Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae).

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.

Predicting spatial patterns of plant biodiversity : from species to communities

Understanding the distribution and composition of species assemblages and being able to predict them in space and time are highly important tasks io investigate the fate of biodiversity in the current global changes context. Species distribution models are tools that have proven useful to predict the potential distribution of species by relating their occurrences to environmental variables. Species assemblages can then be predicted by combining the prediction of individual species models. In the first part of my thesis, I tested the importance of new environmental predictors to improve species distribution prediction. I showed that edaphic variables, above all soil pH and nitrogen content could be important in species distribution models. In a second chapter, I tested the influence of different resolution of predictors on the predictive ability of species distribution models. I showed that fine resolution predictors could ameliorate the models for some species by giving a better estimation of the micro-topographic condition that species tolerate, but that fine resolution predictors for climatic factors still need to be ameliorated. The second goal of my thesis was to test the ability of empirical models to predict species assemblages' characteristics such as species richness or functional attributes. I showed that species richness could be modelled efficiently and that the resulting prediction gave a more realistic estimate of the number of species than when obtaining it by stacking outputs of single species distribution models. Regarding the prediction of functional characteristics (plant height, leaf surface, seed mass) of plant assemblages, mean and extreme values of functional traits were better predictable than indices reflecting the diversity of traits in the community. This approach proved interesting to understand which environmental conditions influence particular aspects of the vegetation functioning. It could also be useful to predict climate change impacts on the vegetation. In the last part of my thesis, I studied the capacity of stacked species distribution models to predict the plant assemblages. I showed that this method tended to over-predict the number of species and that the composition of the community was not predicted exactly either. Finally, I combined the results of macro- ecological models obtained in the preceding chapters with stacked species distribution models and showed that this approach reduced significantly the number of species predicted and that the prediction of the composition is also ameliorated in some cases. These results showed that this method is promising. It needs now to be tested on further data sets. - Comprendre la manière dont les plantes se répartissent dans l'environnement et s'organisent en communauté est une question primordiale dans le contexte actuel de changements globaux. Cette connaissance peut nous aider à sauvegarder la diversité des espèces et les écosystèmes. Des méthodes statistiques nous permettent de prédire la distribution des espèces de plantes dans l'espace géographique et dans le temps. Ces modèles de distribution d'espèces, relient les occurrences d'une espèce avec des variables environnementales pour décrire sa distribution potentielle. Cette méthode a fait ses preuves pour ce qui est de la prédiction d'espèces individuelles. Plus récemment plusieurs tentatives de cumul de modèles d'espèces individuelles ont été réalisées afin de prédire la composition des communautés végétales. Le premier objectif de mon travail est d'améliorer les modèles de distribution en testant l'importance de nouvelles variables prédictives. Parmi différentes variables édaphiques, le pH et la teneur en azote du sol se sont avérés des facteurs non négligeables pour prédire la distribution des plantes. Je démontre aussi dans un second chapitre que les prédicteurs environnementaux à fine résolution permettent de refléter les conditions micro-topographiques subies par les plantes mais qu'ils doivent encore être améliorés avant de pouvoir être employés de manière efficace dans les modèles. Le deuxième objectif de ce travail consistait à étudier le développement de modèles prédictifs pour des attributs des communautés végétales tels que, par exemple, la richesse en espèces rencontrée à chaque point. Je démontre qu'il est possible de prédire par ce biais des valeurs de richesse spécifiques plus réalistes qu'en sommant les prédictions obtenues précédemment pour des espèces individuelles. J'ai également prédit dans l'espace et dans le temps des caractéristiques de la végétation telles que sa hauteur moyenne, minimale et maximale. Cette approche peut être utile pour comprendre quels facteurs environnementaux promeuvent différents types de végétation ainsi que pour évaluer les changements à attendre au niveau de la végétation dans le futur sous différents régimes de changements climatiques. Dans une troisième partie de ma thèse, j'ai exploré la possibilité de prédire les assemblages de plantes premièrement en cumulant les prédictions obtenues à partir de modèles individuels pour chaque espèce. Cette méthode a le défaut de prédire trop d'espèces par rapport à ce qui est observé en réalité. J'ai finalement employé le modèle de richesse en espèce développé précédemment pour contraindre les résultats du modèle d'assemblage de plantes. Cela a permis l'amélioration des modèles en réduisant la sur-prédiction et en améliorant la prédiction de la composition en espèces. Cette méthode semble prometteuse mais de nouveaux tests sont nécessaires pour bien évaluer ses capacités.

Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology

The pace of on-going climate change calls for reliable plant biodiversity scenarios. Traditional dynamic vegetation models use plant functional types that are summarized to such an extent that they become meaningless for biodiversity scenarios. Hybrid dynamic vegetation models of intermediate complexity (hybrid-DVMs) have recently been developed to address this issue. These models, at the crossroads between phenomenological and process-based models, are able to involve an intermediate number of well-chosen plant functional groups (PFGs). The challenge is to build meaningful PFGs that are representative of plant biodiversity, and consistent with the parameters and processes of hybrid-DVMs. Here, we propose and test a framework based on few selected traits to define a limited number of PFGs, which are both representative of the diversity (functional and taxonomic) of the flora in the Ecrins National Park, and adapted to hybrid-DVMs. This new classification scheme, together with recent advances in vegetation modeling, constitutes a step forward for mechanistic biodiversity modeling.

The role of phylogeny in the spatial distributions and assembly of mountain plant communities.

A major challenge in community ecology is a thorough understanding of the processes that govern the assembly and composition of communities in time and space. The growing threat of climate change to the vascular plant biodiversity of fragile ecosystems such as mountains has made it equally imperative to develop comprehensive methodologies to provide insights into how communities are assembled. In this perspective, the primary objective of this PhD thesis is to contribute to the theoretical and methodological development of community ecology, by proposing new solutions to better detect the ecological and evolutionary processes that govern community assembly. As phylogenetic trees provide by far, the most advanced tools to integrate the spatial, ecological and evolutionary dynamics of plant communities, they represent the cornerstone on which this work was based. In this thesis, I proposed new solutions to: (i) reveal trends in community assembly on phylogenies, depicted by the transition of signals at the nodes of the different species and lineages responsible for community assembly, (ii) contribute to evidence the importance of evolutionarily labile traits in the distribution of mountain plant species. More precisely, I demonstrated that phylogenetic and functional compositional turnover in plant communities was driven by climate and human land use gradients mostly influenced by evolutionarily labile traits, (iii) predict and spatially project the phylogenetic structure of communities using species distribution models, to identify the potential distribution of phylogenetic diversity, as well as areas of high evolutionary potential along elevation. The altitudinal setting of the Diablerets mountains (Switzerland) provided an appropriate model for this study. The elevation gradient served as a compression of large latitudinal variations similar to a collection of islands within a single area, and allowed investigations on a large number of plant communities. Overall, this thesis highlights that stochastic and deterministic environmental filtering processes mainly influence the phylogenetic structure of plant communities in mountainous areas. Negative density-dependent processes implied through patterns of phylogenetic overdispersion were only detected at the local scale, whereas environmental filtering implied through phylogenetic clustering was observed at both the regional and local scale. Finally, the integration of indices of phylogenetic community ecology with species distribution models revealed the prospects of providing novel and insightful explanations on the potential distribution of phylogenetic biodiversity in high mountain areas. These results generally demonstrate the usefulness of phylogenies in inferring assembly processes, and are worth considering in the theoretical and methodological development of tools to better understand phylogenetic community structure.

Plant genetic diversity, irrigation and nutrient cycling in traditional mountain oases of northern Oman

Little is known about plant biodiversity, irrigation management and nutrient fluxes as criteria to assess the sustainability of traditional irrigation agriculture in eastern Arabia. Therefore interdisciplinary studies were conducted over 4 yrs on flood-irrigated fields dominated by wheat (Triticum spp.), alfalfa (Medicago sativa L.) and date palm (Phoenix dactylifera L.) in two mountain oases of northern Oman. In both oases wheat landraces consisted of varietal mixtures comprising T. aestivum and T. durum of which at least two botanical varieties were new to science. During irrigation cycles of 6-9 days on an alfalfa-planted soil, volumetric water contents ranged from 30-13%. For cropland, partial oasis balances (comprising inputs of manure, mineral fertilizers, N2-fixation and irrigation water, and outputs of harvested products) were similar for both oases, with per hectare annual surpluses of 131 kg N, 37 kg P and 84 kg K at Balad Seet and of 136 kg N, 16 kg P and 66 kg K at Maqta. Respective palm grove surpluses, in contrast were with 303 kg N, 38 kg P, and 173 kg K ha^-1 yr^-1 much higher at Balad Seet than with 84 kg N, 14 kg P and 91 kg K ha^-1 yr^-1 at Maqta. The results show that the sustainability of these irrigated landuse systems depends on a high quality of the irrigation water with low Na but high CaCO3, intensive recycling of manure and an elaborate terrace structure with a well tailored water management system that allows adequate drainage.

Novel management to enhance spider biodiversity in existing grass buffer strips

Grass buffer strips have been widely sown to mitigate against intensive agricultural management practices that have negatively impacted on invertebrate and plant biodiversity in arable farming systems. Typically, such strips are floristically species poor and are dominated by grasses. In the present study, we developed management practices to enhance the floristic and structural diversity of these existing strips for the benefit of spiders, a key provider of natural pest control in crops. Across three UK arable farms, we investigated the benefits of: (i) scarification to create germination niches into which wildflower seeds were sown and (ii) the effect of graminicide applications to suppress grass dominance. Spiders were sampled twice per year (July and September) during 2008 and 2009. The combination of scarification with wildflower seeds, as well as graminicide, resulted in the greatest wildflower cover and lowest grass cover, with a general trend of increased abundance of adult and juvenile spiders. The abundance of Pachygnatha degeeri, Bathyphantes gracilis and juvenile wolf spiders of the genus Pardosa was positively correlated with wildflower cover, probably reflecting increased prey availability. Sward structure was negatively correlated with Erigone atra, Oedothorax fuscus and juvenile Pardosa abundance. Management that utilizes existing commonly adopted agri-environment options, such as grass buffer strips, represents a potentially important conservation tool for increasing the quantity and quality of invertebrate habitats. This can maximize opportunities for the provision of multiple ecosystem services, including pest regulation by predators such as spiders. These management practices have the potential to be incorporated into existing U.K. and European agri-environment schemes.

Effects of experimental nitrogen additions on plant diversity in an old-growth tropical forest

Response of plant biodiversity to increased availability of nitrogen (N) has been investigated in temperate and boreal forests, which are typically N-limited, but little is known in tropical forests. We examined the effects of artificial N additions on plant diversity (species richness, density and cover) of the understory layer in an N saturated old-growth tropical forest in southern China to test the following hypothesis: N additions decrease plant diversity in N saturated tropical forests primarily from N-mediated changes in soil properties. Experimental additions of N were administered at the following levels from July 2003 to July 2008: no addition (Control); 50 kg N ha−1 yr−1 (Low-N); 100 kg N ha−1 yr−1 (Medium-N), and 150 kg N ha−1 yr−1 (High-N). Results showed that no understory species exhibited positive growth response to any level of N addition during the study period. Although low-to-medium levels of N addition (≤100 kg N ha−1 yr−1) generally did not alter plant diversity through time, high levels of N addition significantly reduced species diversity. This decrease was most closely related to declines within tree seedling and fern functional groups, as well as to significant increases in soil acidity and Al mobility, and decreases in Ca availability and fine-root biomass. This mechanism for loss of biodiversity provides sharp contrast to competition-based mechanisms suggested in studies of understory communities in other forests. Our results suggest that high-N additions can decrease plant diversity in tropical forests, but that this response may vary with rate of N addition.

Trade-offs between timber production and biodiversity in rainforest plantations: Emerging issues and an ecological perspective

During the past two centuries there have been three major paradigm shifts in the management of Australian rainforests and the use of their timbers: from felling native forests towards growing plantations; from viewing forests and plantations as mainly providers of timber to viewing them as sources of multiple benefits (e.g. timber, biodiversity, carbon sequestration, catchment protection, recreation, regional economic development); and from timber plantations being developed mainly by government on public land towards those established by private citizens, companies, or joint venture arrangements, on previously-cleared freehold land. Rainforest timber plantations are increasingly established for varied reasons, and with multiple objectives. Landholders are increasingly interested in the biodiversity values of their plantations. However, there are few guidelines on the changes to plantation design and management that would augment biodiversity outcomes, or on the extent to which this might require a sacrifice of production. [Abstract extract]

Natural regeneration of Atlantic Forest species in the understory of Eucalyptus saligna Smith. in a former forest production unit at the Parque das Neblinas, Bertioga, SP

This study aimed at characterizing the potential for natural regeneration of native vegetation in the under-story of an earlier Eucalyptus saligna Smith production stand. The study was carried out at the Parque das Neblinas, Bertioga municipality, SP, in a 45 ha third rotation stand; which had been abandoned 15 years ago for natural regeneration to occur. The sampling was done in 24 plots of 20 x 40 m. The sampled area was of 19,200 m(2), with inventory made of 100% of the eucalyptus trees. All regeneration trees with a height >= 1.30 m and DBH >= 5.0 cm were measured, as well as adult individuals with DBH >= 5.0 cm; surveyed in two size classes. 1,417 individuals of E. saligna were measured, with a density of 738,02 individuals/ha and a basal area of 22.69 m(2)/ha. Among 2,763 natural regeneration individuals, 111 species belonged to 66 genera and 34 botanical families. The species represented 43.7% of the tree richness of neighboring native forest fragments. The total estimated density and the basal area were respectively 1,052.6 individuals/ha and 6.4 m(2)/ha of autochthonous trees with DBH >= 5.0 cm (Class 1); while for regeneration there were 3,864.58 individuals/ha, and 2.76 m(2)/ha of individuals with a height >= 1.30 m and DBH <5.0 cm (Class 2). Shannon diversity (H`) was 2.83 and 3.68, respectively, for Classes 1 and 2, and the corrected species richness for a 1000-individual sample (R(1000)) were 75.6 and 87.29 (Fisher`s a index) for the same classes. The majority of the species (34.84%) was typical from the understory of wet tropical forest and had zoochoric fruit dispersal (67.57%). The results indicate that, under these conditions, a eucalyptus forest is able to provide adequate regeneration niches for native vegetation, and may represent a sink habitat for local populations.

Percurso pedestre no Rio Este: contribuição para a educação ambiental e promoção do ensino experimental

O ensino praticado nas nossas escolas necessita ser mais consentâneo com os princípios e valores veiculados pela Educação Ambiental. Pretende-se, com este trabalho, levar os alunos a percepcionar a natureza com um olhar diferente, a estabelecer uma nova relação com o meio, adoptando uma postura pró-activa na defesa do espaço ribeirinho. Por meio de um percurso investigativo ao longo da margem esquerda de um troço do rio Este, na zona envolvente da Escola, os alunos de uma turma do 5º ano estudaram a flora autóctone existente na zona ribeirinha e recolheram amostras de água onde puderam aplicar processos de tratamento. Os temas abordados pertencem aos conteúdos leccionados nas aulas de Ciências da Natureza. Considerando que estas actividades podem ser importantes ferramentas na educação para o ambiente, elaborou-se para o grupo experimental um caderno de campo, que serviu de orientação ao estudo da flora, realizou-se uma actividade prática no laboratório, com a amostra da água recolhida. Posteriormente aplicou-se um teste, para conhecer o grau de conhecimento adquirido após a actividade e, no final, os alunos responderam a um inquérito para se conhecer o seu grau de satisfação. Ainda que os resultados do teste não mostrem diferenças significativas na aquisição de conhecimento em relação à turma não participante no projecto, a interpretação da paisagem mostrou-se um meio eficaz de envolver os alunos, desenvolver sensibilidades, construir conceitos, promover atitudes positivas que vão de encontro a uma Educação Ambiental ligada à cidadania.

Azores marine algal flora: how endangered is it?

Unesco chair for "Conservation of plant biodiversity in Macaronesia and the West of Africa", Gran Canaria, 27-28 November 2013.

Elaboració de nous recursos docents en el camp de la biologia vegetal, mitjançant l'ús de noves tecnologies de microscòpia com làser confocal i multifotó

Aquest projecte s'ha realitzat al Servei de Microscòpia de la Universitat Autònoma de Barcelona, i ha tingut una durada de dos anys (2007-2009). Els objectius concrets d'aquest projecte assolits per a les diferents assignatures ha estat l'anàlisi de característiques citològiques, característiques morfològiques i anatòmiques de les estructures vegetatives dels diferents nivells d’organització, característiques morfològiques i anatòmiques de les estructures reproductores. El material docent obtingut en aquest projecte està sent utilitzat en les assignatures següents: Botànica Farmacèutica, Biodiversitat vegetal marina, Recursos vegetals aquàtics: les algues, Plantes d'ús alimentari, Conserv. i gestió de poblacions i comunitats marines, Usos i cultius de recursos algals marins, B. i diversitat de criptògames, Biologia II, Tècniques Exp. de biologia II, Botànica, Biologia animal i vegetal. Per a la realització de l’estudi, s'ha obtingut una col·lecció d’imatges al MLC, MER i MET per aclarir els criteris sistemàtics. Durant el primer any s’han adquirit totes les imatges necessàries, per tal de poder elaborar el material didàctic en suport digital. Durant el segon any s’ha implementat aquest material a les respectives classes pràctiques i s’ha avaluat la seva importància en la millora de la formació dels alumnes i del suport al professor. L’aplicació del material elaborat a la docència pràctica durant el tot segon any ha permès fer un primer estudi per valorar la seva eficàcia i fer-hi les correccions oportunes. Durant tot el projecte, el treball conjunt de professors i tècnics ha estat bàsic per a l’obtenció de material didàctic adequat a la realitat dels estudis actuals i a la docència pràctica.