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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.

The aim of this paper is to investigate the threshold effect of foreign direct investment (FDI) on environmental degradation. In empirical analysis, FDI and environmental degradation are jointly determined under the given threshold variable and other exogenous variables. Using carbon dioxide (CO2) emissions per capita as a proxy for environmental degradation, the results show that increasing FDI worsens CO2 emissions after a threshold level of corruption has been reached. Our results demonstrate that increasing FDI will increase CO2 emissions when the degree of corruptibility is relatively high. The study suggests that further FDI and improved environmental quality are competing rather than compatible objectives in high-corruption countries and are compatible rather than competing objectives in low-corruption countries. Higher trade liberalization in low-corruption countries could contribute to negative environmental consequences because of the increased output or economic activity which results from increased trade. The robustness estimation confirms the evidence that pollution and economic development increase together up to a certain income level, after which the trend reverses.

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."]}

Sustainable nitrogen (N) management in agriculture is one of the most important issues affecting the environmental performance of modern agriculture. It is actually well perceived that coordinated efforts and holistic approaches are required to regulate N use by farmers. The purpose of this study was to provide an initial examination of stakeholders’ views in Japan regarding N use in agriculture and challenges to increase its sustainability. The analysis was based on a questionnaire study of five types of stakeholders (farmers, advisors, researchers, suppliers, policy makers). By means of multivariate analysis techniques it was revealed that consensus was lacking either in the acknowledgment of the causes and effects of unsustainable N management or in the challenges that need to be addressed. N losses from farms and the effects of N use were perceived but not conceived equally by all stakeholders. Organic farming and mandatory measures were the most controversial challenges, while those involving awareness, training and advisory were the most popular. This study cannot provide safe conclusions that can be generalized in the Japanese context, but it indicates domains where further research is required and orientations for future policy design towards more sustainable N use.

Abstract Despite the significant growth in the number of published life-cycle assessments of biofuels, important aspects have not captured sufficient attention, namely soil carbon emissions from land use change (LUC) and uncertainty analysis. The main goal of this article is to evaluate the implications of different LUC scenarios and uncertainty in the life-cycle energy renewability efficiency and GHG (greenhouse gases) intensity of wheat-based bioethanol replacing gasoline. A comprehensive assessment of different LUC scenarios (grassland or cropland converted to wheat cultivation) and agricultural practices is conducted, which results in different carbon stock change values. The types of uncertainty addressed include parameter uncertainty (propagated into LC (life-cycle) results using Monte-Carlo simulation) and uncertainty concerning how bioethanol co-product credits are accounted for. Results show that GHG emissions have considerably higher uncertainty than energy efficiency values, mainly due to soil carbon emissions from direct LUC and N2O release from cultivated soil. Moreover, LUC dominates the GHG intensity of bioethanol. Very different GHG emissions are calculated depending on the LUC scenario considered. Conversion of full- or low-tillage croplands to wheat cultivation results in bioethanol GHG emissions lower than gasoline emissions, whereas conversion of grassland does not contribute to bioethanol GHG savings over gasoline in the short- to mid-term.

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.

Biomass pre-treatment is a key step in achieving the economic competitiveness of biomass conversion. In the present work, an imidazole pre-treatment process was performed and evaluated using wheat straw and eucalyptus residues as model feedstocks for agriculture and forest-origin biomasses, respectively. Results showed that imidazole is an efficient pre-treatment agent; however, better results were obtained for wheat straw due to the recalcitrant behavior of eucalyptus residues. The temperature had a stronger effect than time on wheat straw pre-treatment but at 160 °C and 4 h, similar results were obtained for cellulose and hemicellulose content from both biomasses (ca. 54% and 24%, respectively). Lignin content in the pre-treated solid was higher for eucalyptus residues (16% vs. 4%), as expected. Enzymatic hydrolysis, applied to both biomasses after different pre-treatments, revealed that results improved with increasing temperature/time for wheat straw. However, these conditions had no influence on the results for eucalyptus residues, with very low glucan to glucose enzymatic hydrolysis yield (93% for wheat straw vs. 40% for eucalyptus residues). Imidazole can therefore be considered as a suitable solvent for herbaceous biomass pre-treatment.