Water framework directive implementation: intercalibration exercise for biological quality elements: a case study for the south coast of Portugal

This work summarises the Intercalibration Exercise (IE) required for the Common Implementation Strategy of the Water Framework Directive (WFD; 2000/60/EC) that was carried out in Portugal, and applied to a coastal region. The WFD aims to achieve good ec ological status for all waters in the European Community by 2015. The Ecological Status of a water body is determined us ing a range of Hydromorphological and Physico-Chemical Quality Elements as well Biological Quality Elements (BQE ). In coastal waters, the Biological Elements include Phytoplankton, Other Aquatic Flora and Benthic Inverteb rate Fauna. Good cooperation with the other Member States allowed the IE to proceed without a complete da ta set, and Portugal was ab le to intercalibrate and harmonise methods within the North Ea st Atlantic Geographica l Intercalibration Group for most of the BQE. The appropriate metrics and corre sponding methods were agreed under the framework of the RECITAL (Reference Conditions and Intercalibra tion) project, funded by the Port uguese Water Institu te, INAG. Some preliminary sampling was undertaken, but not su fficient to establish the Reference Conditions. The study area was a coastal lagoon in the southern part of Portugal. The focus was on the Phytoplankton Quality Element, but other BQE were also taken into account. Two sampli ng stations in Ria Formosa coastal lagoon were considered in this exercise: Ramalhete a nd Ponte. The metrics adopted by the Intercalibration Exercise groups were applied enabli ng the classification for the two sta tions of Good/High Status for the majority of the BQE parameters.

Effects of mixture of nanoparticles under different salinity in the clams Ruditapes philippinarum and Ruditapes decussatus

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidadde do Algarve, 2015

Preenchimento sedimentar de duas zonas de dinâmica diferenciada no sapal de Castro Marim

Dissertação de mest. em Estudos Marinhos e Costeiros Ramo Gestão Costeira, Faculdade de Ciências do Mar e do Ambiente, Univ. do Algarve, 2002

Dinâmica dos nutrientes na Ria Formosa: efeitos da interacçäo da laguna com as suas interfaces na reciclagem do azoto, fósforo e sílica

Tese de dout. em Ciências do Mar, Instituto de Investigação das Pescas e do Mar, Univ. do Algarve, 1996

Bioaccumulation and effects of TBT on molluscs from southern Portugal

Tese de dout. Ciências e Tecnologias do Ambiente, Faculdade de Ciências do Mar e do Ambiente, Univ. do Algarve, 2004

Allozyme and mtDNA variation of white seabream Diplodus sargus populations in a transition area between western and eastern Mediterranean basins (Siculo-Tunisian Strait)

To investigate the possible influence of the Siculo-Tunisian Strait on the genetic structure of white seabream Diplodus sargus, 13 polymorphic allozyme loci and a fragment of the cytochrome b mitochondrial DNA were analysed. Allozyme data indicated a moderate but significant differentiation between some north-eastern (Bizerta, Ghar El Melh Lagoon and Mahdia) and southern (Gabes Gulf and El Biban Lagoon) samples. This heterogeneity was also highlighted after removing PGM* and PGI-1* loci which may be under selection. These results can be explained by the chaotic genetic patchiness hypothesis. In contrast, the mtDNA data indicated genetic homogeneity among localities showing the absence of structure in white seabream populations across the Siculo-Tunisian Strait. Historical demography of this species suggests that it has undergone a recent population expansion as a consequence of a bottleneck event during the Pleistocene glaciations.

Phosphoglucose isomerase variability of Cerastoderma glaucum as a model for testing the influence of environmental conditions and dispersal patterns through quantitative ecology approaches

Extreme conditions of coastal lagoons could directly modify the genetic patterns of species. The aim of this work was to investigate the influence of environmental conditions and small scale dispersal patterns on the phosphoglucose isomerase (PGI*) genetic variability of Cerastoderma glaucum from the Mar Menor coastal lagoon. For this purpose, 284 cockles were collected around the perimeter of the lagoon. Vertical polyacrylamide gel electrophoresis was used to scan for PGI* polymorphisms, giving a total of seven alleles. The spatial genetic distribution of the PGI* variability, which seems to be marked by the main circulation in the lagoon, discriminates four hydrological basins. In the central basin, a gradient of allelic composition reflects the circulation forced by the dominant winds and the main channel communicated to the open sea. This result is well supported by the salinity GAM model that defines this gradient. The other three basins are defined by the distribution of fine sand in a more complex model that tries to explain the isolation of the three sites localized inside these basins. The southern, western and northern basins show the lowest degree of interconnection and are considered the most confined areas of the Mar Menor lagoon. This situation agrees with the confinement theory for benthic assemblages in the lagoon. The greater degree of differentiation seen in the Isla del Ciervo population is probably due to recent human intervention on the nearby Marchamalo channel, which has been drained in recent years thus altering the influence of the Mediterranean Sea on the southern basin.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.

Elysia timida (Risso, 1818) three decades of research

Elysia timida (Risso, 1818) three decades of research.— During the last 30 years, studies on Elysia timida (Risso, 1818) have addressed various aspects related to food sources, photosynthetic efficiency of kleptoplasts, population genetics, chemical ecology and reproductive biology, both in the Mediterranean Sea and in the Mar Menor coastal lagoon. E. timida shows a strong specific interaction with Acetabularia acetabulum, retaining functional chloroplasts for at least 45 days and obtaining extra energy in periods when food resources are scarce. It shows control of parapodia, avoiding pigment photodestruction under oversaturated light conditions. The chemical ecological relationships established between E. timida and its potential predator fish, Thalassoma pavo, have also been evaluated, and it has been found that that the extracts of the mollusc contain repellent and unpalatable polypropionate compounds. Population genetics has demonstrated the genetic divergence between populations showing high and significant values of FST and genetic distances, and at least six privative alleles that are not shared with Mediterranean populations have been detected in lagoon populations. This sacoglossan is a poecilogonic species, and its lagoon populations show a greater reproductive output than Mediterranean populations; they produce a greater number of egg masses and embyros per individual, and the capsules have a wider diameter.

In two waters: contemporary evolution of lagoonal and marine white seabream (Diplodus sargus) populations

Brackish water ecosystems are often exposed to wide variations in environmental variables, including temperature and salinity, which may cause strong selective pressures on organisms modifying the genetic patterns of species. The aim of this work was to test whether there is a ‘divergence-with-gene flow’ in coastal lagoon populations of white seabream (Diplodus sargus) (Ria Formosa, S Portugal and Mar Menor, SE Spain) respect to four marine populations, by using partial sequences of cyt b mitochondrial gene and information from nine microsatellite loci. Genetic diversity was highest in both coastal lagoons (Mar Menor and Ria Formosa) considering mitochondrial and nuclear markers. Although some of FST population pairwise comparisons were not significant, analyses of molecular variance (AMOVAs) detected differences between groups (coastal lagoon and marine) close to significance. Also, only two haplotypes (Cytb-17 and Cytb-18) were detected in both coastal lagoon sampling sites and these localities (Mar Menor and Ria Formosa) showed the highest number of singletons, some of them with a high number of mutations, as has been already described for other Mar Menor populations (Pomatochistus marmoratus and Holothuria polii). Also, several tests detected significant positive and balancing selection considering mtDNA and microsatellite data. These data support the hypothesis of selection as one of the drivers of the genetic differences found between coastal lagoon and marine populations. The life strategy adopted by Diplodus sargus in coastal lagoons allows it to decrease its mortality rate and improve the heritability of its genes. Also, the increase time spent in coastal lagoons with different temperatures and salinities favours the fitness selection and the maintenance of exclusive haplotypes and genotypes in coastal lagoon inhabitants favouring the ‘divergence-with-gene-flow’.

Spatial distribution patterns and movements of Holothuria arguinensis in the Ria Formosa (Portugal)

Holothurian populations are under pressure worldwide because of increasing demand for beche-de-mer, mainly for Asian consumption. Importations to this area from new temperate fishing grounds provide economic opportunities but also raise concerns regarding future over-exploitation. Studies on the habitat preferences and movements of sea cucumbers are important for the management of sea cucumber stocks and sizing of no-take zones, but information on the ecology and behavior of temperate sea cucumbers is scarce. This study describes the small-scale distribution and movement patterns of Holothuria arguinensis in the intertidal zone of the Ria Formosa national park (Portugal).Mark/recapture studieswere performed to record theirmovements over time on different habitats (sand and seagrass). H. arguinensis preferred seagrass habitats and did not show a size or life stage-related spatial segregation. Its density was 563 ind. ha−1 and mean movement speed was 10 m per day. Movement speed did not differ between habitats and the direction of movement was offshore during the day and shoreward during the night. Median home range size was 35 m2 and overlap among home ranges was 84%. H. arguinensis' high abundance, close association with seagrass and easy catchability in the intertidal zone, indicate the importance of including intertidal lagoons in future studies on temperate sea cucumber ecology since those systems might require different management strategies than fully submerged habitats.

Small-scale genetic structure of Cerastoderma glaucum in a lagoonal environment: potential significance of habitat discontinuity and unstable population dynamics

Environmental heterogeneity in coastal lagoons is expected to facilitate local adaptation in response to different ecological conditions, causing significant genetic structuring within lagoon populations at a small scale and also differentiation between lagoons. However, these patterns and processes of genetic structuring are still poorly understood. The aims of our study were (1) to seek genetic structure at a small scale in Cerastoderma glaucum inside the Mar Menor coastal lagoon using a mitochondrial DNA marker (COI) that has previously detected genetic differentiation inside the lagoon in other species and (2) to evaluate the influence of extreme environmental conditions and habitat discontinuity on its genetic composition. The results indicate high levels of haplotype diversity and low values of nucleotide diversity. COI data provide evidence of significant population differentiation among some localities within the lagoon. Limited gene flow and unstable population dynamics (i.e. fluctuations in population size caused by local extinction and recolonization), probably due to the high environmental heterogeneity, could generate the small-scale genetic divergence detected between populations within the lagoon.

Population genetics of Cerastoderma edule in Ria Formosa (southern Portugal): the challenge of understanding an intraspecific hotspot of genetic diversity

Coastal lagoons are highly variable environments that may act as hotspots of genetic diversity as a consequence of their ecological role as nursery habitats of marine species with both ecological and fisheries importance. The edible cockle (Cerastoderma edule) is a commercially important shellfish resource inhabiting coastal lagoons in Europe and their fisheries management urgently needs genetic studies to design appropriate strategies to promote the recovery of exploited populations. The aim of this study was to assess the C. edule genetic diversity and population structure at a small geographic scale, inside Ria Formosa coastal lagoon (southern Portugal) using mitochondrial cytochrome oxidase I sequences in six locations. Outcomes pointed to a common pattern of high haplotype diversity and non-significant genetic structuring inside the Ria Formosa lagoon. A high level of gene flow was detected between all localities and the presence of a single stock from a genetic point of view may be considered for fisheries management purposes. The existence of a high number of haplotypes and high values of haplotype diversity of C. edule in Ria Formosa lagoon could be consistent with the hypothesis that higher genetic diversity is expected in populations occurring in coastal lagoons, suggesting that lagoons could increase standing genetic variation and an adaptive potential of lagoon populations as an ecological response to a highly variable environment.

Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species

Coastal lagoons are considered one of the most productive areas of our planet harboring a large variety of habitats. Their transitional character, between terrestrial and marine environments, creates a very particular ecosystem with important variations of its environmental conditions. The organisms that are able to survive on these ecosystems frequently experience strong selective pressures and constrictions to gene flowwith marine populations, which could contribute to genetic divergence among populations inhabiting coastal lagoon and marine environments. Therefore, the main aims of this study are to asses the genetic diversity and population structure of Holothuria arguinensis across geographical ranges, to test the hypothesis of coastal lagoons as hotspots of genetic diversity in the Ria Formosa lagoon, and to determine the role of exporting standing genetic variation from the lagoon to open sea and their implications to recent geographical expansion events. To reach these objectives, we investigate the genetic structure of H. arguinensis using two mitochondrial DNA markers (COI and 16S) at different spatial scales: i) small, inside Ria Formosa coastal lagoon, South Portugal; 2) large, including most of the geographical distribution of this species (South and Western Portuguese coast and Canary islands); these results will allow us to compare the genetic diversity of lagoonal and marine populations of H. arguinensis. On this framework, its recent geographical expansion events, recorded by Rodrigues (2012) and González-Wangüemert and Borrero-Pérez (2012), will be analyzed considering the potential contribution from lagoonal genetic pool. Non-significant genetic structure and high haplotypic diversity were found inside the Ria Formosa coastal lagoon. Both genes were unable to detect significant genetic differentiation among lagoonal and marine localities, suggesting a high rate of gene flow. The results supported our hypotheses that coastal lagoons are not only acting as hotspots of genetic diversity, but also contributing for the genetic variability of the species, working as a source of new haplotypes and enhancing adaptation to the high variable conditions. Different genetic patterns of colonization were found on H. arguinensis, but they must be studied more deeply.

Age and growth, mortality, reproduction and relative yield per recruit of the bogue, Boops boops Linne, 1758 (Sparidae), from the Algarve (south of Portugal) longline fishery

Samples of Boops boops ranging from 7.4 to 30.5 cm were obtained mainly by longline, supplemented by beach seining in the Ria Formosa lagoon, and by market sampling in the Algarve (southern Portugal). The macroscopic analyses of the gonads and the gonad somatic index showed that the south coast of Portugal B. boops spawn mainly from late winter to spring, between February and May. The length at first maturity was similar for males and females and the value for both sexes combined was estimated to be 15.22 cm, corresponding to an age range of 1-3. Age was determined by reading growth bands on otoliths. Age determination was validated by marginal increment analysis. The estimated parameters were L-infinity = 28.06, K = 0.22 and t(0) = -1.42. Mortality rates were calculated for fish captured with longlines, and the estimated parameters were M = 0.33, Z = 1.04 and F = 0.71. Relative yield per recruit analysis and sensitivity analysis showed that the resource is moderately exploited. From the perspective of sustainability, these results provide support for the use of longlines as a gear that is among the least harmful for species such as the bogue.