Using niche modelling of indicator species to predict the distribution of xerophitic shrub dune communities in South-Western Portugal

Inland sand dune systems are amongst the most threatened habitat types of Europe. Affected by severe conditions, these habitats present distinct community compositions, which makes them excellent for studying possible interactions among their integrating species and the environment. We focus on understanding the distribution and cooccurrence of the species from dune plant assemblages as a key step for the adequate protection of these habitats. Using data from an extensive survey we identified the shrub species that could be considered indicators of the different xerophytic scrub dune communities in South West Portugal. Then, we modelled the responses of these species to the environmental conditions using Ecological Niche Factor Analysis. We present some preliminary results elucidating whether using species distribution models of indicator species at a regional scale is a valid approach to predict the distribution of the different types of communities inhabiting these endangered habitats.

Can we use niche models of indicator species to predict the distribution of endangered communities?

European-wide conservation policies are based on the identification of priority habitats. However, research on conservation biogeography often relies on the results and projections of species distribution models to assess species' vulnerability to global change. We assess whether the distribution and structure of threatened communities can be predicted by the suitability of the environmental conditions for their indicator species. We present some preliminary results elucidating if using species distribution models of indicator species at a regional scale is a valid approach to predict these endangered communities. Dune plant assemblages, affected by severe conditions, are excellent models for studying possible interactions among their integrating species and the environment. We use data from an extensive survey of xerophytic inland sand dune scrub communities from Portugal, one of the most threatened habitat types of Europe. We identify indicator shrub species of different types of communities, model their geographical response to the environment, and evaluate whether the output of these niche models are able to predict the distribution of each type of community in a different region.

Thesis abstract. Applying species distribution modeling for the conservation of Iberian protected invertebrates

This article outlines the approaches to modeling the distribution of threatened invertebrates using data from atlases, museums and databases. Species Distribution Models (SDMs) are useful for estimating species’ ranges, identifying suitable habitats, and identifying the primary factors affecting species’ distributions. The study tackles the strategies used to obtain SDMs without reliable absence data while exploring their applications for conservation. I examine the conservation status of Copris species and Graellsia isabelae by delimiting their populations and exploring the effectiveness of protected areas. I show that the method of pseudo‐absence selection strongly determines the model obtained, generating different model predictions along the gradient between potential and realized distributions. After assessing the effects of species’ traits and data characteristics on accuracy, I found that species are modeled more accurately when sample sizes are larger, no matter the technique used.

Assessing the effects of pseudo-absences on predictive distribution model performance

Modelling species distributions with presence data from atlases, museum collections and databases is challenging. In this paper, we compare seven procedures to generate pseudoabsence data, which in turn are used to generate GLM-logistic regressed models when reliable absence data are not available. We use pseudo-absences selected randomly or by means of presence-only methods (ENFA and MDE) to model the distribution of a threatened endemic Iberian moth species (Graellsia isabelae). The results show that the pseudo-absence selection method greatly influences the percentage of explained variability, the scores of the accuracy measures and, most importantly, the degree of constraint in the distribution estimated. As we extract pseudo-absences from environmental regions further from the optimum established by presence data, the models generated obtain better accuracy scores, and over-prediction increases. When variables other than environmental ones influence the distribution of the species (i.e., non-equilibrium state) and precise information on absences is non-existent, the random selection of pseudo-absences or their selection from environmental localities similar to those of species presence data generates the most constrained predictive distribution maps, because pseudo-absences can be located within environmentally suitable areas. This study showsthat ifwe do not have reliable absence data, the method of pseudo-absence selection strongly conditions the obtained model, generating different model predictions in the gradient between potential and realized distributions.

Large-scale prediction of seagrass distribution: the case of Cymodocea nodosa (Mediterranean-Atlantic)

Understanding the factors that affect seagrass meadows encompassing their entire range of distribution is challenging yet important for their conservation. We model the environmental niche of Cymodocea nodosa using a combination of environmental variables and landscape metrics to examine factors defining its distribution and find suitable habitats for the species. The most relevant environmental variables defining the distribution of C. nodosa were sea surface temperature (SST) and salinity. We found suitable habitats at SST from 5.8 ºC to 26.4 ºC and salinity ranging from 17.5 to 39.3. Optimal values of mean winter wave height ranged between 1.2 m and 1.5 m, while waves higher than 2.5 m seemed to limit the presence of the species. The influence of nutrients and pH, despite having weight on the models, was not so clear in terms of ranges that confine the distribution of the species. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. By contrasting predictive approaches, we defined the variables affecting the distributional areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. These findings are encouraging for its use in future studies on climate-related marine range shifts and meadow restoration projects of these fragile ecosystems.

Hydrodynamic and sediment fluxes through the inlets of the Ria Formosa

Tese de dout., Ciências do Mar, da Terra e do Ambiente (Ciências do Mar-Oceanografia Física), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011

The role of hypoxia in the regulation of membrane transporters

ATP binding cassette (ABC) and solute carrier (SLC) transporters are responsible for the majority of the transcellular movement of various substrates, including drugs, among epithelial cells. Despite the well characterized regulation of influx (SLC) and efflux (ABC) transporters by endogenous mediators, such as inflammatory cytokines, little is known about how changes in oxygen levels may affect expression of these transporters. In this study we showed that the expression of SLC22A4, SLC22A5, SLC22A1, SLC02B1, SLC10A2, ABCC2 and ABCC3 transporters is upregulated by hypoxia in HT29 colon carcinoma cells, but not in HepG2 hepatocarcinoma cells. Moreover, OCTN1 (SLC22A4), OCT1 (SLC22A1) and OATP-B (SLC02B1) transporter expression is also induced by inflammatory cytokines but in a smaller extent than in hypoxia. Furthermore our experiments indicate that there is no cross talk between HIF-1 and NF-κB pathways in HT-29 cells, but these two pathways act simultaneously activating common genes, such as, some SLC and ABC transporters. Our preliminary results from studies with an in vivo murine model of colitis, suggest that HIF-1is stabilized and OCTN1 is strongly induced during severe inflammation, which can be relevant for a recovery from the inflammatory process. We have also been interested in the distribution of HIF-1α variants among different ethnic groups as well as their contribution for cancer risk. Thus, we have demonstrated that there is an ethnicity-related variation in the frequency of the C1772T (P582S) single nucleotide polymorphism (SNP) in the HIF-1α gene. Furthermore, we performed a case-control study in a breast cancer population and our results suggest that there is no association between this SNP or the rare G1790A (A588T) SNP and the incidence of breast cancer. Taken together, the results obtained in this study contribute to a better knowledge of drug influx and efflux during hypoxia and inflammation as well as to the understanding of the pharmacogenetic variability of the HIF-1.

The effect of conservation measures on the spatial and temporal variation of rocky fish assemblages in the Arrábida Marine Park

Marine protected areas (MPAs) have been widely proposed for conservation purposes and as a tool for fisheries management. The Arrábida Marine Park is the first MPA in continental Portugal having a management plan, fully implemented since 2009. The main objective of this study was to evaluate the effect of protection measures on rocky reef fish assemblages and target invertebrates through before-after and control-effect (no-take vs. fished areas) underwater visual surveys and analysis of landings trends. Second, we used surveys before, during and after implementation of the management plan to understand fishers‟ preferences for fishing grounds and adaptation to the new rules, and evaluated the reserve effect through analysis of both ecological responses and fishing effort density. Third, we identified the main oceanographic drivers influencing the structure of reef fish assemblages and predicted the community structure for the last 50 years, in light of climatic change. Overall results suggest positive responses in biomass but not yet in numbers of some commercial species, with no effects on non-target species. The reserve effect is reinforced by the increase in landings of commercial species, despite increased fishing effort density in some areas, especially with octopus traps. Fishing grounds are mainly chosen based on the distribution of target species and associated habitats, but distance to port, weather conditions and safety also influence fishers‟ choices. Moreover, different fisheries respond differently to the protection measures, and within each fishery, individual fishers show distinct strategies, with some operating in a broader area whereas others keep preferred territories. Our results also show that wind stress and temperature are the main oceanographic drivers for rocky reef fish assemblages, with tropicalization of assemblages and polewards movements of species over the last 50 years consistent with temperature trends. We believe this study provides significant lessons for marine conservation and management of coastal systems.