Browsing by Author "Paulo, Diogo"
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- Complete mitochondrial genome of the branching octocoral Paramuricea grayi (Johnson, 1861), phylogenetic relationships and divergence analysisPublication . Coelho, Márcio; Ledoux, Jean-Baptiste; Boavida, Joana; Paulo, Diogo; Gómez-Gras, Daniel; Bensoussan, Nathaniel; López-Sendino, Paula; Cerrano, Carlo; Kipson, Silvija; Bakran-Petricioli, Tatjana; Garrabou, Joaquim; A, Serrão; Pearson, GarethThe Gray's sea fan, Paramuricea grayi (Johnson, 1861), typically inhabits deep littoral and circalittoral habitats of the eastern temperate and tropical Atlantic Ocean. Along the Iberian Peninsula, where P. grayi is a dominant constituent of circalittoral coral gardens, two segregating lineages (yellow and purple morphotypes) were recently identified using single-copy nuclear orthologues. The mitochondrial genomes of 9 P. grayi individuals covering both color morphotypes were assembled from RNA-seq data, using samples collected at three sites in southern (Sagres and Tavira) and western (Cape Espichel) Portugal. The complete circular mitogenome is 18,668 bp in length, has an A + T-rich base composition (62.5%) and contains the 17 genes typically found in Octocorallia: 14 protein-coding genes (atp6, atp8, cob, cox1-3, mt-mutS, nad1-6, and nad4L), the small and large subunit rRNAs (rns and rnl), and one transfer RNA (trnM). The mitogenomes were nearly identical for all specimens, though we identified a noteworthy polymorphism (two SNPs 9 bp apart) in the mt-mutS of one purple individual that is shared with the sister species P. clavata. The mitogenomes of the two species have a pairwise sequence identity of 99.0%, with nad6 and mt-mutS having the highest rates of non-synonymous substitutions.
- Field studies of seahorse population density, structure and habitat use in a semi-closed north-eastern Mediterranean marine area (Stratoni, north Aegean Sea)Publication . Correia, Miguel; Paulo, Diogo; Samara, Elina; Koulouri, Panayota; Mentogiannis, Vasilis; Dounas, CostasThe present study was carried out in the marine area of Stratoni, Greece, where two seahorse species are present (Hippocampus hippocampus and H. guttulatus). Two surveys were conducted (September 2016, May 2019) to gather information regarding seahorse species’ abundance, distribution and habitat characteristics. Four different seahorse natural and artificial habitat types were identified. Results revealed that the abundance of H. hippocampus was relatively high, especially at sites with artificial structures, while the presence of H. guttulatus was rare. Data collected can provide baseline information for future population assessments.
- First description of seagrass distribution and abundance in Sao Tome and PrincipePublication . Alexandre, Ana; Silva, João; Ferreira, Rogério; Paulo, Diogo; Serrao, Ester; Santos, RuiSeagrass meadows in Sao Tome and Principe, eastern Atlantic Ocean, are described here for the first time. Specifically, we quantified the biomass and density of seagrasses, characterized the plant morphology and measure their nutrient content as a proxy of the nutrient environmental conditions where the meadows develop. The seagrass Halodule wrightii was found in two locations of the northeastern coast of the island of Sao Tome: 1) developing throughout an estimated area of 1500 ha surrounding Cabras islet, at a depth range of 4-10 m, on sandy bottom; and 2) at Santana bay with an area of 1500 m(2) at 5-10 m depth, on sandy bottom. A highly morphologically different population of Halodule wrightii was found on the northeastern coast of the island of Principe, off Abade beach, covering an area of 135 m2 at 4 m depth. Further research is needed to assess if this is a different species. Shoot biomass and density was 10 and 4-fold higher in Sao Tome than in Principe, respectively. CN ratios of above and belowground tissues of plants collected in Sao Tome were also significantly higher than in Principe. The carbon content of Halodule leaves from Sao Tome and Principe (41%) was much higher than that reported for other Halodule species, suggesting that meadows may have an important ecological role for carbon fixation. The presence of H. wrightii in Sao Tome and Principe raises ecological and evolutionary questions that warrant further research.
- Less is more: seagrass restoration success using less vegetation per areaPublication . Mourato, Carolina; Padrão, Nuno; Serrao, Ester A.; Paulo, DiogoSeagrass restoration in open coast environments presents unique challenges. Traditional sod transplant designs, though relatively successful in these environments, are impractical for large-scale restoration due to high biomass requirements. Here, we develop the checkers design, which aims to optimise the usage of biomass by transplanting fewer sods in a checkerboard pattern. We established six plots (9 m2 each) for each species (Zostera marina and Zostera noltei), with 25 sods in each plot. The area, percent cover, density, and leaf length were measured at 1, 6, and 12 months. The plots located on the seaward end of the transplant design vanished over the winter, suggesting location-dependent survival influenced by winter storms. Nevertheless, both species exhibited increased percentages of cover, density, and vegetated area after one year, with variations between species. Z. noltei showed a slower expansion but greater resilience to winter, while Z. marina displayed a higher density and cover over the first 6 months but experienced area loss during the winter. Despite these differences, both species survived and increased vegetated areas after one year, indicating the viability and promise of the checkers method for large-scale restoration. However, careful consideration of location or storm-mitigating measures is essential for the successful implementation of this method.
- Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversificationPublication . Coelho, Márcio; Pearson, Gareth; Boavida, Joana R. H.; Paulo, Diogo; Aurelle, Didier; Arnaud‐Haond, Sophie; Gómez‐Gras, Daniel; Bensoussan, Nathaniel; López‐Sendino, Paula; Cerrano, Carlo; Kipson, Silvija; Bakran‐Petricioli, Tatjana; Ferretti, Eliana; Linares, Cristina; Garrabou, Joaquim; Serrão, Ester A.; Ledoux, Jean‐BaptisteThe accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.
- Open coast seagrass restoration. Can we do it? Large scale seagrass transplantsPublication . Paulo, Diogo; Cunha, Alexandra H.; Boavida, Joana; Serrao, Ester; Gonçalves, Emanuel J.; Fonseca, MarkSome of the major challenges in seagrass restoration on exposed open coasts are the choice of transplant design that is optimal for coastlines periodically exposed to high water motion, and understanding the survival and dynamics of the transplanted areas on a long time-scale over many years. To contribute to a better understanding of these challenges, we describe here part of a large-scale seagrass restoration program conducted in a Marine Park in Portugal. The goal of this study was to infer if it was possible to recover seagrass habitat in this region, in order to restore its ecosystem functions. To infer which methods would produce better long term persistence to recover seagrass habitat, three factors were assessed: donor seagrass species, transplant season, source location. Monitoring was done three times a year for 8 years, in which areas and densities of the planted units were measured, to assess survival and growth. The best results were obtained with the species Zostera marina transplanted during spring and summer as compared to Zostera noltii and Cymodocea nodosa. Long-term persistence of established (well rooted) transplants was mainly affected by extreme winter storms but there was evidence of fish grazing effects also. Our results indicate that persistence assessments should be done in the long term, as all transplants were successful (survived and grew initially) in the short term, but were not resistant in the long term after a winter with exceptionally strong storms. The interesting observation that only the largest (11 m(2)) transplanted plot of Z marina persisted over a long time, increasing to 103 m(2) in 8 years, overcoming storms and grazing, raised the hypothesis that for a successful shift to a vegetated state it might be necessary to overpass a minimum critical size or tipping point. This hypothesis was therefore tested with replicates from two donor populations and results showed effects of size and donor population, as only the larger planting units (PUs) from one donor population persisted and expanded. It is recommended that in future habitat restoration efforts large PUs are considered.
- Photosynthetic responses of Haalophila stipulacea to a light gradient. I. In situ energy partitioning of non-photochemical quenchingPublication . Runcie, John W.; Paulo, Diogo; Santos, Rui; Sharon, Yoni; Beer, Sven; Silva, JoãoThe quantum yield of photosystem II (phi(II), also termed Delta F/F-m' or F-v/F-m in light- or dark-acclimated plants, respectively) of the tropical seagrass Halophila stipulacea was measured in situ using modulated fluorescence techniques over diel periods at a range of depths. Photosynthetic electron transport rates (ETRs), as derived from phi(II) values at specific ambient photosynthetically available radiation (PAR) irradiances, increased in direct proportion to increasing irradiance in the morning and, at shallow sites (7 to 10 m), reached saturating rates and then declined in the afternoon with lower PAR-specific ETRs. On the other hand, plants at 32 to 33 m showed no saturation even at midday, and the percentage reduction in PAR-specific afternoon ETRs was less than that of the shallower plants. The use of an automated shutter in the measuring device enabled non-photochemical quenching due to down-regulation and basal intrinsic non-radiative decay to be distinguished. While midday values of down-regulation were lower in deeper water, basal intrinsic non-radioactive decay remained fairly constant at 30 to 40% at all depths, with more variation in shallow waters. The maximal phi(II) (i.e. F-v/F-m) reached similar values at midnight regardless of depth. H. stipulacea acclimates to the widely varying irradiances across this depth gradient by regularly modulating down-regulation-based non-photochemical quenching processes, while dissipating a large proportion of light energy through intrinsic decay regardless of depth.
- Recruit survival of Cymodocea nodosa along a depth gradientPublication . Paulo, Diogo; Manent, Pablo; Barrio, Juan M.; Serrão, Ester; Alberto, FilipeClonal plants can reproduce sexually and clonally, expressing different proportions of these different life histories in distinctive environments. In seagrass meadows, light attenuation hinders marine plant colonization in deeper areas of its vertical distribution. Therefore it is expected that the fluorescence maximum quantum yield of seedlings will be higher at deep limits of the meadow relative to shallower depths. We hypothesized that seagrass seedlings experience higher mortality in deeper areas of the meadows than at shallower levels. Our objective was to test survival of seagrass seedlings along a depth gradient in meadows of Cymodocea nodosa in the Canary Islands. Seedlings germinated in laboratory conditions, were transplanted to a natural meadow at three water depths: shallow (5 m), medium (8 m) and deep (12 m). Transplanted seedlings were monitored by measuring maximum quantum yield, leaf length, number of leaves per shoot and survival. Our data suggest that light does not hinder survival of seedlings along the depth gradient of the meadow. Before establishing clonal growth, seedlings in deeper areas had higher survival rates than those in shallow areas. Even though seeds are present at shallow depths and sexual allocation is high, sexual contribution can be lower than expected due to seedling loss.
- Restoration of animal forests: a novel transplantion method for coastal octocorals in the NE AtlanticPublication . Padrão, Nuno; Vieira Mourato, Carolina; Maria Rakka; Serrao, Ester A.; Paulo, DiogoOctocorals are among the main habitat‐engineering species, generating complex three‐dimensional ecosystems of unquestioned importance. Despite their importance, octocoral habitats have dramatically declined in the last decades due to several stressors. Consequently, octocoral gardens are internationally recognized as Vulnerable Marine Ecosystems. In the last decade, several octocoral restoration methodologies were the object of study, yet long‐term success was sparsely achieved or lacked assessment. To reverse the actual scenario, it is important to develop cost‐efficient methodologies to recover impacted, endangered octocoral habitats. In this 4‐year study, we developed and tested the Direct Substrate Attachment (DSA) method. This novel octocoral transplant method was trialed with two size classes of the species Paramuricea grayi and extended with a third class (20–40 cm) using Leptogorgia sarmentosa . With a recorded 95% attachment success, yearly annual positive growth, and a survival of 75% after 4 years, we prove the suitability of the DSA methodology in habitat restoration. Moreover, transplant size did not influence success; all transplants had verifiable holdfast and growth rates of up to 8.34 ± 1.7 cm. Seasonal growth and health status were monitored and compared to further assess the success of the transplant. The transplant performed with the DSA method is to date the first successful octocoral transplant in the Atlantic temperate seas with proven long‐term success. The results achieved are especially important in a moment where ecological degradation and mitigation efforts are a hot topic among decision‐makers. Using the DSA methodology, octocoral transplantation is possible and should be considered in conservation and restoration efforts.
- Sexual reproduction vs. clonal propagation in the recovery of a seagrass meadow after an extreme weather eventPublication . Paulo, Diogo; Diekmann, Onno; Ramos, Ana; Alberto, Filipe; Serrao, EsterMarine flowering plants can reproduce sexually and clonally, and the relative contribution of these two modes can be dependent on the environmental conditions. Zostera marina, a seagrass widely distributed in the northern hemisphere, can form annual and perennial meadows with different proportions of sexual versus clonal propagation depending on the environmental disturbance regime. We study the hypothesis that the contribution of sexual propagation varies during the recovery of a seagrass meadow. In this case study, we compare the proportion of sexual versus clonal propagation of a perennial Z. marina meadow before its disappearance due to winter storms and after recovery. Before disturbance, genotypic diversity was high, indicating frequent sexual reproduction events likely to create an abundant seed bank. Seedling germination allowed the population to recover after the extreme disturbance. As months passed, seedlings became rare and finally absent, giving place to adult shoots. In an advanced stage of colonization, the shoots colonized the area by vegetative growth, which lowered the genotypic diversity. Despite this reduction over time, the genotypic diversity of the new meadow is still high, demonstrating the importance of sexual reproduction in meadow recovery and persistence.