Rubim Almeida
@up.pt
Professor Dept. of Biology, Faculty of Sciences
University of Porto
EDUCATION
Ph.D. in Filogeny and Evolution of Scilla
RESEARCH INTERESTS
Phylogeny and evolution; taxonomy, Monocots, Asparagaceae
Urban vegetation, Landscape architecture, Photography
Scopus Publications
Scopus Publications
Luís Seabra, Andrés Teira-Brión, Inés López-Dóriga, María Martín-Seijo, Rubim Almeida, and João Pedro Tereso
Public Library of Science (PLoS)
Some of the earliest Western European macroremains of rye (Secale cereale) have been recently recovered in Northwest Iberia. However, the chronological and cultural contexts of these remains have not been yet exhaustively analysed. To address this gap of research, previous and unpublished assemblages have been reviewed and analysed through an analytical set of methods: biometry, radiocarbon dates and integrating the remains of rye in the broad archaeobotanical record of the region. Results show the earliest macroremains of rye in the Iberian Peninsula date to a period between the 3rd century and the first half of the 1st century BCE. Rye was usually found in assemblages dominated by spelt and other cereals, in whose fields it was likely acting as a weed. There is no record of rye for about the two following centuries, after which it is probably reintroduced, now as a crop. It is found in several sites from the 3rd-4th centuries CE onwards, suggesting it is a staple crop as in other regions in Europe. Significant differences in grain size are only recorded in a 10th-11th century settlement, suggesting few changes in grain morphometry before Medieval times.
Carlos Martins Vila-Viçosa, Jorge Henrique Capelo, Paulo Alves, Rubim Silva Almeida, and Francisco Maria Vázquez
Universidad Complutense de Madrid (UCM)
We present a comprehensive taxonomic and nomenclatural review of the Portuguese oaks (Quercus L.), issuing from throughout biogeographical, historical, bibliographic, field and herbarium data. We propose a new annotated checklist for all taxa and nothotaxa belonging to Quercus L. genus in the Portuguese national territory, extending the analysis to the broader biogeographical context of Western Mediterranean Subregion. Fifteen herbaria collections were exhaustively studied and complemented by information retrieved from digital collections, resulting in the recognition of eleven native oaks. Further treatment at infraspecific level includes one subspecies and additional 23 nothotaxa. We designate 21 names as types and add a preliminary list of 150 cultivated trees, concurring to a total of 185 oak taxa, in total, found in Portugal.
 Moreover, we clarify the taxonomical status and reinstate both Quercus calliprinos Webb and Q. pseudococcifera Desf. as native for the Western Mediterranean subregion. We recover the concept of Q. faginea Lam., as the widespread Gall oak in Portugal and update its synonym list. We propose Q. broteroana and Q. estremadurensis as autonomous species within the European Q. robur s.l. broad group, alongside two newly circumscribed subsections inside Section Quercus. We describe three nothotaxa as new (Q. ×alvesii, Q. ×capeloana and Q. ×sampaioana) and approach the nomenclatural resolution of the remaining natural hybrids. Lastly, we provide an identification key, intelligible for non-specialists, including both native taxa and most frequent nothotaxa.
 We emphasise the importance of historical and literature review, combined with accurate biogeographical information, as paramount to coherent taxonomical resolution. Both specimens and their associated records were found of crucial significance to a taxonomical model that is, in the end, useful to biodiversity conservation.
Sara Silva, Ana Isabel Oliveira, Agostinho Cruz, Rita Ferraz Oliveira, Rubim Almeida, and Cláudia Pinho
MDPI AG
There is an increase in the popularity of craft beer, which is produced by small, independent, and traditional breweries. Since craft beer popularity is rising in Portugal this research focused on assessing physicochemical parameters, total phenolic content (TPC) and the antioxidant capacity of Portuguese craft beers and raw materials used in beer production. In this experimental study, 19 beer samples were analyzed. Parameters such as pH, Total Acidity, Reducing Sugar Content and TPC were evaluated. For the determination of antioxidant activity, DPPH scavenging activity and metal chelating activity (MCA) were analyzed in all samples. Craft beers demonstrated a high phenolic content (ranging from 343.78 mg GAE/L to 2172.49 mg GAE/L), significantly different from industrial beers. Craft beers demonstrated a higher inhibition of DPPH radicals and higher MCA than the raw materials. DPPH inhibition ranged from 36.5% to 96.0% for malt and 64.7% to 79.6% in hops samples. MCA also varied between the different samples, with results of 12.0% to 24.8% in malt samples and 3.8% to 23.5% in hops. Raw materials can potentially influence the antioxidant activity of the resulting beer. Positive correlations between TPC and physicochemical properties can be useful to help consumers choose beers with added value for health.
L. Seabra, P. Pereira, M. Salgado, M. Martín-Seijo, R. Almeida-da-Silva, and J.P. Tereso
Elsevier BV
Carlos Martins Vila-Viçosa, Cristiana Vieira, Francisco Márquez, Rubim Almeida, and Francisco María Vázquez
Universidad Complutense de Madrid (UCM)
We examined specimens from René Louiche Desfontaines, deposited in the “Herbier de la Flore Atlantique”(P-Desf) from MNHN-P and homologue specimens from P-Lam, LINN-HS, MPU, FI-Webb, and B-W, to assess three names of western Mediterranean oaks (Quercus L.) that are distributed across across the Iberian Peninsula and North Africa. Specifically, we bring insights to the names Quercus ballota, Q. pseudococcifera., and Q. pseudosuber, after a thorough examination of the original specimens, combined with the analysis of the respective protologues. The results highlight the need for wider and detailed natural history and classic herbaria surveys to promote the discussion and better understanding of species delimitation and biogeographic awareness, especially in crucial groups, that are still involved in taxonomic andevolutionary discussion, as the trees that form the potential climacic forests of the Northern Hemisphere.
Carlos Vila-Viçosa, Salvador Arenas-Castro, Bruno Marcos, João Honrado, Cristina García, Francisco M. Vázquez, Rubim Almeida, and João Gonçalves
MDPI AG
The Iberian Peninsula hosts a high diversity of oak species, being a hot-spot for the conservation of European White Oaks (Quercus) due to their environmental heterogeneity and its critical role as a phylogeographic refugium. Identifying and ranking the drivers that shape the distribution of White Oaks in Iberia requires that environmental variables operating at distinct scales are considered. These include climate, but also ecosystem functioning attributes (EFAs) related to energy–matter exchanges that characterize land cover types under various environmental settings, at finer scales. Here, we used satellite-based EFAs and climate variables in species distribution models (SDMs) to assess how variables related to ecosystem functioning improve our understanding of current distributions and the identification of suitable areas for White Oak species in Iberia. We developed consensus ensemble SDMs targeting a set of thirteen oaks, including both narrow endemic and widespread taxa. Models combining EFAs and climate variables obtained a higher performance and predictive ability (true-skill statistic (TSS): 0.88, sensitivity: 99.6, specificity: 96.3), in comparison to the climate-only models (TSS: 0.86, sens.: 96.1, spec.: 90.3) and EFA-only models (TSS: 0.73, sens.: 91.2, spec.: 82.1). Overall, narrow endemic species obtained higher predictive performance using combined models (TSS: 0.96, sens.: 99.6, spec.: 96.3) in comparison to widespread oaks (TSS: 0.80, sens.: 92.6, spec.: 87.7). The Iberian White Oaks show a high dependence on precipitation and the inter-quartile range of Normalized Difference Water Index (NDWI) (i.e., seasonal water availability) which appears to be the most important EFA variable. Spatial projections of climate–EFA combined models contribute to identify the major diversity hotspots for White Oaks in Iberia, holding higher values of cumulative habitat suitability and species richness. We discuss the implications of these findings for guiding the long-term conservation of Iberian White Oaks and provide spatially explicit geospatial information about each oak species (or set of species) relevant for developing biogeographic conservation frameworks.
Carlos Vila-Viçosa, João Gonçalves, João Honrado, Ângela Lomba, Rubim S. Almeida, Francisco Maria Vázquez, and Cristina Garcia
Springer Science and Business Media LLC
AbstractMarcescent forests are ecotones distributed across southern Europe that host increased levels of biodiversity but their persistence is threatened by global change. Here we study the range dynamics of these forests in the Iberian Peninsula (IP) during the Late Quaternary, a period of profound climate and anthropic changes. We modeled and compared the distribution of eight oak taxa for the present and two paleoclimatic environments, the Last Glacial Maximum (LGM, ~ 21 kya) and the Mid-Holocene (MH, ~ 6 kya). Presence records were combined with bioclimatic and topographic data in an ensemble modelling framework to obtain spatial projections for present and past conditions across taxa. Substantial distribution shifts were projected between the three studied periods, that were explained by precipitation, winter cold and terrain ruggedness. Results were congruent with paleoclimatic records of the IP and showed that range shifts of these contact zones concurred with range dynamics of both Submediterranean and Temperate oaks. Notably, the distribution ranges of hybrid oaks and marcescent forests matched throughout the late Quaternary. This study contributes to unveil the complex Late-Quaternary biogeography of the ecotone belt occupied by marcescent forests and, more broadly, of Mediterranean oaks. Improved knowledge of species’ responses to climate dynamics will allow us to anticipate and manage future range shifts driven by climate change.
CARLOS VILA-VIÇOSA and RUBIM ALMEIDA
Magnolia Press
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FRANCISCO MARÍA VÁZQUEZ, ALLEN COOMBES, RUBIM ALMEIDA, DAVID GARCIA-ALONSO, FRANCISCO MÁRQUEZ-GARCÍA, and CARLOS VILA-VIÇOSA
Magnolia Press
The nomenclature of some species of Quercus described by Lamarck from the Iberian Peninsula is reviewed. Five names are lectotypified and two epitype are designated.
J. Rocha, R. Ramírez, M. Díaz, M. Martins, I. García-Cabral, F. Amich, R. Almeida, V. Carnide, I. Castro, and A. L. Crespí
Informa UK Limited
Abstract Very similar morphologies have always been pointed out for subsections Natrix and Viscosae of the genus Ononis L. Morphological, environmental and biogeographic approaches do not show significant differences between taxa of both subsections, and only life form was pointed out as biological descriptor to explain taxonomic and ecological strategies for these taxa: Natrix is composed by perennial life forms, while Viscosae is solely represented by annual life forms. The discussion of results was conducted through the insurance hypothesis, according to which resilient or resistant behaviours, here represented by taxonomic diversity and morpho-environmental variability, described the ecological strategies for these taxa. In this way, wider morpho-environmental variability induced more responses (higher taxonomic diversity and life forms), i.e. more resilience. On contrary, the narrower morpho-environmental variability induced less taxonomic diversity and only perennial life forms, i.e. more resistance. Two future climate change scenarios were also used to confirm these resilience and resistance strategies for both subsections.
Ana Claudia Moreira Teodoro, Lia Duarte, Rubim Almeida, and Sara Mendes
SPIE
Forests are dynamic, complex and multidimensional ecosystems and play an irreplaceable role in social, economic, environmental, ecological and cultural context. Eucalyptus is the most common exotic species in Portugal forests. This species is fundamental in the industries related to the pulp paper production and the concern about their effects in ecosystems is growing. Geographical Information Systems (GIS) combined with Remote Sensing (RS) data can help to understand this complex ecosystem. Moreover, GIS and RS are commonly used in forest management. GIS allows the manipulation, analysis, and generation of considerable amounts of environmental information. This information can be used in the evaluation of ecosystems’ conditions and for decision making. The study case of this project was the municipal lands included in “Serras do Porto” and Valongo’s Nature 2000 network (Porto district, Portugal). The study zone considered in this work is a landscape of extreme relevance to Porto Metropolitan Area. For decades this area was extensively explored with eucalyptus plantations in order to produce cellulose for paper industry. Due to the characteristics of the area and its extension (40 hectares) the use of GIS became the most accurate and reliable alternative to characterize it. The combination of GIS tools and RS data allows the characterization of terrain relief, namely the analysis of altimetry, hypsometry, hydrography, the creation of environmental indexes such as Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI) and Normalized Difference Water Index (NDWI), and the Digital Elevation Model (DEM). RS technology offer the potential to explore the effects of land-use changes and disturbances on forest dynamics at large spatial scales. A Sentinel-2A image was used to produce NDVI, EVI, and NDWI environmental indexes and to generate the Land Use Land Cover (LULC) map, through Semi-Automatic Classification Plugin from QGIS software using Minimum Distance algorithm. The LULC was classified with two classes because the study area only presents two types of species: eucalyptus and bare soil. The LULC map obtained was validated through field points collected in the study area with a GPS receptor. An overall accuracy of 92.98% and a kappa statistic of 0.842 was obtained. Also, some of the geographic information obtained in the field was then integrated in QGIS software. Moreover, a phenological study was performed using NDVI values obtained from Sentinel-2A images, to understand the eucalyptus behavior in a certain period of time.. Because of that RS data provided useful information about the landscape dynamics allowing the assess to forest cover change and land use helping to create decision making plans and forest conservation measures.
João Pedro Tereso, Ana M.S. Bettencourt, Pablo Ramil-Rego, Andrés Teira-Brión, Inés López-Dóriga, António Lima, and Rubim Almeida
Elsevier BV
Joana Marques, João Gonçalves, Cláudia Oliveira, Sergio E. Favero-Longo, Graciela Paz-Bermúdez, Rubim Almeida, and Beatriz Prieto
Wiley
Contradictory evidence from biogeomorphological studies has increased the debate on the extent of lichen contribution to differential rock surface weathering in both natural and cultural settings. This study, undertaken in Côa Valley Archaeological Park, aimed at evaluating the effect of rock surface orientation on the weathering ability of dominant lichens. Hyphal penetration and oxalate formation at the lichen-rock interface were evaluated as proxies of physical and chemical weathering, respectively. A new protocol of pixel-based supervised image classification for the analysis of periodic acid-Schiff stained cross-sections of colonized schist revealed that hyphal spread of individual species was not influenced by surface orientation. However, hyphal spread was significantly higher in species dominant on northwest facing surfaces. An apparently opposite effect was noticed in terms of calcium oxalate accumulation at the lichen-rock interface; it was detected by Raman spectroscopy and complementary X-ray microdiffraction on southeast facing surfaces only. These results suggest that lichen-induced physical weathering may be most severe on northwest facing surfaces by means of an indirect effect of surface orientation on species abundance, and thus dependent on the species, whereas lichen-induced chemical weathering is apparently higher on southeast facing surfaces and dependent on micro-environmental conditions, giving only weak support to the hypothesis that lichens are responsible for the currently observed pattern of rock-art distribution in Côa Valley. Assumptions about the drivers of open-air rock-art distribution patterns elsewhere should also consider the micro-environmental controls of lichen-induced weathering, to avoid biased measures of lichen contribution to rock-art deterioration.
C. Alves, C. Vieira, R. Almeida, and H. Hespanhol
Elsevier BV
Márcia CARVALHO, João ROCHA, Valdemar CARNIDE, Sandra MARTINS, Maurici MUS, Francisco AMICH, Rubim ALMEIDA, Cláudia MACHADO, Berta GONÇALVES, Eunice BACELAR,et al.
The Scientific and Technological Research Council of Turkey (TUBITAK-ULAKBIM) - DIGITAL COMMONS JOURNALS
Iberian Buxus spp. are represented by B. sempervirens, restricted to the Cantabrian, eastern Iberian Peninsula, and northeastern mountain systems, emerging scarcely in Portugal, and by B. balearica that occurs in the Betic deep river valleys and in the Balearic islands. The genetic affinity existent between fifteen populations of B. sempervirens was evaluated by seven ISSRs primers. Moreover, leaf morpho- anatomical measurements indicative of leaf performance (such as leaf area, leaf mass per unit area, width, length, shape factor, tissues thickness, stomatal density, and quantification of epi- and intracuticular waxes) and environmental characterization were conducted to get insight into the functional ecology of the genus Buxus. Six populations of B. balearica and 15 of B. sempervirens, collected in the Iberian Peninsula and the Balearic islands, were included to establish the interspecific ranges. A functional ecological description by morpho-anatomical analysis of leaves and a genetic and environmental approach exposed differences between Pyrenaean-Cantabrian- Portuguese and Iberian B. sempervirens populations. Genetic relationships among Buxus populations were investigated using inter- simple sequence repeat (ISSR) markers. Seven ISSR primers generated a total of 159 unambiguous and repeatable bands, of which 156 (98.1%) were polymorphic. These divergences for Iberian B. sempervirens are explained by the isolation in their distributions since the Oligocene. Previsions for future climate change scenarios confirm those biogeographic divergences for the Iberian B. sempervirens.
Vanessa Ferreira, Isaura Castro, João Rocha, António L. Crespí, Olinda Pinto-Carnide, Francisco Amich, Rubim Almeida, and Valdemar Carnide
Elsevier BV
Rubim Almeida da Silva, João Rocha, Ana Silva, Isabel García-Cabral, Francisco Amich, and António L. Crespí
American Society of Plant Taxonomists
Abstract Six different morphotypes for the Scilla species in western Europe have been distinguished based on leaf width, length of the basal bract, number of flowers per inflorescence, and length of bulbs: (1) S. peruviana; (2) S. hyacinthoides; (3) S. lilio-hyacinthus; (4) S. ramburei + S. beirana; (5) S. verna + S. paui + S. odorata + S. merinoi + S. monophyllos; and (6) S. obtusifolia + S. numidica + S. autumnalis. Two biogeographic trends have been circumscribed in terms of monthly precipitation averages (the most discriminating parameter). One trend, characterized by lower annual regimes of precipitation and distributions around the Mediterranean basin, is represented by S. peruviana, S. hyacinthoides, S. obtusifolia, and S. numidica. The second trend, associated with higher average precipitation along the extreme western coast of Europe, is represented by the S. verna group and S. lilio-hyacinthus. Scilla autumnalis exhibits an intermediate environmental behaviour. Future climate change scenarios point towards an increase in the potential habitat area of species distributed along the Mediterranean basin (S. peruviana, S. hyacinthoides, S. obtusifolia, S. numidica, and S. autumnalis) and a decrease in the potential habitat area for the western-most likely morphotypes (S. ramburei, S. verna, S. monophyllos, and S. lilio-hyacinthus).
Joana Marques, Helena Hespanhol, Graciela Paz-Bermúdez, and Rubim Almeida
Elsevier BV
João Pedro Tereso, Pablo Ramil-Rego, Teresa Pires De Carvalho, Rubim Almeida-da-Silva, and Filipe Costa Vaz
Springer Science and Business Media LLC
João Pedro Tereso, Pablo Ramil-Rego, Yolanda Álvarez González, Luis López González, and Rubim Almeida-da-Silva
Elsevier BV
João Pedro Tereso, Pablo Ramil-Rego, and Rubim Almeida-da-Silva
Elsevier BV
J. Rocha, A L. Crespí, M. García-barriuso, G. Kozlowski, R. Almeida, J. Honrado, S. Talavera, and F. Amich
Informa UK Limited
Abstract The genus Baldellia Parl. has always been a complex taxon. Three species and three subspecies have been proposed for the Iberian Peninsula. The morphological variation of this genus in the Iberian Peninsula, Balearic islands and northern Morocco, and its thermo-pluviometric and altitudinal correlation are the focus of this contribution. Twenty-eight morphological variables were examined and subjected to a multivariate statistical analysis. The three morphotypes observed (Form 1, which includes B. ranunculoides subsp. repens and B. alpestris; Form 2, which includes B. ranunculoides and Form 3 – for the new combination B. ranunculoides subsp. ranunculoides var. tangerina (Pau) J. Rocha, A. Crespí, M. García-Barriuso, R. Almeida, J. Honrado, comb. nova proposed here for the first time) seem to represent different reproductive strategies. Morphological variables related with the presence or absence of stolons and the architecture of the inflorescence; the size and number of fruits are the most discriminating variables. Form 1 represents the asexual morphotype; Forms 2 and 3 correspond to morphotypes for which sexual reproduction is preferential. The environmental approach revealed that the asexual form (Form 1) grows in temperate, in more humid conditions, and within a broad altitudinal range. In contrast, the two sexual forms are more common in warmer and drier conditions, and occur over a narrower interval of altitudes.
João Rocha, António Crespí, Rubim Almeida, and Francisco Amich
Informa UK Limited
Abstract Background: Detailed knowledge of a species' autecology as well as information on the availability of suitable habitats and the impacts of climate change on the species and its habitat are requirements for adequate conservation planning. For this purpose, species distribution modelling has been suggested as an effective tool to assess the potential geographic distributions of species under different climate scenarios. Aims: The aim of this study was to generate suitability maps and predictive maps based on scenarios of climate change to identify areas with the most value for conservation for the western Iberian endemics Silene acutifolia, S. foetida subsp. foetida and S. foetida subsp. gayana. Methods: Maxent software was used to model and predict the distribution of the species based on environmental variables under climate change scenarios. Results: Our analysis indicated that the models performed well, predicting with high accuracy the current distributions of the species. Under two scenarios of increasing CO2, the species were predicted to be susceptible to a major reduction of suitable habitat; both S. foetida subspecies were shown to be at risk of extinction. Conclusions: Our findings suggest that the inclusion of S. foetida in national conservation and long-term monitoring programmes must be considered.