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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.
- 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.
- Genetic hypervariability of a Northeastern Atlantic venomous rockfishPublication . Francisco, Sara M.; Castilho, Rita; Lima, Cristina S.; Almada, Frederico José Oliveira de; Rodrigues, Francisca; Šanda, Radek; Vukic, Jasna; Pappalardo, Anna Maria; Ferrito, Venera; Robalo, JoanaBackground: 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 phylogeographical 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.
- Against all odds: a tale of marine range expansion with maintenance of extremely high genetic diversityPublication . Robalo, Joana; Francisco, Sara M.; Vendrell, Catarina; Lima, Cristina S.; Pereira, Ana; Brunner, Benedikt P.; Dia, Mamadou; Gordo, L. S.; 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.
- The First Report of Holothuria (Thymiosycia) impatiens (Forsskål, 1775), (Holothuroidea: Holothuriidae) from Tunisia (Mediterranean Sea): Taxonomic, Morphological, and Molecular Data CompilationPublication . Kalthoumi, Donia; Francisco, Sara M.; Miladi, Malek; Ruiz-Canales, Antonio; AZZOUNA, Atf; Robalo, JoanaAbstract: For the first time, specimens of Holothuria impatiens are reported from the Tunisian coast, supported by molecular (COI sequencing) and morphological (examination of ossicles) analyses. For comparative purposes, Holothuria impatiens samples were genetically analyzed with existing data from Spain, Italy, and the Red Sea. In addition to their external morphology, an external substance covering the individuals is described, besides the new ossicle structure described in the body wall of H. impatiens samples. The results of the morphometry of the specimens from the Tunisian coast revealed that, for two shapes of ossicles, the size of the individuals does not influence their structures. Low genetic diversity was observed in Tunisia, with two haplotypes; one of both haplotypes was reported for the first time exclusively in Tunisia. The phylogenetic tree showed that the haplotypes were shared across all locations, revealing that the Mediterranean and Red Sea individuals were clearly distinct. Further studies on the genetic diversity of H. impatiens are crucial for the evaluation of the singularity of Mediterranean populations.