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Digital Annex for the following thesis: Vila-Viçosa, C. (2023). Natural History, Biogeography and Evolution of the Iberian white oak syngameon (Quercus L. Sect. Quercus). Ph.D. Thesis, Faculdade de Ciências da Universidade do Porto, Portugal Abstract: The genus Quercus L. is one of the most diverse and important group of woody plants, particularly when considering that they are the trees that rule the Northern Hemisphere forests. Oaks have an intricate Biogeography that criss-crosses diverse climatic and edaphic gradients, encompassing a huge ambiguity in terms of species delimitation. Frequently, the taxonomic proposals brought by traditional Linnaean Botany are either insufficient or rather inflate the number of species and nomenclatural assignments, which are further diluted into inconsistent taxonomic ranks, varying from species to subspecies and varieties. The supremacy given to morphological characters that are inherently fragile and plastic, spread across the distribution areas of distinct lineages, may carry ambiguity on the identification and proper species delimitation. From the oaks that are distributed across the Western Palearctic region, the ones that are deciduous or brevi-deciduous present higher levels of ambiguity in terms of species number and their delimitation. This ambiguity is particularly strong in the circummediterranean region and in the transitional areas between the two major biogeographic Regions of the western Palearctic region, the Euro-Siberian and Mediterranean. This degree of uncertainty, which increases towards the Southern European Peninsulas, is amplified by the ease that the different species of oaks tend to hybridize among them. The present work provides a holistic framework that covers multiple areas, from the taxonomic and evolutive study of this genus, to biogeography and molecular characterization. Its major objective was to resolve the species delimitation of the Iberian deciduous and marcescent oaks and putative introgression among them, enhancing the available knowledge about species diversity, which can foster suitable species and forest conservation. A specific objective was to cross-reference the natural history revision and the different taxonomic treatments brought by distinct authors, with personal observations. These data were then incorporated into ecological modelling and molecular characterization, which in the end fed a newly updated taxonomic proposal. In Section A we obtained results from extensive field, herbaria, and literature review, updating the nomenclature of the Portuguese and western Mediterranean oaks. Section B was supported by Section A’s in-depth review and enabled finer species distribution models, nurturing both hindcast (since ca. 20 Kyr) and forecast (2070-2100) exercises of the range dynamics of Mediterranean oaks species. The study of past and future range shifts solved important pending biogeographic questions, especially related to past range-shifts. Such past-range shifts improved our knowledge on species responses to climate dynamics and allowed a better anticipation of future responses of range shifts driven by climate change. Section C encompassed the molecular characterization of Iberian white oak species and their hybrids, whose delimitation is often faltering when one intends to infer about species rank, or hypothesize about the participation of parent taxon in natural hybrid swarms. This work allowed us to solve the phylogenetic backbone of western Palearctic white oaks, suggesting a significant segregation of the Iberian pedunculate oaks and unveiling two subsections inside Section Quercus. These subsections are biogeographically well-segregated and present diverse levels of introgression among species. Results demonstrated the efficiency of RADSeq for rebuilding the reticulate phylogeny of the Eurasian white oaks, showcasing the significance of the Iberian Peninsula as a major hotspot for oak diversity. We implemented a circular approach to these methods, which retro-fed themselves in terms of insight generation, enabling a powerful strategy to solve the evolutionary history of this difficult groups of plants. We estimate that the reticulate historical biogeography of the western Palearctic white oaks deserves further scrutiny by adding vicariant oak populations from northern Africa, the Near East and southern European Peninsulas. Methods should again follow this similar additive and sequential process of adjoining deep Natural History examination, with extensive fieldwork in type populations and genome-wide molecular surveys, in order to solve this group of plants. With the present work, we were able to significantly improve on the depiction of the basic unit of Biodiversity (the Species), in the complex Quercus genus. We provided tools to enable further efforts for the conservation of the Mediterranean oak forests, which overwhelm one of the most important (and one of the most threatened) Biomes for plant conservation at the global scale.

Aim: Animal migration strategies balance trade-offs between mortality and reproduction in seasonal environments. Knowledge of broad-scale biogeographical patterns of animal migration is important for understanding ecological drivers of migratory behaviours. Here we present a flyway-scale assessment of the spatial structure and seasonal dynamics of the Afro-Palearctic bird migration system and explore how phenology of the environment guides long-distance migration. Location: Europe and Africa. Time period: 2009–2017. Major taxa studied: Birds. Methods: We compiled an individual-based dataset comprising 23 passerine and near-passerine species of 55 European breeding populations where a total of 564 individuals were tracked migrating between Europe and sub-Saharan Africa. In addition, we used remote sensed observations on primary productivity (NDVI) to estimate the timing of vegetation green-up in spring and senescence in autumn across Europe. First, we described how individual breeding and non-breeding sites and the migratory flyways link geographically. Second, we examined how migration timing along the two major Afro-Palearctic flyways is tuned with vegetation phenology en route and at the breeding sites. Results: While we found the longitudes of individual breeding and non-breeding sites to be strongly positively related, the latitudes of breeding and non-breeding sites were negatively related. In autumn, timing of migration was similar along the Western and the Eastern flyways and happened ahead of the autumnal senescence of vegetation. In spring, migration timing was approximately two weeks later along the Eastern flyway than on the Western flyway which coincided with the later spring green-up in Eastern Europe. Main Conclusions: Migration of the Afro-Palearctic landbirds follows a longitudinally parallel leap-frog migration pattern where migrants track vegetation green-up in spring and depart before vegetation senescence in autumn. However, the ongoing global change have the potential to disrupt this spatiotemporal synchronization between migration timing and spring green-up with variable effects on different migrant populations.

Complete dataset (part 1) of daily climate variables (daily precipitation, maximum temperature and minimum temperature) for a historical (1989-2005) and future period (2021-2050), of four climate models (CNRM-CERFACS-CNRM-CM5, ICHEC-EC-EARTH, IPSL-IPSL-CM5A-MR and MPI-M-MPI-ESM-LR) under two Representative Concentration Pathways (RCP 4.5 and 8.5). The climatic variables are provided at 9x9 km resolution for the Iberian Peninsula and at 1x1 km and for the Transboundary Biosphere Reserve of Meseta Ibérica (Portugal-Spain). {"references": ["Jacob, D., Teichmann, C., Sobolowski, S., Katragkou, E., Anders, I., Belda, M., ... & Wulfmeyer, V. (2020). Regional climate downscaling over Europe: perspectives from the EURO-CORDEX community. Regional environmental change, 20(2), 1-20.", "Cornes, R. C., van der Schrier, G., van den Besselaar, E. J., & Jones, P. D. (2018). An ensemble version of the E\u2010OBS temperature and precipitation data sets. Journal of Geophysical Research: Atmospheres, 123(17), 9391-9409."]}

A palmeira é uma cultivar usada na produção de óleos alimentares vegetais, cosméticos e encontra-se em crescente aplicação na produção de biodiesel. Há aumento da consciência que as cultivares são vulneráveis à possível prática criminosa pela introdução intencional de microrganismos patogênicos nas lavouras. De um modo geral, as palmeiras são propensas à degradação quando atacada pelo fungo Ganoderma, conhecido como fungo da podridão branca, por degradar a lignina. É de grande importância considerar este tipo de podridão da palmeira quando atacada pelos microrganismos em questão, de modo a ser estabelecido um controle efetivo.No entanto, na literatura são encontrados trabalhos que ressaltam a importância: (a) de estar-se atento ao modo de proliferação desta praga e (b) de conhecer-se a biologia molecular do Ganoderma. A alta humidade presente no solo litorâneo favorece o surgimento do fungo Ganoderma. A alta salinidade e o baixo pH do solo surge como um ambiente desfavorável para a proliferação deste tipo de microrganismo. Atualmente, o melhor método de controle do Ganoderma é a extinção dos campos de palmeiras por ele contaminados. A melhor estratégia para o futuro estaria no desenvolvimento de palmeiras tolerantes ao ataque das referidas pragas, sendo uma possibilidade a alteração da lignina produzida nas palmeiras. Desta forma, conclui-se que o Ganoderma da palmeira está se tornando em um problema cada vez maior e o seu controle levaria à resolução de questões como a podridão branca. Oil palm (OP) is a major crop for the production of vegetable oil used in foods, cosmetics and increasingly biodiesel. There is an increasing awareness that crops are vulnerable to nefarious introduction of pathogenic microorganisms. Oil palms are prone to a rot by the fungus Ganoderma. White rot fungi are capable of degrading lignin. It is necessary to consider this mode of attack for effective control. Nevertheless, the existing literature is concerned with the (a) mode of spread and (b) molecular biology of Ganoderma. The high moisture content of coastal soil favour Ganoderma. High salinity and low soil pH appear to discourage the disease. The optimum current method of control is to rid fields of decayed OP. The optimal future approach may be to develop tolerant OP and altering lignin in OP may be possible. In conclusion, Ganoderma of OP is becoming increasingly virulent and control would benefit from consideration of the process as one of white rot.

In this master thesis, a single-stage anaerobic co-digestion system was operated treating a mixture of leachate and tannery wastewater, increasing salinity from 5 to 15 g Na+ L-1. Biogas production (1.6 ± 0.3 – 3.0 ± 0.3 L d-1) increased as salinity increased up to 10 g Na+ L-1 as well as CH4 yield (0.29 ± 0.03 – 0.33 ± 0.03 L CH4 g-1 COD). At 15 g Na+ L-1, a decrease in biogas production and granules fragmentation were observed. Overall, the results showed that the microbial community was able to withstand salinities up to 15 g Na+ L-1, presenting a good performance on the co-treatment of leachate and tannery wastewater. The second part of this master thesis was focused on the effect of combining metal organic frameworks (MOF-5), with high adsorption properties towards CO2 when compared with CH4, with a combination of different poly(ionic liquid)/ionic liquid (PIL/IL) membranes for biogas upgrading. The MOF-5 was incorporated at different loadings (10, 20 and 30 wt%), and mixed matrix membranes (MMMs) were prepared by solvent evaporation method. The results showed that MOF-5 particles were uniformly dispersed into the PIL/IL matrix, except for PIL C(CN)3/40 [C2MIM][C(CN)3]. The prepared PIL/IL/MOF-5 membranes revealed suitable thermal stability (Tonset up to 300-380ºC) for biogas upgrading, but a loss of mechanical stability was found after the incorporation of MOF-5. Nevertheless, increasing MOF-5 content in the MMMs resulted in an improvement on CO2 permeability, which increased 133% for PIL Tf2N/40 [C2MIM][BETi]/30 MOF-5 when compared to PIL Tf2N/40 [C2MIM][BETi]. It was therefore possible to demonstrate the improvement of CO2/CH4 separation performance of this MMMs system using MOF-5, which opens the perspective of using these materials for biogas upgrading.

The objective of the WADI project is to analyse the sustainability of irrigated agriculture in Europe in the context of post Agenda 2000 agricultural policies and in the context of the implementation of the European Water Framework Directive. The approach followed to evaluate the sustainability of irrigation integrates the concepts of environmental sustainability and economic and social sustainability. This work analyses the implications that the Water Framework Directive (WFD) may have on three major irrigation regions of Portugal – Baixo Alentejo, Lezíria do Tejo and Baixo Mondego– when a volumetric tariff is applied to irrigation water under different policy scenarios. The first sections provide a general description of the main features of agriculture and irrigated agriculture in Portugal; describes the selected study regions and characterizes some typologies within these regions; and explains the methodology used in this study. Later on the impacts of policy change, particularly concerning prospective future scenarios and the impact caused by WFD implementation via a volumetric tariff, are presented at a regionally aggregated level.

Wind turbines and solar panels are becoming second nature in Portugal, as its occurrence in the country becomes ubiquitous. Somehow, one could argue that renewable energy in Portugal is in the process of ‘naturalisation’ as part of a new – mechanised, but environmentally benign – landscape. Portuguese Institute for the Conservation of Nature and Biodiversity (ICNB) has shown an ambiguous stance on this issue, defending global concerns towards renewable energy, while at the same time attempting to engage locals in the preservation of extensive ‘classified areas’. In the course of this research, we tried to focus on these incongruities and to analyse how they are impacting local communities during the process of wind power installation.

Bioconversion of recalcitrant biomass/waste into bulk chemicals or biofuels is not practicable. Gasification of these materials produces syngas (mainly composed of CO2, CO and H2) that can be converted to products of interest, both by thermochemical or microbial processes. Thus far, industrial microbial processes focus on syngas conversion to ethanol, but other products such as butanol, acetic acid, butyric acid, hydrogen and methane can be obtained as well. In this work, microbial syngas conversion by anaerobic mixed cultures was explored. The physiology and microbial composition of mesophilic (37ºC) and thermophilic (55ºC) communities degrading syngas were analyzed. Cultures were incubated in batch and, upon syngas conversion, transferred to bottles with increasing CO partial pressure (from 5% to 50% CO, total pressure 1.75 bar). Syngas utilization and fatty-acids and alcohols formation were monitored. Microbial composition was analyzed by PCR-DGGE and the 16S rRNA gene of predominant microorganisms sequenced. Under mesophilic conditions, CO could not be used at partial pressures higher than 10%. However, thermophilic enrichment cultures could convert CO at partial pressures up to 50%. Acetate and CO2 were the main products formed by the mixed cultures. Predominant microorganisms in syngas-degrading communities were closely related to Thermoanaerobacter, Thermoanaerobacterium, Desulfotomaculum and Thermincola species. Syngas conversion in batch assays was rather slow and possibly limited by gas-liquid mass-transfer rate. Presently we are optimizing CO-water mass transfer and mixing performance using gas lift and oscillatory reactors. The final purpose is the development of a continuous process for efficient syngas conversion by mixed cultures.

Microbial electrolysis cells (MECs) are an innovative and emerging technique based on the use of solid-state electrodes to stimulate microbial metabolism for wastewater treatment and simultaneous production of value-added compounds (such as methane). This research studied the performance of a two-chamber MEC in terms of organic matter oxidation (at the anode) and methane production (at the cathode). MEC‟s anode had been previously inoculated with an activated sludge, whereas the cathode chamber inoculum was an anaerobic sludge (containing methanogenic microorganisms). During the experimentation, the bioanode was continuously fed with synthetic solutions in anaerobic basal medium, at an organic load rate (OLR) of around 1 g L-1 d-1, referred to the chemical oxygen demand (COD). At the beginning (Run I), the feeding solution contained acetate and subsequently (Run II) it was replaced with a more complex solution containing soluble organic compounds other than acetate. For both conditions, the anode potential was controlled at -0.1 V vs. standard hydrogen electrode, by means of a potentiostat. During Run I, over 80% of the influent acetate was anaerobically oxidized at the anode, and the resulting electric current was recovered as methane at the cathode (with a cathode capture efficiency, CCE, accounting around 115 %). The average energy efficiency of the system (i.e., the energy captured into methane relative to the electrical energy input) under these conditions was over 170%. However, reactor‟s performance decreased over time during this run. Throughout Run II, a substrate oxidation over 60% (on COD basis) was observed. The electric current produced (57% of coulombic efficiency) was also recovered as methane, with a CCE of 90%. For this run the MEC‟s average energy efficiency accounted for almost 170 %. During all the experimentation, a very low biomass growth was observed at the anode whereas ammonium was transferred through the cationic membrane and concentrated at the cathode. Tracer experiments and scanning electron microscopy analyses were also carried out to gain a deeper insight into the reactor performance and also to investigate the possible reasons for partial loss of performance. In conclusion, this research suggests the great potential of MEC to successfully treat low-strength wastewaters, with high energy efficiency and very low sludge production.