Mycorrhizal fungi are soil-borne organisms that form symbiotic associations with the majority of land plants. These fungi gather and exchange mineral nutrients with plants for photosynthetically derived carbohydrates. Mycorrhizal fungi can also confer other benefits onto plants, e.g. defense against pathogens, improved water relations, tolerance to heavy metal toxicity and herbivory. The influence of mycorrhizal fungi on plant mineral nutrition and response to stress suggests that these organisms may have a role to play sustainable agriculture as well as in bioremediation and ecosystem restoration. In contributing to this important research, I investigated host-specific interactions between mycorrhizal fungi and the sex morphs of the gynodioecious perennial herb Polemonium foliosissimum (Polemoniaceae) and their mycorrhizal associates in the field. I hypothesized that the genders of this species differed in their associations with mycorrhizal fungi in benefits received. I performed a full factorial simulated herbivory experiment and evaluated the extent of mycorrhizal colonization in the roots as well as the concentrations of nutrients in leaf tissue. Mycorrhizal colonization and leaf nutrient concentrations did not differ between the genders nor were influenced by the experimental treatments. This suggests that the genders of Polemonium foliosissimum do not interact differently with mycorrhizal fungi, and thus do not represent different "hosts". Also, I investigated local adaptation of mycorrhizal associations by exploring the effect of large herbivore grazing on plant-mycorrhizal associations. I hypothesized that grazing by large herbivores results in locally adapted symbioses that enhance plant response to herbivory. I grew the perennial bunchgrass Themeda triandra (Poaceae) in inoculum prepared from soils collected from three field exclosures with differing histories of large herbivore exclusion in the Kenya Long Term Exclosure Experiment. I conducted a full factorial simulated herbivory experiment in which plants were subject to two clipping events over the course of 5-months, and evaluated plant regrowth as well as mycorrhizal colonization for plants in the experiment. Plants grown in inoculum from exclosures in which large herbivores have had access produced more root mass when mycorrhizal fungi were present. Further, I found equivalent biomass production of clipped and non-clipped plants in inoculum prepared from the exclosure with only native large herbivore access while equivalent biomass production was not found in the substrate prepared from areas with a history of large herbivore exclusion. This suggests that mycorrhizal fungi mediate plant growth and response to herbivory in this system.

Doctor of Philosophy / Department of Division of Biology / John Blair / The feasibility of restoration, which traditionally targets historical conditions, is questionable in the context of global change. To address this, my dissertation investigated (Chapter 2) the patterns of restoration establishment along a chronosequence of restored prairies with respect to nearby remnant prairies, (Chapters 3-4) responses of plant communities in restorations initiated using different methods (levels of species richness and sowing density) to drought, which is projected to increase in frequency, and (Chapters 5-6) the effects of propagule source and variation (mixing among sources) on restoration establishment and the generality of restoration outcomes across variable environments using reciprocal common gardens of multi-species restoration seedings. Chapter 2, published in Restoration Ecology, showed that restoration led to the recovery of desirable characteristics within several years, but restorations utilizing primarily fall-collected seeds likely diminished the representation of early phenology species, so biodiversity may be further enhanced by including early phenology species in seeding mixes. Chapters 3 and 4, published respectively in Ecological Applications and Applied Vegetation Science, examined the establishment of native plant communities after seeding and their responses to experimentally imposed drought. Both high seed mixture richness and high density seeding resulted in greater establishment of native, seeded species compared to low richness and low density treatments, and exotic species were less prevalent in high richness and high density treatments. However, we found little evidence of differential drought resistance, recovery, and resilience among treatments. This result coupled with increases in exotic species following drought suggest that other forms of active management may be needed to produce restored plant communities that are robust to climate change. Chapter 5 (published in Ecosphere) iii and Chapter 6 found that seed source affects individual species establishment, community structure, and productivity. However, there was no consistent advantage for any source, including local sources, across sites or species. This suggests that source effects on single species or effects observed at single locations should not be broadly generalized. Together, this dissertation shows that restoration can recover many characteristics of native prairies and that manipulation of seeding practices (seed mixture richness, seeding density, seed source) influence grassland establishment in terms of productivity, community structure, invasion, and the abundance and survival of individual species.

Doctor of Philosophy / Department of Biology / Michael Tobler / Extremophiles are organisms with the ability to survive in environments characterized by strong physicochemical stressors lethal to most other organisms, providing excellent models to further our understanding of life's capacities and limitations to deal with far-from-average conditions. I studied how physiological processes varied among fish residing in starkly different environmental conditions to understand how organisms cope with extreme environments and disentangle the roles of short-term plastic responses and evolved population differences in shaping physiological responses. I used the Poecilia mexicana model, a series of extremophile fish populations that has colonized toxic hydrogen sulfide (H₂S) rich springs and caves, to address three major objectives: (1) I investigated the energetic consequences of life in extreme environments and tested whether predicted reductions in organismal energy demands evolved repeatedly along replicated environmental gradients. (2) I characterized variation in gene expression among populations and organs to test for interactive effects between different stressors and identify potential physiological mechanisms underlying adaptation to H₂S and cave environments. (3) I conducted common garden and H₂S-exposure experiments to test how evolutionary change and plasticity interact to shape variation in gene expression observed in nature. To address these objectives, I measured variation in metabolic physiology and quantified variation in physiological processes through genome-wide gene expression analyses. I found that adaptation to extreme environments directly impacts energy metabolism, with fish living in extreme environments consistently expending less energy overall. Reductions in energy demand have evolved in convergence and were primarily mediated through a life history shift (reduction in body mass). The quantification of gene expression across divergent habitats and organs revealed organ-specific physiological responses in H₂S-rich and cave habitats. Gene expression variation in the relevant genes was primarily shaped by evolutionary change in gene regulation, and ancestral plastic responses play a minor role in causing the observed expression differences between replicated sulfidic and nonsulfidic populations in nature. Overall, my research has implications for understanding the capacities and constraints that shape life in extreme environments and aids in our understanding of modifications in physiological pathways mediating adaptation to elevated H₂S and perpetual darkness.

A distribuição e riqueza de espécies ao redor do globo intriga o ser humano desde os tempos antigos. Algumas teorias para explicar tais padrões se baseiam no conceito de adaptação local, procurando avaliar o desempenho relativo dos indivíduos nativos de uma dada localidade perante ao desempenho de indivíduos imigrantes. Este desempenho diferenciado ocorreria devido à heterogeneidade espacial encontrada no ambiente, gerando gradientes de seleção natural. Estas pressões de seleção levariam a adaptação às condições locais dos indivíduos das espécies. No caso de gradientes altitudinais, vários fatores ambientais estão correlacionados com a elevação, caracterizando pressões seletivas diferenciadas e espacialmente distribuídas. Para organismos que ocorrem nestes gradientes, os limites de distribuição geográfica pode estar ligada a variação nas condições ambientais. Neste estudo escolhemos um par de espécies irmãs de Rhipsalis (R. crispata e R. oblonga - Rhipsalideae, Cactaceae) que se distribui ao longo de um gradiente altitudinal na Mata Atlântica brasileira, R. oblonga até 1000m de altitude e R. crispata até 700m de altitude, para verificar a capacidade adaptativa das espécies às mudanças de algumas condições ambientais associadas a variação altitudinal. Para verificar a capacidade adaptativa das espécies, realizamos experimentos de transplante, com mais de 4000 plantas para áreas de diferentes altitudes. As estações experimentais foram montadas em três altitudes (50m, 100m e 825m), replicadas duas vezes em pontos distintos da serra do mar, onde havia variação natural das condições de microhabitat em cada altitude. Nós esperávamos que R. oblonga apresentasse desempenho biológico, avaliado pelos dados de crescimento e sobrevivência, superior que o de R. crispata com o aumento da altitude, e que R. crispata apresentasse seu melhor desempenho nas áreas de baixa altitude. Nossos resultados indicaram que R. oblonga apresenta melhor desempenho que R. crispata na maioria dos ambientes e que o melhor crescimento de R. crispata ocorreu em áreas baixa costeiras. R. oblonga apresenta uma distribuição geográfica mais ampla, assim também é mais tolerante à mudanças ambientais. Enquanto que R. crispata, por apresentar distribuição geográfica menor, também é menos tolerante a mudanças ambientais, o que fica claro ao observar as respostas das espécies, segundo as variação nas condições de microhabitat. Nossos resultados indicam que distribuição altitudinal das espécies pode ser explicada por diferenças na capacidade adaptativa das espécies / Old and relevant questions exist in relation to species distribution and richness in the earth planet. Some theories to explain these patterns are based on the concept of local adaptation, i.e., difference on the performance of individuals due to environment spatial heterogeneity related to gradients of natural selection. Selective pressures could lead to adaptation to local conditions by populations of a given species. In altitudinal gradients, various environmental factors change according to the changes in elevation. In this study we selected a pair of Rhipsalis\' sister species (R. crispata and R. oblonga - Rhipsalideae, Cactaceae), distributed across altitudinal gradient in the Brazilian Atlantic Forest to verify, by transplant experiments, the species adaptive capacity to environmental conditions associated with elevation.. The experimental stations were set up in three altitudes levels (50m, 100m and 825m), replicated twice in Serra do Mar. We expected that R. crispata presents a better biological performance (growth and survival) than R. oblonga in lower elevation, and vice versa.. Our results indicated that R. oblonga exceeds R. crispata in most environments, but R. crispata was better than R. oblonga in the low coastal altitude sites. Rhipsalis oblonga presents broad geographic distributions, so it is more tolerant to environmental changes and R. crispata, due to its less widely geographic distribution, is less tolerant to environmental changes. Our results indicate that altitudinal species distribution could be explained by differences in species adaptive capacity

Le potentiel évolutif des populations naturelles à répondre aux changements environnementaux détermine leur capacité à s'adapter et à survivre. Pour achever une évolution adaptative, la fitness doit être héritable, i.e. doit être transmise des parents à leurs descendants par des gènes. Pour pouvoir mesurer le potentiel évolutif d'une population en milieu naturel, il est primordial d'avoir au préalable des informations sur la fitness des individus qui la composent, mais aussi de connaître la fitness de leurs descendants. Les mesures de fitness sont extrêmement rares, en particulier pour les espèces marines, où les relations entre les générations sont rarement connues. Dans cette thèse, je présente le premier pedigree construit pour une population de poissons marins sur la base du suivi génétique mené depuis plus de 10 ans sur les poissons-clowns orange de l'île de Kimbe (Papouasie-Nouvelle Guinée). Le pédigrée comprend 2927 individus et révèle une philopatrie natale sur 5 générations. L'approche en génétique quantitative révèle que la fitness locale a une très faible valeur d'héritabilité (<1%). La variation génétique additive et les effets maternels sont également très faibles (<1%). En revanche, l'habitat est le principal facteur qui explique les différences de fitness locale observées entre les individus (jusqu'à 96,5%). Ensemble, ces résultats suggèrent que, bien que l'environnement impose une forte pression de sélection sur la fitness locale, la population de poissons-clowns orange a un très faible potentiel d'évolution face aux changements environnementaux. / The evolutionary potential of wild populations to respond to environmental change will determine their capacity to adapt and survive. However, in order to achieve evolutionary change, variation in the contribution of an individual to the next generation — its fitness — must have a genetic basis and be heritable. The study of the evolutionary potential of populations requires longitudinal and relatedness data with different environments to partition the contribution of genes, maternal effects and environment on fitness. Estimates of genetic heritability of fitness traits are extremely rare, especially for marine species, where inter-generational relationships are rarely known. Here, we present the first multi-generational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) over a 10-year period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. We show that local reproductive success has a very low (<1%) but significant heritability. We also show that additive genetic variation and maternal effects on local fitness are both extremely low (<1%). Habitat is the major driver that explain differences in the contribution of individuals to the next generation in the local population (until 96.5%). Together these results suggest that while the environment imposes strong selection pressures on the local fitness, the low heritability indicates the orange clownfish population has little evolutionary potential to adapt to local environmental changes.

Current and emerging threats to trees and forest ecosystems require a re-evaluation of the way forest genetic resources are managed. Governments in the United Kingdom and elsewhere are committed to the restoration, expansion and creation of new woodlands. Tree populations are often adaptively differentiated from one another, so a key question underpinning the success of planting schemes is the choice of seed origin. A long held understanding is that locally sourced seeds will have the best opportunity to tolerate conditions of the planting site (local provenancing). However, the rate at which the environment is changing introduces a great deal of uncertainty into decision making and there is concern that climate change is proceeding at rates faster than those with which locally adapted trees would be able to cope. As such, there are suggestions that seed collected from areas already experiencing the anticipated future conditions will improve the adaptability of forests (predictive provenancing). This thesis investigated outstanding questions relating to the merits of the local provenancing and predictive provenancing approaches, and the practical implementation of seed sourcing policy in British forestry. The validity of existing seed zone boundaries used under local provenancing was analysed for ancient semi-natural Scots pine Pinus sylvestris L. forests of Scotland. Vegetation description and analyses of climatic covariates revealed that the existing series of seed zones used to guide selection of planting stock for restoration do not necessarily environmentally match seed sources to planting sites under current conditions. Additional disparity is introduced when edaphic variation (or proxies for this) is considered. To determine whether future adaptation under local provenancing may be restricted by limited pollen flow among populations of native Scots pine in Scotland, the timing of pollen production in five populations was estimated by repeatedly measuring strobilus development on a series of twenty trees over three consecutive springs. Differences in the mean predicted date of pollen production were found, with populations in the warmer west shedding pollen earliest each year, although the timing and differences in timing among populations varied from year to year, with shedding taking place earliest in the warmest of the three years and latest in the coolest year. A theoretical multi-patch, ecological genetic individual-based model (IBM) was developed to investigate the utility of different seed sourcing strategies (local versus non local provenance) and their capacity to help populations adapt to directional climate change. As well as being adapted to climate, which varied in a clinal pattern, individuals also had to be well adapted to the habitat conditions of the planting site in order to survive hard selection at the seedling stage. The model showed that population size of a new planting was reduced when planting stock adapted to the future conditions but not to current conditions was deployed. The differences were most severe when selection acted simultaneously on both the climate-related and the habitat-related phenotype. Finally, a series of in-depth qualitative surveys conducted with members of the domestic forest nursery and seed supply sector in Great Britain found that there are many difficulties associated with seed sourcing and the supply of trees. These problems arise due to a very limited ability to predict demand at the time of seed sowing, and lead to waste when demand is overestimated and importation of planting stock when demand is underestimated. Confidence and competitiveness in the domestic sector could be greatly improved by updating seed sourcing guidelines and by simplifying certain aspects of the process by which forest planting projects are funded.

The Government of Malawi, through delegates from the Department of Disaster Management Affairs, has on several occasions advised smallholder farmers who live in flood prone areas to relocate to upland areas that are safe from floods. Smallholder farmers have refused to do so and continue to live in the flood prone areas despite experiencing on-going flooding. Smallholder farmers living in flood prone areas in Malawi insist that flash floods bring fertile soils from upland areas that enhance crop production in the flood prone areas. These fertile soils allow smallholder farmers to grow a variety of crops, fruits and vegetables throughout the year, some of which they sell. Within this context, my research critically explores how smallholder farmers perceive their vulnerability to floods and seeks to understand the factors and processes that motivate them to live in the flood prone areas. It also examines the realities and dynamics of local adaptation in the flood prone areas in Malawi through opportunities, challenges, barriers and limitations. The research uses 57 in-depth interviews, a household survey involving 227 households, participant observations and 12 focus group discussions with smallholder farmers. Findings show that firstly, smallholder farmers are not ready to abandon their land and relocate upland because floods are part of their lives and livelihood strategies. Secondly, that power dynamics at household and community levels based on gender roles and culture need to be understood and accounted for in local adaptation strategies in order to effectively enhance local adaptive capacity. Thirdly, that social networks and interdependence between the smallholder farmers living in flood prone areas and those living in upland areas play a significant role in the adoption of local adaptation strategies and adaptation to floods and droughts through temporary migration. This thesis reveals that the perception and extent of vulnerability to floods is dynamic and differentiated based on several factors. The thesis also reveals that local adaption is a complex process such that in some cases, the realities of power dynamics at both the household and community level affects local adaptive capacity to floods. Transformational adaptation that incorporates specific and contextual adaptation strategies is therefore recommended as one of the best approaches towards achieving successful adaptation to climate variability and resilience.

<p>Understanding the diversity of life is one of the main aims of evolutionary biology, and requires knowledge of the occurrence and causes of adaptive genetic differentiation among geographically distinct populations. Environmental stress caused by acidity may cause strong directional selection in natural populations, but is little explored from an evolutionary perspective. In this thesis, a series of laboratory experiments and field data was used to study evolutionary and ecological responses of amphibians to environmental acidity. </p><p>Local adaptation to acid stress was studied in the moor frog (<i>Rana arvalis)</i>.The results show that acid origin populations have higher acid stress tolerance during the embryonic stages than neutral origin populations, and that acid and neutral origin populations have diverged in embryonic and larval life-histories. The mechanisms underlying adaptive differentiation are partially mediated by maternal effects related to extra-embryonic membranes and egg size. Acid origin females invest in larger eggs and have a stronger egg size-fecundity trade-off than females from neutral areas, likely reflecting adaptive differentiation in maternal investment patterns. </p><p>Potential carry-over effects of low pH, and the effects of UV-b/pH interaction were investigated in the common frog (<i>R. temporaria</i>). The results suggest that amphibian larvae are able to compensate for the negative effects of acidity experienced early in life, if conditions later turn beneficial. <i>R. temporaria</i> populations differed in their sensitivity to synergistic effects of low pH/UV-B, indicating variation in population responses to environmental stress.</p><p>In conclusion, these results suggest rapid evolution in response to human induced environmental change, much of which may be mediated via adaptive maternal effects. Acidification may be a powerful selective force shaping life-history evolution.</p>

<p>This thesis is an attempt to describe how different environmental factors influence life history traits in different populations, sexes and developmental stages in the moor frog, <i>Rana arvalis. </i>The studied populations are located along 1100 km latitudinal gradient, with pH varying between 4.0 and 8.5. I have used data from both natural populations and common garden experiments. </p><p>Reproducing moor frogs were larger and older at high latitudes, indicating a selective advantage of large size at high latitudes and/or earlier reproduction at low latitudes. When controlling for age I found that frogs were older and smaller at low pH, which may be a result of a reduced growth rate due to acid stress. The both sexes respond differently to different environments, with the lowest sexual dimorphism in body size found in the acid environments. This is possibly caused by a trade-off between growth and reproduction. Being large is considered to be advantageous, in females due to increased fecundity, and in males due to higher ability to compete for mates, while the cost of high growth is a reduced possibility to survive until the next mating season. Moor frog embryos originating from an acid population survived better under acid stress than embryos from a neutral population. Using quantitative genetic techniques I found strong maternal effects and small additive genetic variation for the traits in acid and non acid populations. The variation in acid stress tolerance owed largely to non-genetic effects. Females from acid localities lay larger eggs, which probably improves the performance of tadpoles under acid conditions. The trade-off between egg size and fecundity was stronger in acid populations indicating that females in acid populations reduced fecundity to increase offspring size. Finally, frogs from acidified environments were more asymmetric in skeletal traits further indicating the developmental stress created by acidification.</p>

<p>The identification of processes governing genetic structure at different spatial scales remains a major challenge in evolutionary biology and is of considerable applied interest in conservation biology. In <i>Euphrasia stricta</i> five varieties have been identified (<i>brevipila</i>, <i>gotlandica</i>, <i>stricta</i>, <i>suecica</i> and <i>tenuis</i>) based on differences in habitat, phenology and morphology. In this thesis, I examined genetic variation at AFLP and microsatellite marker loci in relation to variation in habitat and morphology within and among varieties of <i>E. stricta</i> on the island Gotland in the Baltic Sea. The results are discussed in relation to evolutionary processes acting within this species complex. </p><p>In a study conducted at the regional scale, the two early-flowering varieties <i>suecica</i> and <i>tenuis</i> each formed a genetically distinct group, while the three late-flowering varieties <i>brevipila</i>, <i>gotlandica</i> and <i>stricta</i> formed a third group. The results suggest that <i>suecica</i> and <i>tenuis</i> have ancient origins since they are genetically different both from the <i>brevipila</i>/<i>gotlandica</i>/<i>stricta</i> group and from each other despite their similar habitat preferences. This pattern was obtained using both marker systems. Discrepancies between AFLP and microsatellites were found in patterns of isolation by distance and in estimates of expected heterozygosity, <i>H</i>_e.</p><p>Focusing on the mixed genetic group <i>brevipila</i>/<i>gotlandica</i>/<i>stricta</i> and the causes behind their clustering together despite differences in morphology and habitat preferences, I performed a study at a smaller geographic scale. Studying a population of <i>E. stricta</i> I found that, although gene flow within the population was strong, it had not prevented the formation of genetic groups associated with micro-habitat properties. </p><p>An important result for conservation of the rare variety <i>suecica</i> is its distinct genetic separation from variety <i>tenuis</i>. If the aim of conservation is to preserve the uniqueness of <i>suecica,</i> the two varieties should be treated as separated entities. </p>