Global plant characterisation and distribution with evolution and climate

Since Arrhenius published seminal work in 1921, research interest in the description of plant traits and grouped characteristics of plant species has grown, underpinning diversity in trophic levels. Geographic exploration and diversity studies prior to and after 1921 culminated in biological, chemical and computer-simulated approaches describing rudiments of growth patterns within dynamic conditions of Earth. This thesis has two parts:- classical theory and multidisciplinary fusion to give mathematical strength to characterising plant species in space and time.Individual plant species occurrences are used to obtain a Species-Area Relationship. The use of both Boolean and logic-based mathematics is then integrated to describe classical methods and propose fuzzy logic control to predict species ordination. Having demonstrated a lack of significance between species and area for data modelled in this thesis a logic based approach is taken. Mamdani and T-S-K fuzzy system stability is verified by application to individual plant occurrences, validated by a multiple interfaced data portal. Quantitative mathematical models are differentiated with a genetic programming approach, enabling visualisation of multi-objective dispersal of plant strategies, plant metabolism and life-forms within the water-energy dynamic of a fixed time-scale scenario. The distributions of plant characteristics are functionally enriched through the use of Gaussian process models. A generic framework of a Geographic Information System is used to visualise distributions and it is noted that such systems can be used to assist in design and implementation of policies. The study has made use of field based data and the application of mathematic methods is shown to be appropriate and generative in the description of characteristics of plant species, with the aim of application of plant strategies, life-forms and photosynthetic types to a global framework. Novel application of fuzzy logic and related mathematic method to plant distribution and characteristics has been shown on a global scale. Quantification of the uncertainty gives novel insight through consequent trophic levels of biological systems, with great relevance to mathematic and geographic subject development. Informative value of Z matrices of plant distribution is increased substantiating sustainability and conservation policy value to ecosystems and human populations dependent upon them for their needs.Key words: sustainability, conservation policy, Boolean and logic-based, fuzzy logic, genetic programming, multi-objective dispersal, strategies, metabolism, life-forms

Predicting areas of potential conflicts between bearded vultures (Gypaetus barbatus) and wind turbines in the Swiss Alps

The alarming increase in global temperature observed over the last hundred years, driven by the use of fossil fuels, has prompted a shift towards “greener” energy production. An extensive expansion of wind power exploitation is expected in the coming years, which makes its effect on vulnerable species an issue of growing conservation concern. Among the wildlife affected by wind turbines, vultures are probably the most vulnerable avian ecological guild. They have experienced a sharp decline during the last decades and their survival in many areas is the result of targeted recovery and conservation actions. The bearded vulture (Gypaetus barbatus) represents an emblematic example. After having been extirpated from the European Alps, the species once again inhabits its former habitat, thanks to the massive long-lasting effort of a dedicated reintroduction programme. There are concerns, however, that the sprawl of wind turbines in the Alpine massif will jeopardise this successful population recovery. The main goal of this PhD thesis was therefore to predict areas in the Swiss Alps where conflicts between bearded vulture conservation and wind energy development are likely to occur, thus allowing for a more biodiversity-friendly spatial planning of wind turbines. Using a spatially explicit modelling framework with combined information of casual observations and GPS data, I predicted species’ potential distribution as well as its flight behaviour in relation to landscape, wind, and foraging conditions. First, I investigated the species ecological requirements in relation to season and age and translated these into distribution maps covering the whole Swiss Alpine arc. Here the focus was on evaluating the ability of the models to predict the possible future expansion of the species, a crucial point for anticipating potential conflicts arising from the spread of wind energy. During this process, I secondly had to delve into methodological challenges, especially with regard to taking objective decisions for model tuning. Based on the example of modelling the distribution of the bearded vulture, I introduced a new genetic algorithm for hyperparameters tuning, which drastically reduces computation time while achieving a model performance comparable or equal to that obtained with standard methods. Moreover, I generalised the developed routines so as to make them applicable to the most common species distribution modelling techniques and compiled the solutions in an R package now available to the scientific community. Thirdly, I explored the flight height patterns of bearded vultures to identify key factors driving low-height flight activity and delineated areas where the species is likely to fly within the critical height range that is typically swept by the blades of modern wind turbines. Overall, I found that food availability is an important driver of both distribution and low-height flight activity of bearded vultures. Habitat selection differed between seasons and between age classes during the cold season. While food availability and geological substrates were the main drivers of the distribution during the warm season, I observed a shift in the requirement of adult birds in the cold season, where habitat selection was mainly influenced by climatic conditions. This suggests that adult birds may be constrained by favourable winter conditions for the selection of breeding territories. Combining the ecological requirements of both age classes and seasons I found that 40% of the Swiss Alps offers suitable habitat for the species. The model trained with species data collected between 2004 and 2014 was able to accurately predict new breeding territories established in 2015 – 2019, and thus adequately delineated areas where the spreading population will likely to occur in the future and where conflicts with wind energy development might arise. The flight-height analysis of the GPS-tagged birds revealed that bearded vultures mainly fly within the critical height range swept by the turbine blades (77.5% of GPS locations), which poses the species at high risk of collision. Flying at low heights most frequently occurred along south exposed mountainsides and in areas with a high probability of ibex (Capra ibex) presence, a key food source for bearded vulture. Synthesising the information on bearded vulture distribution with the flight height behaviour allowed identifying and mapping areas where the species is likely to fly at risky height within its habitat. This high resolution, spatially explicit information represents a valuable tool for planners involved in wind energy development as well as a first basis for detailed impact assessments, while the methodological framework I developed represents a transferable approach for scientists studying potential conflicts between the development of aerial infrastructure and other target organisms

Population Structure of Lethrinus Lentjan (Lethrinidae, Percoidei) Across the South China Sea and the Philippines Is Detected With Lane-Affected RADSeq Data

Southeast Asia includes the Coral Triangle, a marine biodiversity hotspot that supports important fishery resources experiencing varied threats. Patterns of speciation and population structure in the Coral Triangle have been examined to test hypotheses relating to the historical geologic processes that may have influenced this biodiversity phenomenon. This study investigates the genetic population structure of the Pink-ear Emperor Snapper, Lethrinus lentjan (Lacepède, 1802), across the Philippines and the South China Sea. The species is fished throughout the Coral Triangle by subsistence and commercial fishers and their landings have been in decline for several years, which could be indicative of depleted stocks. Six locations were sampled representing the northeastern, southeastern, central, and western Philippines, and central and southern Vietnam. This study used restriction-site associated DNA sequencing (RADSeq) to sample single nucleotide polymorphism markers from throughout the genome. Here, RADseq data is successfully used to detect structuring within the Philippines where a previous study of L. lentjan mitochondrial control region sequences did not. Genetic structure analyses revealed significant divergence along the boundaries of repeatedly isolated ocean basins, as observed in several Indo-Pacific species. Pleistocene vicariance is a suspected driving factor in lineage diversification for this species, supporting the hypothesis that the Coral Triangle is a center of origin. Before management or conservation strategies can be implemented, a stock assessment should be completed for L. lentjan, including research on its life history, ecosystem services, and metapopulation dynamics. This study also used STRUCTURE analysis to detect a strong Illumina sequencer lane effect, where the genotype of a fish is associated with the sequencer lane used to generate the data. To control and remove this lane effect, the data was parsed into two clusters, a new method for salvaging lane-affected data. It is recognized that RADSeq is prone to lane effects that can result in erroneous conclusions, and several strategies are outlined for identifying, mitigating, and avoiding them in future high-throughput RADSeq studies