Caren Vega-Retter

Finding patterns of distribution for freshwater phytoplankton, zooplankton and fish, by means of parsimony analysis of endemicity

Durante las ultimas decadas, los estudios limnologicos en sistemas chilenos han contribuido al conocimiento de la composicion de especies y de las principales variables ambientales de muchos cuerpos de agua distribuidos sobre un amplio intervalo latitudinal, desde los 18o a los 53o S. Asimismo, aun carecemos de una vision comprensiva acerca de la estructura y funcionamiento de las aguas dulces regionales. En este trabajo revisamos la informacion sobre la biota pelagica de las cuencas de Chile, con el proposito de revelar patrones de distribucion de especies y su posible asociacion con variables ambientales. Construimos matrices de presencia-ausencia para fitoplancton, zooplancton y peces en lagos y cuencas. Desde esta base de datos, realizamos analisis de parsimonia de endemismo, como medio para determinar patrones fundamentales de distribucion de la biota dulceacuicola. Tambien, determinamos la relacion entre la presencia de especies y algunas variables relevantes de los sitios. Nuestros resultados sugieren que la latitud ejerce una fuerte influencia en la distribucion de especies, aunque tambien la altitud, longitud y el area ejercen efectos significativos en algunos grupos. Por otro lado, los resultados sugieren una relacion entre el grado de vagilidad de los grupos y el grado de estructuracion de la metacomunidad, relacionada con el numero de areas de endemismos.

Genetic effects of living in a highly polluted environment: the case of the silverside Basilichthys microlepidotus (Jenyns) (Teleostei: atherinopsidae) in the Maipo River basin, central Chile

Freshwater systems are one of the environments most impacted by human activity, with pollution being a highly important factor. In Chile, several rivers exhibit varied levels of pollution, one of which is the Maipo River basin where the city of Santiago is located. The silverside Basilichthys microlepidotus (Jenyns) is an endemic fish species that inhabits this basin, thus we hypothesized that pollution has affected gene diversity and migration in populations of B. microlepidotus from the Maipo River basin. The aim of this study was to identify the population structure of B. microlepidotus in this basin and to determine if the populations of the silverside inhabiting polluted sites present differences in gene diversity and gene flow compared to populations inhabiting non-polluted areas. Using the variability of eight microsatellites, five populations of silverside were detected; three inhabiting non-polluted sites and two inhabiting polluted sites. From this, it was inferred that B. microlepidotus has been able to tolerate pollution in the Maipo River basin. No differences in gene diversity or migration were detected between polluted and non-polluted sites but comparison with historical estimation revealed an increase in the current migration rate when all the data from the basin were compared. A reduction in current effective population size was also observed when compared to historical values, and this is probably due to river degradation. Despite the disappearance of other fish species recorded at this basin, our results suggest that B. microepidotus is tolerant to pollution, thus indicating that native species respond differently to this environmental factor.

Heavy Metal Content in Chilean Fish Related to Habitat Use, Tissue Type and River of Origin

In this study, we analyze the concentration of ten metals in two freshwater fish—the benthic catfish Trichomycterus areolatus and the limnetic silverside Basilichthys microlepidotus—in order to detect possible accumulation differences related to fish habitat (benthic or pelagic), tissue type (gill, liver and muscle), and the river of origin (four different rivers) in central Chile. The MANOVA performed with all variables and metals, revealed independent effects of fish, tissue and river. In the case of the fish factor, Cu, Cr, Mo and Zn showed statistically higher concentrations in catfish compared with silverside for all tissues and in all rivers (p < 0.05). In the case of the tissue factor, Al, Cr, Fe and Mn had statistically higher concentrations in liver and gills than in muscle (p  < 0.05). For the river effect, the analysis showed higher concentrations of Cr, Mn and Pb in the Cogoti river and the lower concentrations in the Recoleta river. These results suggest that not all metals have the same pattern of accumulation; however, some metals tend to accumulate more in readily catfish, probably due to their benthic habit, and in liver and gill tissue, probably as a result of accumulation from food sources and respiration.

Liver transcriptome characterization of the endangered freshwater silverside Basilichthys microlepidotus (Teleostei: Atherinopsidae) using next generation sequencing

Twenty eight out of 44 Chilean freshwater fishes have been considered to fall within the vulnerable or threatened category. Thus, information about the biology, ecology and the effects of the anthropic activity on these species is fundamental to take appropriate conservation measures. In Chile the endemic silverside Basilichthys microlepidotus inhabits mainly rivers surrounded by cities; during the last 10years it was categorized as an endangered species, thus more basic information is needed in order to elaborate a plan of protection for this species. To this end, the transcriptome of B. microlepidotus was sequenced, assembled and characterized. A total of 7.8 million reads (1.05Gb) were obtained from the sequencing and 5.93 million reads (0.83Gb) were used for the de novo assembly, obtaining a total of 31,523 contigs. Of these, 13,724 contigs with expression in all the individuals used were retained for the functional annotation. 7938 sequences were successfully annotated; the biological processes class was the most highly represented, followed by molecular function and cellular component. These sequence data provide a useful new molecular resource for future studies on gene expression and the effects of the human activity on B. microlepidotus, which will facilitate obtaining more information about that, as well as the developing of appropriate conservation strategies for this species.

Next generation sequencing yields the complete mitochondrial genome of the Endangered Chilean silverside Basilichthys microlepidotus (Jenyns, 1841) (Teleostei, Atherinopsidae), validated with RNA-seq.

Abstract The complete sequence of the mitochondrial genome for the Chilean silverside Basilichthys microlepidotus is reported for the first time. The entire mitochondrial genome was 16,544 bp in length (GenBank accession no. KM245937); gene composition and arrangement was conformed to that reported for most fishes and contained the typical structure of 2 rRNAs, 13 protein-coding genes, 22 tRNAs and a non-coding region. The assembled mitogenome was validated against sequences of COI and Control Region previously sequenced in our lab, functional genes from RNA-Seq data for the same species and the mitogenome of two other atherinopsid species available in Genbank.

The hidden costs of living in a transformed habitat: Ecological and evolutionary consequences in a tripartite mutualistic system with a keystone mistletoe

Land use change is one of the most important anthropogenic drivers of biodiversity loss. Nevertheless, the ecological and evolutionary consequences of habitat transformation remain less understood than those from habitat fragmentation. Transformed habitats are structurally simpler, altering species composition and their ecological interactions, potentially compromising gene flow and genetic diversity. We focused on a tripartite mutualistic system composed of a mistletoe (Tristerix corymbosus), its pollinator (Sephanoides sephaniodes) and its seed disperser (Dromiciops gliroides) to assess changes in their ecological and evolutionary dynamics as a result of habitat transformation. We used eight microsatellite markers to compare genetic diversity, relatedness and gene flow among five mistletoe groups inhabiting native and transformed habitats (abandoned Eucalyptus globulus plantations). We found that these groups were genetically structured, with greater allelic richness and genetic diversity in their native habitat. Also, we found higher relatedness among mistletoe individuals in transformed habitats, which varied as a function of the geographic distance among plants, probably as a result of larger resource availability, which influenced mutualist visitation rates. We did not find differences in the current migration patterns, which suggests that Tristerix corymbosus may be resilient to habitat transformation. Yet, its highly specialized interactions along with changes in its spatial configuration depict a more complex scenario, which probably impose a cost in terms of lower genetic diversity and increased relatedness that might compromise its long-term viability.

Differential gene expression revealed with RNA-Seq and parallel genotype selection of the ornithine decarboxylase gene in fish inhabiting polluted areas

How organisms adapt to unfavorable environmental conditions by means of plasticity or selection of favorable genetic variants is a central issue in evolutionary biology. In the Maipo River basin, the fish Basilichthys microlepidotus inhabits polluted and non-polluted areas. Previous studies have suggested that directional selection drives genomic divergence between these areas in 4% of Amplified Fragment Length Polymorphism (AFLP) loci, but the underlying genes and functions remain unknown. We hypothesized that B. microlepidotus in this basin has plastic and/or genetic responses to these conditions. Using RNA-Seq, we identified differentially expressed genes in individuals from two polluted sites compared with fish inhabiting non-polluted sites. In one polluted site, the main upregulated genes were related to cellular proliferation as well as suppression and progression of tumors, while biological processes and molecular functions involved in apoptotic processes were overrepresented in the upregulated genes of the second polluted site. The ornithine decarboxylase gene (related to tumor promotion and progression), which was overexpressed in both polluted sites, was sequenced, and a parallel pattern of a heterozygote deficiency and increase of the same homozygote genotype in both polluted sites compared with fish inhabiting the non-polluted sites was detected. These results suggest the occurrence of both a plastic response in gene expression and an interplay between phenotypic change and genotypic selection in the face of anthropogenic pollution.

Development and characterization of the first 16 microsatellites loci for Panulirus pascuensis (Decapoda: Palinuridae) from Easter Island using Next Generation Sequencing

The spiny lobster Panulirus pascuensis stands out among the endemic species of Easter Island, due to its cultural and economic importance. A total of 16 microsatellite loci were characterized in 18 individuals, 9 of which were polymorphic. The mean number of alleles per locus was 3.44 (2-6) and the observed heterozygosity ranged from 0.11 to 0.93. None of the loci exhibited significant linkage disequilibrium or departures from HWE. These new microsatellites will be used to obtain information about migration, population structure and genetic diversity of P. pascuensis in order to improve the future sustainable management and conservation plans.

Development of ten microsatellite markers from the keystone mistletoe Tristerix corymbosus (Loranthaceae) using 454 next generation sequencing and their applicability to population genetic structure studies

Tristerix corymbosus (Loranthaceae) is a keystone mistletoe from the South American temperate rainforests. As most mistletoes, T. corymbosus relies on biotic pollination and seed dispersal, which may cause population structure. For a better understanding of its ecology, we isolated and characterized ten polymorphic microsatellite loci for this species. We used 454 Next Generation Sequencing to build a microsatellite library from a high quality DNA sample. We tested 90 sequences from which we obtained ten polymorphic markers. In order to assess their variability, the novel markers were tested in 48 individuals from three locations of the Valdivian Coastal Reserve in Chile. We also estimated genetic differences between pairs of populations using the FST statistic. The mean number of alleles per locus in the 48 individuals studied was 7.1 (2–17 alleles per locus). The observed and expected heterozygosity ranged from 0.298 to 0.634 and from 0.310 to 0.881, respectively. There were genetic differences among the three populations assessed, according to the FST values (ranging from 0.048 to 0.100, all significant) and, the number of alleles per locus ranged from 3.9 to 5.1. These are the first microsatellite markers developed for T. corymbosus, and they arise as a powerful tool for studying population structure, genetic diversity and gene flow at the landscape scale, along its distribution.