Percorrer por autor "Robalo, Joana I."
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- Against all odds: a tale of marine range expansion with maintenance of extremely high genetic diversityPublication . Robalo, Joana I.; Francisco, Sara M.; Vendrell, Catarina; Lima, Cristina S.; Pereira, Ana; Brunner, Benedikt; Dia, Mamadou; Gordo, Leonel; Castilho, RitaThe displacement of species from equatorial latitudes to temperate locations following the increase in sea surface temperatures is among the significant reported consequences of climate change. Shifts in the distributional ranges of species result in fish communities tropicalisation, i.e., high latitude colonisations by typically low latitude distribution species. These movements create new interactions between species and new trophic assemblages. The Senegal seabream, Diplodus bellottii, may be used as a model to understand the population genetics of these invasions. In the last decades, this species has undergone an outstanding range expansion from its African area of origin to the Atlantic coast of the Iberian Peninsula, where now occurs abundantly. Mitochondrial and nuclear markers revealed a striking high haplotypic nucleotide and genetic diversity values, along with significant population differentiation throughout the present-day geographical range of the Senegal seabream. These results are not consistent with the central-marginal hypothesis, nor with the expectations of a leptokurtic distribution of individuals, as D. bellottii seems to be able to retain exceptional levels of diversity in marginal and recently colonised areas. We discuss possible causes for hyperdiversity and lack of geographical structure and subsequent implications for fisheries.
- Asymmetrical dispersal and putative isolation-by-distance of an intertidal blenniid across the Atlantic-Mediterranean dividePublication . Castilho, Rita; Lopes Da Cunha, Regina; Faria, Claudia; Velasco, Eva M.; Robalo, Joana I.Transition zones are of high evolutionary interest because unique patterns of spatial variation are often retained. Here, we investigated the phylogeography of the peacock blenny, Salaria pavo, a small marine intertidal fish that inhabits rocky habitats of the Mediterranean and the adjacent Atlantic Ocean. We screened 170 individuals using mitochondrial and nuclear sequence data from eight locations. Four models of genetic structure were tested: panmixia, isolation-by-distance, secondary contact and phylogeographic break. Results indicated clear asymmetric migration from the Mediterranean to the Atlantic but only marginally supported the isolation-by-distance model. Additionally, the species displays an imprint of demographic expansion compatible with the last glacial maximum. Although the existence of a refugium in the Mediterranean cannot be discarded, the ancestral lineage most likely originated in the Atlantic, where most of the genetic diversity occurs.
- Genetic hypervariability of a Northeastern Atlantic venomous rockfishPublication . Francisco, Sara M.; Castilho, Rita; Lima, Cristina S.; Almada, Frederico; Rodrigues, Francisca; Šanda, Radek; Vukić, Jasna; Pappalardo, Anna Maria; Ferrito, Venera; Robalo, Joana I.Background: Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities’ composition. A hylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins. Methods: In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron. Results: The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.
- Genomics goes deeper in fisheries science: The case of the blackspot seabream (Pagellus bogaraveo) in the northeast AtlanticPublication . Cunha, Regina L.; Robalo, Joana I.; Francisco, Sara M.; Farias, Inês; Castilho, Rita; Figueiredo, IvoneRecent advances in genomics are an essential contributor to the assessment of fish stocks by providing a finescale identification of the species' genetic boundaries. The blackspot seabream, Pagellus bogaraveo, is a commercial sparid distributed across the northeast (NE) Atlantic and the Mediterranean. Within the NE Atlantic, three P. bogaraveo stocks are currently defined: Azores; Atlantic Iberian waters; Celtic Sea and the Bay of Biscay. We used a genotyping-by-sequencing (GBS) approach to better define the spatial scale at which the species occurs in the NE Atlantic. Our findings revealed the existence of an additional genetic cluster in the eastern Atlantic (Gulf of C ' adiz) that was not identified in previous studies based on mitochondrial DNA or microsatellite data. The combined effect of ocean circulation patterns, complex bathymetry and the existence of local upwelling may play an important role on the retention of blackspot seabream larvae and adults, providing an explanation for the genetic differentiation between the specimens caught off the Gulf of C ' adiz and Peniche (Portugal). Results presented here revealed hidden intra-specific genetic differentiation and can inform a finer-scale sampling to determine the new stock boundaries in the Atlantic Iberian coasts.
- Life in a drop: sampling environmental DNA for marine fishery management and ecosystem monitoringPublication . Gilbey, John; Carvalho, Gary; Castilho, Rita; Coscia, Ilaria; Coulson, Mark W.; Dahle, Geir; Derycke, Sofie; Francisco, Sara M.; Helyar, Sarah J.; Johansen, Torild; Junge, Claudia; Layton, Kara K. S.; Martinsohn, Jann; Matejusova, Iveta; Robalo, Joana I.; Rodriguez-Ezpeleta, Naiara; Silva, Goncalo; Strammer, Ilona; Vasemagi, Anti; Volckaert, Filip A. M.Science-based management of marine fisheries and effective ecosystem monitoring both require the analysis of large amounts of often complex and difficult to collect information. Legislation also increasingly requires the attainment of good environmental status, which again demands collection of data to enable efficient monitoring and management of biodiversity. Such data is traditionally obtained as a result of research surveys through the capture and/or visual identification of organisms. Recent years have seen significant advances in the utilisation of environmental DNA (eDNA) in the marine environment in order to develop alternative cost-effective ways to gather relevant data. Such approaches attempt to identify and/or quantify the species present at a location through the detection of extra-organismal DNA in the environment. These new eDNA based approaches have the potential to revolutionise data collection in the marine environment using non-invasive sampling methods and providing snapshots of biodiversity beyond the capacity of traditional sampling. Here we present a non-technical summary of different approaches in the field of eDNA, and emphasise the broad application of this approach, with value for the governance and management of marine aquatic ecosystems. The review focuses on identifying those tools which are now readily applicable and those which show promise but are currently in development and require further validations. The aim is to provide an understanding of techniques and concepts that can be used by managers without genetic or genomic expertise when consulting with specialists to perform joint evaluations of the utility of the approaches.
- Northern refugia and recent expansion in the North Sea: the case of the wrasse Symphodus melops (Linnaeus, 1758)Publication . Robalo, Joana I.; Castilho, Rita; Francisco, Sara M.; Almada, Frederico; Knutsen, Halvor; Jorde, Per E.; Pereira, Ana M.; Almada, Vitor C.Pleistocene climate changes have imposed extreme conditions to intertidal rocky marine communities, forcing many species to significant range shifts in their geographical distributions. Phylogeographic analyses based on both mitochondrial and nuclear genetic markers provide a useful approach to unravel phylogeographic patterns and processes of species after this time period, to gain general knowledge of how climatic changes affect shifts in species distributions. We analyzed these patterns on the corkwing wrasse (Symphodus melops, Labridae), a rocky shore species inhabiting North Sea waters and temperate northeastern Atlantic Ocean from Norway to Morocco including the Azores, using a fragment of the mitochondrial control region and the first intron of the nuclear S7 ribosomal protein gene. We found that S. melops shows a clear differentiation between the Atlantic and the Scandinavian populations and a sharp contrast in the genetic diversity, high in the south and low in the north. Within each of these main geographic areas there is little or no genetic differentiation. The species may have persisted throughout the last glacial maximum in the southern areas as paleotemperatures were not lower than they are today in North Scandinavia. The North Sea recolonization most likely took place during the current interglacial and is dominated by a haplotype absent from the south of the study area, but present in Plymouth and Belfast. The possibility of a glacial refugium in or near the English Channel is discussed.
- On the efficacy of a pre-filtering density separation method for microplastic analysisPublication . Feiteira, Sara; Abrunhosa, Felipe; Corona, Luana; Robalo, Joana I.; Castilho, RitaMicroplastics (particles with a diameter between 1 and 5 mm) in the marine environment are a growing concern due to their involuntary ingestion by fish and other marine species. The small microplastic size makes them easily consumed in the water and hence readily introduced into the marine food chain, with yet unknown bioaccumulative and toxic consequences. The proximity to urban areas, industrial activities, and sewage disposal potentially increases the presence of microplastics in the marine environment. The gastrointestinal tract (GIT) of some species contains high quantities of debris, sediment, and non-digestible materials such as calcium carbonate resulting from their dietary or behavioral habits. This study aims to assess the efficacy of a pre-filtering density separation method using a hypersaline solution to facilitate the subsequent filtration procedure. This additional step is expected to accelerate the procedure as a whole, improving the filtering process and ensuring a more accurate detection of microplastics.
- Resolving the population structure and demographic history of the European anchovy in the northeast atlantic: tracking historical and contemporary environmental changesPublication . Martin Pujolar, José; Gardiner, Courtney E. C.; Heyden, Sophie von der; Robalo, Joana I.; Castilho, Rita; Lopes da Cunha, Regina; Henriques, Romina; Nielsen, Einar E.The spatial distribution of the European anchovy has expanded in the northern part of its range in the Northeast Atlantic in recent decades. However, whether this results from a northward range shift of southern conspecifics or the expansion of a local northern population is unknown. Using for the first time whole-genome sequencing, we explore current patterns of genetic diversity and population sub-structuring of European anchovy in the Northeast Atlantic, with special focus on recently expanded North Sea areas. Genomic data suggested three distinct groups: Northern (North Sea and Kattegat), Southern (Ireland and Central Portugal) and Cadis (South Portugal). Despite most of the genome being homogenised by high levels of gene flow characteristic of small pelagic fish, several large regions of high genetic differentiation were observed. This suggests that genomic population boundaries might be maintained by local adaptation within chromosome structural variants (inversions). Admixture analysis indicates that the ongoing northern range shift involves both migrants of southern origin and expansion of the local North Sea population. Historical demographic inference suggests that anchovies survived the last glacial period with small population sizes, followed by a split into the current Northern and Southern groups at the end of the last glacial maximum. The Southern group then expanded into the North Sea as the ice sheets retreated, in an expansion involving a large number of individuals, which is consistent with the retention of most of the genetic diversity. In comparison with other small pelagic fish, the genetic patterns found in anchovies (deeply divergent groups, no loss of genetic diversity during expansion, mixing between groups) align well with those found in European sprat, while sardines fit the pattern of expansion of a leading-edge population, with reduced genetic diversity and much shallower divergence between populations. This study contributes to a better understanding of population structure, range shifts and local adaptation in small pelagic fish under climate change, informing conservation and management efforts.
- Sex‐linked differentiation in commercially exploited fishes: rethinking population structure in dynamic marine environmentsPublication . Gardiner, Courtney E. C.; Heyden, Sophie von der; Matthee, Conrad A.; Nielsen, Einar E.; Pujolar, José M.; Robalo, Joana I.; Castilho, Rita; Lopes da Cunha, Regina; Durholtz, Deon; Fairweather, Tracey P.; Kathena, Johannes N.; Henriques, RominaUnderstanding how genomic structure links with ecological and evolutionary processes is critical for forecasting species responses to dynamic marine environments, especially in commercially exploited marine species, where fishing pressure can impact genomic integrity. Here we investigate Merluccius paradoxus, a commercially exploited demersal fish that appears to be undergoing a range expansion along the southern African coastline. Using whole-genome sequence data of individuals from across the species' distribution (n=37), we reveal that sex-linked divergence, rather than geography, is the principal driver of genomic variation, challenging conventional assumptions of regional geographic population structure. Divergence was concentrated on autosomal regions (primarily large regions on Chromosomes 1 and 2), rather than known sex-determining (SD) regions (Chromosome 9), and did not have structural variants or extended linkage disequilibrium (LD). Instead, patterns were consistent with sex-specific directional selection acting on genes enriched for neuronal function, metabolism and muscle development, traits that are likely linked to behaviour, physiology and environmental tolerance. Males had reduced nucleotide diversity (π), low observed heterozygosity (Ho ) and longer runs of homozygosity (ROH) in these regions, suggesting recent selective sweeps or a reduced effective population size (Ne ). Together with spatial differences in sex distribution and genomic diversity metrics, results suggest that males and females may differ in both range dynamics and adaptive potential. As M. paradoxus continues to shift its distribution across geo-political boundaries, sex-biased adaptation may have important consequences for reproductive output, resilience and sustainable fisheries management under a changing climate. This study highlights the need to incorporate sex-linked genomic variation into conservation planning, particularly in transboundary systems vulnerable to cumulative pressures of fishing and environmental change.
- Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distributionPublication . Cunha, Regina L.; Faleh, Abderraouf Ben; Francisco, Sara; Šanda, Radek; Vukić, Jasna; Corona, Luana; Dia, Mamadou; Glavičić, Igor; Kassar, Abderrahmane; Castilho, Rita; Robalo, Joana I.Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cadiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almeria-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.