Browsing by Author "Figueiredo, Ivone"
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- Dataset of the complete mitogenome of the deep-sea sailfin roughshark, Oxynotus paradoxus Frade, 1929Publication . Matos, Ana; Gomes-dos-Santos, André; Graça Aranha, Sofia; Dias, Ester; Veríssimo, Ana; Teodosio, Maria; Figueiredo, Ivone; Castro, L. Filipe C．; Froufe, ElsaChondrichthyans comprise a diverse group of vertebrate species with extraordinary ecological relevance. Yet, multiple members of this evolutionary lineage are associated with sig-nificant extinction risk. The sailfin roughshark Oxynotus para-doxus is a deep-water benthic shark currently listed as vul-nerable due to population declines in parts of its range. Here we provide the first complete mitochondrial genome of O. paradoxus, comprising also the first record for the genus and family Oxynotidae. These data can facilitate future monitor-ing of the genetic diversity in this and related species. Ge-nomic DNA was extracted from O. paradoxus collected in the eastern North Atlantic off western Portugal (37.59 degrees N, 9.51 degrees W) and sent for Illumina Paired-End (2 x 150 bp) library con-struction and whole genome sequencing on a Novaseq60 0 0 platform. Trimmomatic (version 0.38) was used to remove adapters and MitoZ (version 3.4) to assemble and anno-tate the mitogenome. This mitogenome with 17 100 bp has a total of 38 genes, 13 of which are protein-coding genes, 23 transfer RNA genes, and 2 ribosomal RNA genes. Eight transfer RNAs and 1 protein-coding gene (NADH de-hydrogenase subunit 6, NAD6) are in the complementary strand. In the provided phylogenetic inference, with all avail-able and verified Squalomorphii mitogenomes, the four or-ders are well separated, and as expected, O. paradoxus is placed in the Squaliformes order. This data reinforces the need for more genomic resources for the Oxynotidae family.(c) 2023 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
- Designing a coastal monitoring marine biodiversity survey, using trammel nets and gillnets in PortugalPublication . Rufino, Marta M.; Maia, Catarina; Dinis, David; Farias, Inês; Moura, Teresa; Gomes, Pedro; Quaresma, Ivania; Martins, Rogélia; Figueiredo, Ivone; Serra-Pereira, Bárbara; Gaspar, Miguel; Moreno, AnaAlthough coastal areas are of great importance, they often lack long term monitoring surveys, which are essential for effective management, fisheries sustainability, and marine spatial planning. To address this, we conducted two experimental surveys aimed at assessing communities and their biodiversity, with the objective of designing a monitoring program for marine coastal biodiversity, based on gear type, depth, sampling arrangement, total net length, and panel position within the haul. Depth was found to be the most important factor shaping biodiversity, while gear type had the greatest impact on assessing species richness. Overall, both number of species and diversity increased with depth, though significant differences were only found between hauls deployed at 10 m and deeper (30-50 m). Trammel nets caught a larger number of species compared to gillnets, and there was evidence of an interaction between depth and gear, in terms of abundance and at the community level; samples taken deeper than 10 m showed more gear-related differences. We found that neither the panel position within the haul nor the number of nets had any impact on species diversity or abundance. Similarly, there was no evidence for an effect related to the arrangement of nets, as results were consistent whether using separated or continuous net panels. However, the number of nets used as a sampling unit significantly influenced the results, as the variation in species abundance and diversity with depth and gear type was similar, when 20 or 30 nets were used, but became more variable when only 10 nets were used, even with increased replication. We concluded that both trammel nets and gillnets should be included in a coastal biodiversity monitoring program, as each catches a different set of species, including both demersal and pelagic taxa. Further, we recommend using a minimum of 20 nets (ideally 30+) per station, with replication. The evaluated monitoring system has a minimal impact on the ecosystem, can be easily deployed using commercial vessels and effectively captures a large number of species, being thus, highly recommended to be used in coastal monitoring surveys.
- 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.
- How is the morphology of the oviducal gland and of the resulting egg capsule associated with the egg laying habitats of Rajidae species?Publication . Maia, Catarina; Serra-Pereira, Bárbara; Erzini, Karim; Figueiredo, IvoneEgg capsules of Rajidae species vary in size, shape and adornments. These differences can be used as a taxonomic tool to differentiate species. Furthermore, since egg capsule external morphology is adapted to the environment where they are laid, it can be used make inferences on egg-laying grounds. In the present study, oviducal glands and egg capsules of seven species of skates (Leucoraja naevus, Raja brachyura, Raja montagui, Raja microocellata, Raja miraletus, Raja clavata and Raja undulata) are described and compared, and a taxonomic key developed. The resulting taxonomic key constitute a useful tool to identify skate species inhabiting Portuguese continental waters and, therefore, to improve our knowledge of egg laying habitatsproviding useful information for conservation and management.
- Identification of potential essential fish habitats for skates based on fishers' knowledgePublication . Serra-Pereira, Bárbara; Erzini, Karim; Maia, Catarina; Figueiredo, IvoneUnderstanding of spatio-temporal patterns of sensitive fish species such as skates (Rajidae) is essential for implementation of conservation measures. With insufficient survey data available for these species in Portuguese Continental waters, this study shows that fishery-dependent data associated with fishers' knowledge can be used to identify potential Essential Fish Habitats (EFH) for seven skate species. Sites with similar geomorphology were associated with the occurrence of juveniles and/or adults of the same group of species. For example, sites deeper than 100 m with soft sediment include predominantly adults of Raja clavata, and are the habitat for egg deposition of this species. Raja undulata and R. microocellata are the more coastal species, preferring sand or gravel habitats, while coastal areas with rocks and sand seabed are potential nursery areas for R. brachyura, R. montagui and R. clavata. The main output of this study is the identification of preferential fishing sites enclosing potential EFH for some species, associated with egg-laying and nursery grounds. The location of these areas will be considered for future seasonal closures, and studies will be conducted to evaluate the biological and socio-economic impacts of such measures. As in the past, fishermen will collaborate in the process of evaluating those impacts, since they have practical and applied knowledge that is extremely valuable for evaluating the advantages and disadvantages of such closures. In conclusion, this study is a first contribution to the understanding and identification of EFH for skate species, associated with nursery and egg deposition sites, with direct application to management.
- Temperature and food-mediated variability of European Atlantic sardine recruitmentPublication . Garrido, Susana; Silva, Alexandra; Marques, Vitor; Figueiredo, Ivone; Bryere, Philippe; Mangin, Antoine; Santos, A. Miguel P.The influence of the environmental conditions during larval development on the resulting recruitment strength was investigated for European sardine (Sardina pilchardus) at Atlanto-Iberian waters. Satellite-derived Sea Surface Temperature (SST) and Chlorophyll-a concentration (Chla) data from the previous spawning seasons (January to March/April and October to December of the previous year) were related to recruitment success data in the main recruitment hotspots. Recruitment data was taken from yearly acoustic scientific cruises and from the ICES recruitment index estimated by an age-structured model for the entire stock. A linear discriminant analysis model using SST, Chla, and the abundance of spawners during the spawning season identified years of high and low recruitment for all the recruitment hotspots with an accuracy of >= 79%. In general, high recruitment years were associated with high Chla and low SST, although the most important variables to discriminate between the groups were area-specific. High recruitment years were mostly related to high food availability (Chla), particularly during the last quarter of the previous year. In Western Iberia and in the Gulf of Cadiz, high recruitment years were also associated to lower SST, whereas in the Bay of Biscay, where SST during the winter was generally below the optimal range approximate to 11-12 degrees C for sardine larval development, higher recruitment was associated with high SST. For ICES data of the southern European sardine stock, lower SST and higher Chla during the last quarter of the previous year were associated with high recruitment years and SST alone was able to discriminate between the two recruitment groups with 73% accuracy. Although the time-series of available data are still small, these significant relationships are consistent with field and laboratory studies relating larval growth and mortality with main environmental drivers. These relationships should be further investigated in the following years to evaluate if they can be used to construct reliable indicators to predict the level of recruitment and abundance with sufficient advance to help in the management of this important fishing resource.
- The use of caudal thorns for ageing Raja undulata from the Portuguese continental shelf, with comments on its reproductive cyclePublication . Moura, Teresa; Figueiredo, Ivone; Farias, Inês; Serra-Pereira, Bárbara; Coelho, Rui; Erzini, Karim; Neves, Ana; Gordo, Leonel SerranoThe present study focuses on age estimation, with reproductive information contributing to the better understanding of the growth and the biology of Raja undulata. In the age and growth study, two calcified structures were used: caudal thorns and central vertebra. Results of readings showed that there were no significant differences in age estimates between the two structures. Both von Bertalanffy and Gompertz growth models were fitted to size-at-age data by sex and geographical area. No significant differences were found between sexes for the two models but significant differences were found between geographical areas ( P = 0.05). The Gompertz growth function was selected as the best model to describe R. undulata growth because it presented the best fit and the most reasonable biological estimates. Reproductive analysis indicates one annual breeding season for R. undulata. The differences found in the estimates of length at first maturity between geographical areas (TL50% = 838 mm in Peniche and 762 mm in Algarve for females and TL50% = 781 mm in Peniche and 736 mm in Algarve for males), together with the regional differences found between growth parameters estimates ( P = 0.05), may reflect the existence of different local populations of R. undulata on the Portuguese continental shelf.
- Using biological variables and reproductive strategy of the undulate ray Raja undulata to evaluate productivity and susceptibility to exploitationPublication . Serra-Pereira, Bárbara; Erzini, Karim; Figueiredo, IvoneThe present work provides a detailed analysis of the reproductive strategy of the undulate ray Raja undulata in Portuguese mainland waters. The species was found mostly between 30 and 40 m deep on sandy bottoms. Egg-laying sites were observed in the north, centre and south-west regions, mainly at depths below 30 m. The peak of the reproductive season occurred from December to May. Asynchrony between reproductively active females and males appeared to occur, although most adult males were capable of reproducing throughout the year. The estimated length at 50% maturity was 862 cm (87 years) and 768 cm (76 years) total length for females and males, respectively. The maximum potential fecundity was estimated to be 698 follicles per female per reproductive season, which are released in 47 batches of 15 follicles. The life-history and demographic parameters of R. undulata are similar to those of other skate species, while the potential rate of population increase (049) is above the published values for other elasmobranch species. With these new findings, this study makes an important contribution to the understanding of the life history of R. undulata, and provides a first evaluation of the productivity and susceptibility of the species to exploitation.
- Vulnerable marine ecosystems survey pilot missions with EVA Hybrid AUV/ROVPublication . Almeida, Carlos; Martins, Alfredo; Soares, Eduardo; Santos, A. Miguel P.; Matias, Bruno; Silva, Pedro; Pereira, Ricardo; Sytnyk, Denys; Ferreira, António; Lima, Ana Paula; Cunha, Mariana R.; Ramalho, Sofia P.; Rodrigues, Clara F.; Figueiredo, Ivone; Rosa, Marcos; Almeida, JoséFishing for deep-sea species occurs on continental slopes, ridges, and seamounts. Fishing operations using fishing gears that contact the bottom (e.g., trawls and bottom longlines) may have significant impacts on Vulnerable Marine Ecosystems (VMEs). VMEs refer to marine ecosystems with a population or community of sensitive taxa or habitats that are likely to experience substantial alteration from short-term to chronic disturbance and that are unlikely to recover during the timeframe in which the disturbance occurs. The VME concept, introduced in the United Nations General Assembly Resolution 61/105, has been worldwide applied to the management of deep-sea fisheries. However, the effective identification and management of VMEs is highly constrained by the scarcity of data on VME indicator taxa. This data deficiency is usually surpassed by the use of VME predictive modelling. Video footage is a non-destructive method commonly used for exploring and investigating areas of seabed and for characterising and identifying habitat types. Remotely Operated Vehicles (ROVs) are one of the tools for seabed mapping. ROVs range in size from small observation-class to large work-class vehicles. Their sizes determine the payload, manoeuvrability, depth rating and ultimately uses of the vehicle. For epifaunal imaging, ROVs can be used in two modes: qualitative inspections and quantitative assessments. This paper presents the development of an innovative system composed of a compact support research vessel and a hybrid autonomous underwater vehicle capable of accurate georeferenced high-resolution imaging and profiling of the seabed for a detailed survey of the seabed for biodiversity studies. The experimental results obtained by the developed system in field work in real VME survey at 600m depth are presented.