Ph.D. Vera-Escalona, Iván

Las especies del género Anisakis (Nematoda: Anisakidae) son parásitos marinos con ciclo de vida indirecto. Los crustáceos planctónicos actúan como primeros hospedadores intermediarios, mientras que peces y cefalópodos intervienen como segundos hospedadores intermediarios o paraténicos, finalmente el ciclo se cierra en los cetáceos, mamíferos marinos que son los principales hospedadores definitivos del género. En el ciclo de vida, las larvas de Anisakis pueden ser ingeridas por el hombre interviniendo como huésped accidental, lo que puede ocasionar anisakiasis, una zoonosis adquirida a través del consumo de peces y cefalópodos crudos o marinados. Estos nemátodos tienen una distribución cosmopolita, sin embargo, su diversidad ha sido escasamente estudiada en el hemisferio Sur. Por tanto, se evaluó la diversidad de las larvas de Anisakis spp., presentes en dos especies de hospederos de Chile, combinando el análisis morfométrico y genético. Para ello, se recolectaron larvas de Anisakis spp. en la cavidad abdominal de la merluza Merluccius gayi y el calamar Dosidicus gigas, procedentes de terminales pesqueros de la región del Biobío, Chile. La caracterización morfométrica de las larvas de Anisakis spp., consistió en la medición de la longitud del esófago, ventrículo esofágico, cola, longitud total y ancho máximo del cuerpo. Para los análisis genéticos se usó la región molecular nuclear ITS (ITS1-ITS2) y mitocondrial COX2. Los resultados morfométricos revelaron que las larvas extraídas de D. gigas son significativamente de mayor longitud que las recolectadas en M. gayi, sugiriendo una alta variabilidad fenotípica hospedador-dependiente. Los análisis moleculares y filogenéticos determinaron la presencia de Anisakis pegreffii en ambos hospedadores, sin embargo, demostraron una baja diferenciación genética y diversidad nucleotídica entre las secuencias, indicando una escasa variabilidad genética para el conjunto de datos. Este trabajo constituye el primer registro molecular de A. pegreffii en hospedadores intermediario o paraténicos de la costa de Chile.

The introduction and establishment of invasive species in regions outside their native range, is one of the major threats for the conservation of ecosystems, affecting native organisms and the habitat where they live in, causing substantial biological and monetary losses worldwide. Due to the impact of invasive species, it is important to understand what makes some species more invasive than others. Here, by simulating populations using a forward-in-time approach combining ecological and single polymorphic nucleotides (SNPs) we evaluated the relation between propagule size (number of individuals = 2, 10, 100, and 1,000), extinction rate (with values 2%, 5%, 10%, and 20%), and initial heterozygosity (0.1, 0.3, and 0.5) on the population survival and maintenance of the heterozygosity of a simulated invasive crab species over 30 generations assuming a single introduction. Our results revealed that simulated invasive populations with initial propagule sizes of 2–1,000 individuals experiencing a high extinction rate (10–20% per generation) were able to maintain over 50% of their initial heterozygosity during the first generations and that under scenarios with lower extinction rates invasive populations with initial propagule sizes of 10–1,000 individuals can survive up to 30 generations and maintain 60–100% of their initial heterozygosity. Our results can help other researchers better understand, how species with small propagule sizes and low heterozygosities can become successful invaders.

Genetic structure and connectivity information can be used to identify biological corridors and prioritize the conservation of areas that help maintain ecosystem integrity. Some marine fish, especially those of commercial interest, have been proposed as suitable indicators to identify potential marine biological corridors due to their high mobility among habitats and socioeconomic importance. In this study, we assessed the genetic structure of lane snapper populations in the Honduran Caribbean to evaluate connectivity and identify potential environmental barriers. Furthermore, we evaluated the genetic characteristics of the lane snapper on a larger spatial scale, including populations across the rest of its distribution range in the western Atlantic, using mtDNA and nuDNA markers. Our results demonstrate a significant genetic diversity of lane snappers in the Honduran Caribbean. Furthermore, despite their high dispersal potential, we observed genetic structuring in lane snapper populations on a larger spatial scale, resulting in the formation of two distinct groups throughout their distribution range: group 1 from Florida, the Gulf of Mexico, Honduras, and Colombia and group 2 from Puerto Rico and Brazil. This genetic differentiation can be attributed to oceanographic barriers such as river plumes and marine currents. These findings have the potential to significantly impact marine conservation and management efforts in the region, both at local and regional scales. It is anticipated that they will not only inform but also elicit a response, driving further action towards effective conservation measures. At a local scale, we recommend that conservation efforts focus on protecting critical habitats. At a regional scale, lane snappers should be included in the management plans of existing marine protected areas necessary to ensure the long-term sustainability of the species and the marine ecosystems in which it resides.

Non-native species can have profound implications on the survival of native ones. This is especially true for some invasive crabs, such as the green crab Carcinus maenas, a native species to the Northern Hemisphere that has been introduced into southern Argentina, from where it could expand through Argentina, Chile, and the Antarctic Peninsula. Hence, there is interest in forecasting changes in C. maenas habitat suitability through time to predict if potential future invasions might occur. Here, by using a Species Distribution Model (SDM) approach, we estimated the habitat suitability for C. maenas along southern South America and the Antarctic Peninsula under two future climate-change scenarios. Our results reveal that under current conditions, habitat suitability for C. maenas along the Antarctic Peninsula is null and very restricted in Argentina and Chile. Habitat suitability along the Antarctic Peninsula remained null in the short-term (30 years) and long-term future (80 years), despite the climate-change scenario considered. Surprisingly, when considering future conditions, habitat suitability along the coast of Argentina and Chile decreased and became nil for some currently occupied locations. Thus, the SDM results suggest that climate change could have a negative effect on the habitat suitability of C. maenas leading to potential local extinctions.

Natural disturbances can modify extinction-colonization dynamics, driving changes in the genetic diversity and structure of marine populations. Along Chilean coast (36°S, 73°W), a strong hypoxic-upwelling event in 2008, and a mega earthquake-tsunami in 2010 caused mass mortality within the Aphos porosus population, which is a vulnerable species with low dispersal potential. We evaluated the effects of these two major disturbances on the diversity and spatial-temporal genetic structure of Aphos porosus in two neighboring areas that were impacted on different levels (High level: Coliumo Bay; Low level: Itata Shelf). Thirteen microsatellites (from 2008 to 2015) amplified in individuals collected from both locations were used to evaluate the effects of the two disturbances. Results showed that after the strong hypoxic-upwelling event and the mega earthquake-tsunami, Aphos porosus populations exhibited lower genetic diversity and less effective population sizes (Ne < 20), as well as asymmetries in migration and spatial-temporal genetic structure. These findings suggest a rise in extinction-recolonization dynamics in local Aphos porosus populations after the disturbances, which led to a loss of local genetic diversity (mainly in Coliumo Bay area impacted the most), and to greater spatial-temporal genetic structure caused by drift and gene flow. Our results suggest that continuous genetic monitoring is needed in order to assess potential risks for Aphos porosus in light of new natural and anthropogenic disturbances.

Microbes associated with marine invertebrates play a key role in the physiological and biochemical processes of the host, and can be responsible for food-borne diseases in humans. Raw invertebrates are a common component of coastal gastronomy worldwide and their consumption could represent a potential risk to humans if their microbiome hosts infectious bacteria. However, these species’ microbiome composition is usually unknown. In this study, we sequenced the 16S gene to characterise the microbiome of the digestive system and gonads of the commercially-exploited sea snail Phorcus sauciatus from the Macaronesian islands and mainland Portugal. The goal was to identify bacteria that might pose a threat to humans. In total, 910 OTUs were identified, thirty-two of which were found to be classified as Risk level-1 and -2 species. Among these, twenty pathogenic bacterial strains were found in high relative abundance and identified as potential drivers of human diseases, including Micrococcus luteus and Serratia marcescens. Here, we discuss how our findings on the occurrence of these bacteria could seriously affect humans. Our results are relevant beyond the scope of this study, as this work might also pave the way for uncovering further implications on the raw consumption of other shellfish and invertebrate species.

Studies on microbial communities are pivotal to understand the role and the evolutionary paths of the host and their associated microorganisms in the ecosystems. Meta-genomics techniques have proven to be one of the most effective tools in the identification of endosymbiotic communities of host species. The microbiome of the highly exploited topshell Phorcus sauciatus was characterized in the Northeastern Atlantic (Portugal, Madeira, Selvagens, Canaries and Azores). Alpha diversity analysis based on observed OTUs showed significant differences among regions. The Principal Coordinates Analysis of beta-diversity based on presence/absence showed three well differentiated groups, one from Azores, a second from Madeira and the third one for mainland Portugal, Selvagens and the Canaries. The microbiome results may be mainly explained by large-scale oceanographic processes of the study region, i.e., the North Atlantic Subtropical Gyre, and specifically by the Canary Current. Our results suggest the feasibility of microbiome as a model study to unravel biogeographic and evolutionary processes in marine species with high dispersive potential.

Aims Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents. Location Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean). Taxon The limpet Patella aspera. Methods Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t3 to a higher Ne at time t2; and (ii) Scenario 2 considering a reduction of Ne from a time t3 to a time t2. Results Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (Ne). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene. Main conclusions Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.

Life-history traits are among the most important factors affecting population abundance and genetic diversity of species. Here, we analysed the genetic patterns of two Galaxias species with different life-history traits to investigate how these biological differences impacted their evolution in the Valdivia River basin, Southern Chile. We analysed mitochondrial DNA (mtDNA) sequences from 225 individuals of Galaxias maculatus and 136 of G. platei to compare patterns of genetic diversity, structure and demographic growth across the basin. Galaxias maculatus presented higher genetic diversity and higher genetic structure than G. platei. Demographic analyses showed G. maculatus kept a higher population size over time, with a signal of demographic expansion in the last 250 kyr. Whereas Galaxias platei, exhibited lower, but constant population size over time. Furthermore, haplotype networks revealed higher lineage diversity in G. maculatus with a tendency to occupy different areas of the basin. Coalescent simulations ruled out that genetic differences between species could be explained by stochastic processes (genetic drift), suggesting species-specific biological differences as responsible for the observed genetic differences. We discuss how differences in life-history traits and past glaciations interact to shape the evolutionary history of the two Galaxias species.

Galaxiid fishes from South America are represented by three genera (Aplochiton, Brachygalaxias and Galaxias) and eight species. Their genetic patterns have been studied over the last two decades to disentangle how historical and contemporary processes influenced their biogeographic distribution and phylogeographic patterns. Here we review and synthesize this body of work. Phylogeographic approaches reveal the important role played by orogeny and the expansion/melting of glacial ice during the Quaternary. Populations retreated to glacial refugia during glacial times and some systems experienced drainage reversals from the Atlantic to the Pacific following deglaciation. Although most species expanded their populations and increased their genetic diversity during the Holocene, the introduction of salmonids and the construction of dams are likely to lead to a decline in genetic diversity for at least some species. An improvement in our understanding of the processes that influenced historical and contemporary diversity patterns among galaxiid and other native fishes in South America is necessary for addressing the cumulative and synergistic impacts of human activity on this unique freshwater fauna.