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- Genetic population structure of the Blackspot seabream (Pagellus bogaraveo): contribution of mtDNA control region to fisheries managementPublication . Robalo, Joana Isabel; Farias, Inês; M. Francisco, Sara; Avellaneda, Karen; Castilho, Rita; Figueiredo, IvoneMarine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. Pagellus bogaraveo is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975-1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.
- Putting European lampreys into perspective: A global‐scale multilocus phylogeny with a proposal for a generic structure of the PetromyzontidaePublication . Pereira, Ana; Levy, André; Vukić, Jasna; Šanda, Radek; Levin, Boris; Freyhof, Jörg; Geiger, Matthias; Choleva, Lukáš; Francisco, Sara M.; Robalo, JoanaPrevious studies on the phylogenetic relationships between lamprey species relied either on a low number of morphological characters related to the feeding apparatus, or on a low number of molecular mitochondrial DNA markers. Here, we apply a multilocus approach to assess the phylogenetic relationships of northern hemisphere lampreys, with a special emphasis on the 17 European species. The study comprises two mitochondrial (cytochrome c oxidase subunit 1 gene—DNA barcodes, and cytochrome b gene) a nd t wo n uclear (internal transcribed spacers I and II) markers to investigate species' phylogenetic affinities. The phylogeny obtained with mitochondrial markers revealed a clear and highly supported separation of all northern hemisphere lampreys. Among those, our multilocus results show several polyphyletic genera, stressing the need for a taxonomic revision in a near future. Lampetra morii (Berg, 1931) from East Asia, often included in Eudontomyzon, is placed in the genus Lethenteron. Lampetra richardsoni Vladykov & Follett, 1965 and Entosphenus hubbsi (Vladykov & Kott, 1976) should be placed in a new genus, as well as the southern populations of Lethenteron camtschaticum (Tilesius, 1811) and Lethenteron reissneri (Dybowski, 1869). Considering European species, our results argue for a taxonomic revision of Eudontomyzon, with emphasis on Eudontomyzon vladykovi Oliva & Zanandrea, 1959.
- Time matters: genetic composition and evaluation of effective population size in temperate coastal fish speciesPublication . Francisco, Sara M.; Robalo, JoanaExtensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species.
- Sympatric threatened Iberian leuciscids exhibit differences in Aeromonas diversity and skin lesions’ prevalencePublication . Grilo, Miguel; Chambel, Lélia; Marques, Tiago A.; Sousa, Carla; Robalo, Joana; Oliveira, ManuelaAssessments regarding health aspects of Iberian leuciscids are limited. There is currently an information gap regarding effects of infectious diseases on these populations and their role as a possible conservation threat. Moreover, differences in susceptibility to particular agents, such as Aeromonas spp., by different species/populations is not clear. To understand potential differences in Aeromonas diversity and load, as well as in the prevalence and proportion of skin lesions, in fishes exposed to similar environmental conditions, an observational study was implemented. Using a set of 12 individuals belonging to two sympatric Iberian leuciscid species (Squalius pyrenaicus and Iberochondrostoma lusitanicum), the skin lesion score in each individual was analyzed. Furthermore, a bacterial collection of Aeromonas spp. isolated from each individual was created and isolates’ load was quantified by plate counting, identified at species level using a multiplex-PCR assay and virulence profiles established using classical phenotypic methods. The similarity relationships of the isolates were evaluated using a RAPD analysis. The skin lesion score was significantly higher in S. pyrenaicus, while the Aeromonas spp. load did not differ between species. When analyzing Aeromonas species diversity between fishes, different patterns were observed. A predominance of A. hydrophila was detected in S. pyrenaicus individuals, while I. lusitanicum individuals displayed a more diverse structure. Similarly, the virulence index of isolates from S. pyrenaicus was higher, mostly due to the isolated Aeromonas species. Genomic typing clustered the isolates mainly by fish species and skin lesion score. Specific Aeromonas clusters were associated with higher virulence indexes. Current results suggest potential differences in susceptibility to Aeromonas spp. at the fish species/individual level, and constitute important knowledge for proper wildlife management through the signalization of at-risk fish populations and hierarchization of conservation measures.
- Molecular and morphological validation of the species of the genus Actinia (Actiniaria: Actiniidae) along the Atlantic Iberian PeninsulaPublication . Pereira, Ana; Cadeireiro, Emília; Ocaña, Oscar; Vukic, Jasna; Šanda, Radek; Mirimin, Luca; Robalo, Joana IsabelThe discrimination between the several species of the genus Actinia occurring in the Northeastern Atlantic and Mediterranean has been made analyzing morphological characters, with emphasis on external coloration patterns and morphology of cnidom structures. In Iberia, the occurrence of more than two species of Actinia has been suggested, but its validity is yet to be confirmed. In this paper, the identity of the species of the genus Actinia occurring along the Atlantic Iberian coast is investigated, analyzing morphological and molecular procedures. For this purpose, genetic data was collected from 140 individuals and two genetic markers were amplified and sequenced (the nuclear 28S and the mitochondrial 16S ribosomal genes). The genetic identification was corroborated by morphological analysis of individuals representing each of the genetic groups found. This procedure led to the identification of three species occurring in the studied area – Actinia equina (L.), A. fragacea Tugwell and A. schmidti Monteiro, Sole-Cava & Thorpe.
- The potential of Aeromonas spp. from wildlife as antimicrobial resistance indicators in aquatic environmentsPublication . Grilo, Miguel; Santos, Carla Sousa; Robalo, Joana; Oliveira, ManuelaDeclines in freshwater fish populations are occurring at a fast rate, increasing the importance of ex-situ conservation programs supported by sound knowledge of population dynamics and life-history traits of the target species. We analysed the growth and age structure of wild and captive stocks of the western ruivaco Achondrostoma occidentale, a Portuguese endangered cyprinid, targeted for captive breeding and restocking since 2007. Specifically, we compared maximum size, longevity, and length-at-age among captive and wild populations, restocked and non-restocked. We found considerable variation in length-at-age and longevity between captive-bred and wild fish, with the former generally growing faster and living longer. Analysis of length-age distributions among wild populations suggested a positive effect of restocking actions in fish abundance. Results highlight the value of captive breeding for the conservation of endangered cyprinids, and reinforce the need for detailed data on life-history trait variation between captive and wild stocks to assess the efficiency of ex-situ conservation programs.
- Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distributionPublication . Cunha, Regina L.; BEN FALEH, Abderraouf; Francisco, Sara; Šanda, Radek; Vukic, Jasna; Corona, Luana; DIA, Mamadou; Glavicic, Igor; Kassar, Abderrahmane; Castilho, Rita; Robalo, JoanaMarine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specifc life-history traits or oceanographic barriers that prevent gene fow. 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 identifed 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 Cádiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almería-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to afect 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.
- Genomics goes deeper in fisheries science: The case of the blackspot seabream (Pagellus bogaraveo) in the northeast AtlanticPublication . Cunha, Regina L.; Robalo, Joana; 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.
- Interbreeding between local and translocated populations of a cleaner fish in an experimental mesocosm predicts risk of disrupted local adaptationPublication . Gonzalez, Enrique Blanco; Espeland, Sigurd H.; Jentoft, Sissel; Hansen, Michael M.; Robalo, Joana Isabel; Stenseth, Nils Christian; Jorde, Per ErikTranslocation of organisms within or outside its native range carries the risk of modifying the community of the recipient ecosystems and induces gene flow between locally adapted populations or closely related species. In this study, we evaluated the genetic consequences of large‐scale translocation of cleaner wrasses that has become a common practice within the salmon aquaculture industry in northern Europe to combat sea lice infestation. A major concern with this practice is the potential for hybridization of escaped organisms with the local, recipient wrasse population, and thus potentially introduce exogenous alleles and breaking down coadapted gene complexes in local populations. We investigated the potential threat for such genetic introgressions in a large seminatural mesocosm basin. The experimental setting represented a simulated translocation of corkwing wrasse (Symphodus melops) that occurs on a large scale in the Norwegian salmon industry. Parentage assignment analysis of mesocosm's offspring revealed 30% (195 out of 651 offspring) interbreeding between the two populations, despite their being genetically (FST = 0.094, p < 0.05) and phenotypically differentiated. Moreover, our results suggest that reproductive fitness of the translocated western population doubled that of the local southern population. Our results confirm that human translocations may overcome the impediments imposed by natural habitat discontinuities and urge for immediate action to manage the genetic resources of these small benthic wrasses.
- Molecular epidemiology, virulence traits and antimicrobial resistance signatures of aeromonas spp. in the critically endangered iberochondrostoma lusitanicum follow geographical and seasonal patternsPublication . Grilo, Miguel; Isidoro, Sara; Chambel, Lélia; Marques, Carolina S.; Marques, Tiago A.; Sousa-Santos, C.; Robalo, Joana; Oliveira, ManuelaDespite the fact that freshwater fish populations are experiencing severe declines worldwide, our knowledge on the interaction between endangered populations and pathogenic agents remains scarce. In this study, we investigated the prevalence and structure of Aeromonas communities isolated from the critically endangered Iberochondrostoma lusitanicum, a model species for threatened Iberian leuciscids, as well as health parameters in this species. Additionally, we evaluated the virulence profiles, antimicrobial resistance signatures and genomic relationships of the Aeromonas isolates. Lesion prevalence, extension and body condition were deeply affected by location and seasonality, with poorer performances in the dry season. Aeromonas composition shifted among seasons and was also different across river streams. The pathogenic potential of the isolates significantly increased during the dry season. Additionally, isolates displaying clinically relevant antimicrobial resistance phenotypes (carbapenem and fluroquinolone resistance) were detected. As it inhabits intermittent rivers, often reduced to disconnected pools during the summer, the dry season is a critical period for I. lusitanicum, with lower general health status and a higher potential of infection by Aeromonas spp. Habitat quality seems a determining factor on the sustainable development of this fish species. Also, these individuals act as reservoirs of important antimicrobial resistant bacteria with potential implications for public health.