variable environment during its short lifespan in South America and Africa, leading to the death of the entire adult population during the dry season. Austrolebias is a specious genus of the family Rivulidae, with ∼58 currently recognized species, extensively distributed in the temperate Neotropical region. Herein, we reviewed different aspects of the evolutionary biology with emphasis on the genome dynamic linked to the burst speciation process in this genus. Austrolebias constitutes an excellent model to study the genomic evolutionary processes underlying speciation events, since all the species of this genus analyzed so far share an unusually large genome size, with an average DNA content of 5.95 ± 0.45 picograms per diploid cell (mean C-value of about 2.98 pg). The drastic nuclear DNA–increasing would be associated with a considerable proportion of transposable elements (TEs) found in the Austrolebias genomes. The genomic proportion of the moderately repetitive DNA in the A. charrua genome represents approximately twice (45%) the amount of the repetitive components of the highly related sympatric and syntopic rivulinae taxon Cynopoecilus melanotaenia (25%), as well as from other rivulids and actinopterygian fish. These events could explain the great genome instability, the high genetic diversity, chromosome variability, as well as the morphological diversity in species of Austrolebias. Thus, species of this genus represent new model systems linking different evolutionary processes: drastic genome increase, massive TEs genomic representation, high chromosome instability, occurrence of natural hybridization between sister species, and burst speciation events.

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.