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- A call for CARE in animal behaviour: an holistic ethical research frameworkPublication . Badihi, Gal; Taylor-O’Connor, Jennifer; Daly, Gabriela Bezerra de Melo; Komeda, Viola; Daoudi-Simison, Sophia; Rodrigues, Evelina D.; Webster, Michael M.; Altschul, Drew M.; Hobaiter, Catherine; Wiltshire,Charlotte; Klein, Harmonie; Freymann, Elodie; Grund, Charlotte; Soldati, Adrian; Henderson, Matthew; Leroux, Maël M.; Slania, Nora E.; ElseviorDespite increasing awareness of animal welfare, there are vast discrepancies between legal protections and recommended practices for different species, in different countries and at different institutions. While many guidelines are now available, they often target specific research contexts or species, leaving a gap in compre hensive ethical oversight across the entire research process. Within animal behaviour research, there is a bias for considering ethics during only the methodology and design phase. This often means only the immediate impact on animals directly involved in the research is accounted for. Conducting ethical research should extend beyond ensuring animal welfare during data collection and include environmentally sustainable research practices, alongside the ethical treatment of people working within and alongside animal behaviour research. We offer the Consult, Approve, Research and Evaluate (CARE) framework to improve the scientific integrity, transparency and ethical practices within the field of animal behaviour. CARE encourages researchers and academic bodies to (1) Consult existing (academic and traditional) knowledge on the study species, local human—animal interactions, their environment and previously implemented ethical practices and to reflect on personal experience and biases when approaching a study question; (2) seek Approval from relevant bodies (e.g. institutional ethics committees and local and government authorities) even when not mandatory; (3) uphold ethical standards while carrying out Research and (4) Evaluate the short- and long-term impacts of the specific study. Our framework is designed to distribute accountability at every level of the academic system, from individual re searchers to their institutions, funding bodies and publishers. We pitch this framework as a ‘version 1.0’ to recognize the fast-evolving nature of ethical standards in animal behaviour research and to allow space for improvement. CARE provides a necessary infrastructure for addressing systemic biases and ensuring ethically sound, socially responsible and environmentally sustainable animal behaviour research.
- Abiotic stress and induced DNA hypomethylation cause interphase chromatin structural changes in rice rDNA lociPublication . Santos, Ana Paula; Ferreira, Liliana J.; Maroco, João; Oliveira, Maria MargaridaGlobal climate change, i.e. higher and more variable temperatures, and a gain in soil salinity are increasing plant stress with direct consequences on crop yield and quality levels. Rice productivity is strongly affected by abiotic stress conditions. The regulation of chromatin structure in response to environmental stress is poorly understood. We investigated the interphase chromatin organization from rice plants in non-stress versus stress conditions. We have used a cytogenetic approach, based on fluorescence in situ hybridization (FISH) with 45S, 5S rDNA and centromeric probes on rice tissue sections. The abiotic stress conditions included cold, heat and mild salinity and were applied during seed germination. In contrast to cold, saline and heat stresses caused extensive decondensation of 45S rDNA chromatin and also an increase in the distance between the 2 homologous 5S rDNA loci. 5-Azacytidine (5-AC), a DNA hypomethylating drug, greatly increased 45S rDNA chromatin decondensation and interestingly was able to induce polarization of centromeres in rice interphase nuclei. The abiotic stresses tested did not perturb the spatial position of centromeres, typically with circular arrangement around the nucleolus. The results suggest a role for chromatin plasticity in a world of climate changes.
- Accounting for animal density gradients using independent information in distance sampling surveysPublication . Marques, Tiago A.; Buckland, Stephen T.; Bispo, Regina; Howland, BrettDistance sampling is extensively used for estimating animal density or abundance. Conventional methods assume that location of line or point transects is random with respect to the animal population, yet transects are often placed along linear features such as roads, rivers or shorelines that do not randomly sample the study region, resulting in biased estimates of abundance. If it is possible to collect additional data that allow an animal density gradient with respect to the transects to be modelled, we show how to extend the conventional distance sampling likelihood to give asymptotically unbiased estimates of density for the covered area. We illustrate the proposed methods using data for a kangaroo population surveyed by line transects laid along tracks, for which the true density is known from an independent source, and the density gradient with respect to the tracks is estimated from a sample of GPS collared animals. For this example, density of animals increases with distance from the tracks, so that detection probability is overestimated and density underestimated if the non-random location of transects is ignored. When we account for the density gradient, there is no evidence of bias in the abundance estimate. We end with a list of practical recommendations to investigators conducting distance sampling surveys where density gradients could be an issue.
- Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster)Publication . Marum, Liliana; Rocheta, Margarida; Maroco, João; Oliveira, Maria Margarida; Miguel, Célia M.Somatic embryogenesis (SE) is a propagation tool of particular interest for accelerating the deployment of new high-performance planting stock in multivarietal forestry. However, genetic conformity in in vitro propagated plants should be assessed as early as possible, especially in long-living trees such as conifers. The main objective of this work was to study such conformity based on genetic stability at simple sequence repeat (SSR) loci during somatic embryogenesis in maritime pine (Pinus pinaster Ait.). Embryogenic cell lines (ECLs) subjected to tissue proliferation during 6, 14 or 22 months, as well as emblings regenerated from several ECLs, were analyzed. Genetic variation at seven SSR loci was detected in ECLs under proliferation conditions for all time points, and in 5 out of 52 emblings recovered from somatic embryos. Three of these five emblings showed an abnormal phenotype consisting mainly of plagiotropism and loss of apical dominance. Despite the variation found in somatic embryogenesis-derived plant material, no correlation was established between genetic stability at the analyzed loci and abnormal embling phenotype, present in 64% of the emblings. The use of microsatellites in this work was efficient for monitoring mutation events during the somatic embryogenesis in P. pinaster. These molecular markers should be useful in the implementation of new breeding and deployment strategies for improved trees using SE.
- Are tidal lagoons ecologically relevant to larval recruitment of small pelagic fish : an approach using nutritional condition and growth ratePublication . Chícharo, M.A.; Amaral, A.; Faria, A.; Morais, P.; Mendes, C.; Piló, D.; Ben-Hamadou, R.; Chícharo, L.There are numerous studies dealing with larvae of Small Pelagic Fish (SPF), but only a few have actually addressed advanced larval phases. Temperate coastal lagoons are particularly understudied, due to the absence of standard method to capture advanced larval fish in these near shore shallow habitats. Accordingly, this study aims to describe abundances, nutritional condition and in situ growth of postflexion (SPF) from the Ria Formosa, a tidal coastal lagoon in southern Portugal. The nutritional condition and in situ growth were determined through cohort analysis and standardized RNA:DNA ratio (sRD), complemented with feeding incidence (gut content) and fatty acids (FAs, trophic biomarkers) of postflexion larvae sampled sequentially with light traps, from spring 2005 to summer 2006. Simultaneously, environmental parameters such as water temperature, salinity, dissolved oxygen and chlorophyll a were measured. Post-larvae of SPF were captured through the year in important numbers. The dominant species were Sardina pilchardus (50.7%), Engraulis encrasicolus and Atherina presbyter (11.4%). These results are distinct from those based on adult/juvenile surveys or early planktonic phases in the Ria Formosa where clupeiformes were occasionally reported. Sardines were captured mainly in winter, spring and early summer and anchovies mainly during summer and autumn. Sand smelt, a resident species, was present throughout the year. In the early summer, the three species were present and during this period some diet overlapping occurred, the feeding incidence of the clupeiformes was very low, but atherinids always exhibited full guts reflecting the different gut morphology or indicating different lifecycle strategies. The bulk of the diet was mollusks, crustaceans and appendicularians, for sand smelts, sardines and anchovies, respectively. The results of FA analyses showed some contribution of phytoplankton to SPF in the area. All SPF exhibited higher condition (sRD) and growth rates in summer, which are explained by the adequate temperature and higher planktonic productivity. This is especially relevant because the successful development of postflexion larvae in these nursery areas largely determines the successful recruitment to adult fish populations.
- A behavioural study on environmental enrichment in the common octopus, Octopus vulgaris cuvier, 1798Publication . Severino, David Peniche de Carvalho; Gonçalves, Emanuel JoãoA riqueza de estimulação é um dos aspetos mais importantes quando se fala em bem-estar de animais em cativeiro. Neste trabalho pretendemos demonstrar que o enriquecimento ambiental tem uma influência assinalável no comportamento e no bem-estar do polvo comum (Octopus vulgaris). Para uma parte da análise foi usado o etograma da espécie, elaborado a partir da observação de 2 polvos, da costa do Algarve. Foram verificados e descritos 38 padrões comportamentais, em 7 categorias: locomoção, alimentação, social, posturas, abrigo, exploração, padrões de cores e outros. Para a análise do bem-estar, distribuíram-se 12 polvos também apanhados na costa do Algarve por três aquários, com diferentes níveis de enriquecimento: aquário 1 - nenhum, aquário completamente vazio, sem substrato nem objetos (estéril); aquário 2 - fraco, substrato de areia (standard); aquário 3 - forte, enriquecido com substrato de areia, pedras e covos (enriquecido). Foram feitas 4 filmagens por dia (2 vezes durante o dia e 2 à noite) a cada aquário. No aquário enriquecido os polvos foram mais exploratórios, principalmente no período da tarde. No aquário estéril os polvos apresentaram uma maior frequência de comportamentos estereotipados. A preparação de um abrigo parece constituir uma necessidade comportamental, já que este comportamento esteve presente tanto no aquário standard, como no enriquecido.
- Biodiversity vs. geodiversity in landscape appreciation: What do Portuguese and Spanish pre-service teachers value?Publication . Almeida, António; Prieto, Prieto; Fernández, Beatriz GarcíaABSTRACT This study aimed to identify, via questionnaire, the landscape preferences of 336 pre-service teachers—219 from a metropolitan area in Portugal and 117 from a rural area in Spain. Eight natural landscapes were assessed, each characterised by geodiversity, biodiversity, and cultural features. Overall, Portuguese students showed stronger preferences, possibly due to Spanish students’ familiarity with natural surroundings. Landscapes featuring geodiversity with water bodies (such as cascades and caldera lakes) were most favoured, while biodiversity-rich landscapes were pre ferred over those with only geodiversity. Both groups expressed a stronger commitment to landscape preservation than to their preferences, showing a moderate to weak correlation between these factors. Animals significantly attracted interest, and when various natural elements were present, geo diversity features tended to be less noticed. Positive emotions were gen erally associated with the landscapes, though some geological features and educational values were underappreciated. Suggestions for integrating these insights into teacher training are included.
- Bridging sd1 molecular knowledge with recent breeding strategies for the improvement of traditional rice varieties - a japonica case-studyPublication . Negrão, Sónia; Palaniappan, Jayamani; Maroco, João; Lourenço, Tiago; Mackill, David; Oliveira, Maria MargaridaThe rice semidwarfing gene, sd1, also known as the “green revolution gene”, has been studied intensively due to its contribution to the increase of crop production. Although sd1 breeding was extensively applied since the 1960s, the recent advances in the molecular basis of this gene allowed designing a more precise breeding strategy - marker assisted backcrossing (MAB) - to track sd1 introgression in two traditional rice varieties. For selection of sd1 plants we first confirmed the efficiency of specific markers based on Os200 x 2 gene sequence. Background selection was also performed with the help of microsatellites markers (SSR) and a total of 7 breeding lines were recovered containing a higher percentage of recurrent parent genome (RPG). Analysis of Covariance (ANCOVA) using mean progenitor plant height as covariate was performed to compare several agronomic and quality-related parameters in two different environments. The results suggest that plant height differs significantly between the two environments F(1, 220) = 155.336; p < 0.001. From the total variability of plant height we could conclude that 73% is due to the genotype, while 10.4% depends on the environment. In addition, the percentage of RPG seems negatively correlated with plant height (p < 0.005). MAB and background selection thus revealed as useful tools to assist breeding for semidwarfism in traditional rice varieties.
- Control of stomatal aperture and carbon uptake by deficit irrigation in two grapevine cultivarsPublication . Souza, Cláudia R. de; Maroco, João; Santos, Tiago P.; Rodrigues, M. Lucília; Lopes, Carlos Manuel Antunes; Pereira, João Santos; Chaves, Maria Manuelaodels for the Mediterranean region. In recent years, deficit irrigation, including partial root drying (PRD), has been proposed as an irrigation technique to improve water use efficiency and standardize grapevine yield and quality. The objective of this study was to evaluate the impact of deficit irrigation on photosynthetic responses of field grown grapevines of cv. Moscatel and Castela˜o. The treatments were: full irrigation (FI), corresponding to 100% ETc; non-irrigated, but rain fed (NI) and partial root zone drying (PRD) and deficit irrigation (DI), both corresponding to an irrigation of 50% ETc. While in the DI treatment water was applied to both sides of the root system, in the PRD treatment, water was supplied to only one side of the root system, alternating sides periodically. In both cultivars, PRD and DI vines showed intermediate pre-dawn leaf water potential (ψpd) values (around -0.4 MPa) while FI vines, showed ψpd around -0.2 MPa during the growing season. NI showed the lowest cpd, reaching -0.6 MPa in Moscatel and -0.8 MPa in Castelão, at the end of growing season. Water status of PRD vines remained closer to FI than DI, especially at midday. Photosynthetic rates and fluorescence parameters of the deficit irrigation treatments (PRD and DI) did not show significant differences from FI vines, for most of the season. In Moscatel, although PRD generally showed gs, relative stomatal limitation (RSL) and intrinsic water use efficiency (A/gs) values closer to NI than DI, most of the differences between PRD and DI were not statistically significant. Our results showed a stability of the photosynthetic machinery in grapevines under low-to-moderate water availabilities, as demonstrated by the maintenance of the activity of three Calvin Cycle enzymes and of the Vcmax values. However, a decline in Jmax was observed in NI vines, that can be a result either of a decrease in ATP production or, alternatively, of decreased mesophyll conductance to CO2 diffusion. In general terms, stomatal limitation of photosynthesis is likely to be dominant in non-irrigated plants. Deficit irrigation had no negative impact on CO2 assimilation, despite less water application than in full-irrigation. Differences among varieties may be related to differences in sensitivity of stomata, shoot growth and/or the interaction between rootstock and cultivar to soil water availability.
- A deepening understanding of animal culture suggests lessons for conservationPublication . Brakes, Philippa; Carroll, Emma L; Dall, Sasha R X; Keith, Sally Anne; McGregor, Peter; Mesnick, Sarah L.; Noad, Michael; Rendell, Luke Edward; Robbins, Martha M.; Rutz, Christian; Thornton, Alex; Whiten, Andrew; Whiting, Martin J.; Aplin, Lucy M.; Bearhop, Stuart; Ciucci, Paolo; Fishlock, Vicki; Ford, John K. B.; Sciara Di, Giuseppe Notarbartolo; Simmonds, Mark P.; Spina, Fernando; Wade, Paul R.; Whitehead, Hal; Williams, James; Garland, Ellen C.A key goal of conservation is to protect biodiversity by supporting the long-term persistence of viable, natural populations of wild species. Conservation practice has long been guided by genetic, ecological and demographic indicators of risk. Emerging evidence of animal culture across diverse taxa and its role as a driver of evolutionary diversification, population structure and demographic processes may be essential for augmenting these conventional conservation approaches and decision-making. Animal culture was the focus of a ground-breaking resolution under the Convention on the Conservation of Migratory Species of Wild Animals (CMS), an international treaty operating under the UN Environment Programme. Here, we synthesize existing evidence to demonstrate how social learning and animal culture interact with processes important to conservation management. Specifically, we explore how social learning might influence population viability and be an important resource in response to anthropogenic change, and provide examples of how it can result in phenotypically distinct units with different, socially learnt behavioural strategies. While identifying culture and social learning can be challenging, indirect identification and parsimonious inferences may be informative. Finally, we identify relevant methodologies and provide a framework for viewing behavioural data through a cultural lens which might provide new insights for conservation management.