Rapid climate change is a significant threat to the long-term persistence of native tree populations. Concern has been expressed that tree populations might fail to adapt due to rate of change, insufficient adaptive variation in tree populations and limits to dispersal. In contrast, others have contended that most tree species have high phenotypic plasticity, maintain high levels of within-population genetic variation and exhibit effective gene dispersal capability, all characteristics which should enable an adaptive response. To assess the potential adaptability of tree populations we need to understand their genetic diversity and phenotypic plasticity to build on the currently limited evidence base and guide decisions about seed sourcing for establishment of new woodlands desired to meet ambitious planting targets. Currently the seed sourcing system divides the island in four regions of similar size although it is not based on any genetic or ecological information. We discuss the suitability of this system with the insight of the data collected from native tree populations growing in experimental trials. In this thesis we study genetic diversity and phenotypic plasticity patterns in over 30 native tree populations across all Great Britain for three broadleaved species: ash (Fraxinus excelsior), rowan (Sorbus aucuparia), and silver birch (Betula pendula). To obtain these data we assessed the variation in multiple traits in several common garden experiments for each species, which were grown in contrasting environments. There is a tendency in provenance experiments to consider height as a proxy for fitness. We demonstrate that tree height is not enough to understand tree fitness and its adaptability capacity. We assessed our tree populations for growth (survival, tree height, DBH), stem form (number of forks), leaf phenology (leaf flushing and senescence) and leaf anatomical traits (leaf area, stomatal density and stomatal size).Great Britain has very distinct and heterogeneous environments likely to have given rise to adaptive differentiation. Knowing the geographical pattern of the genetic differences we can see the direction selective pressures have had on each of the traits studied, and we compare differences in patterns across the traits and species. Comparing populations growing in different environments we assessed the variation in phenotypic plasticity by trait and the direction of these plasticity. We found that tree populations across Great Britain are highly genetically variable and show genetic differences which have a geographical pattern, and that the patterns and size of the differences vary by species. Phenotypic plasticity varies across traits and interactions between genotype and environment make plasticity in some traits more unpredictable than others. We conclude that tree populations of ash, rowan and birch are well adapted to the diverse and oceanic climate of Great Britain, and that levels of genetic diversity and phenotypic plasticity provide a high capacity to respond to environmental change.

Reef-building corals (Order: Scleractinia) are undergoing rapid taxonomic revision after molecular systematics disputed the relationships at all taxonomic levels within traditional classification. New morphological characters are being used to produce evolutionary relationships supported by molecular phylogenetics. While these characters are providing more congruent taxonomic relationships, their variation has not been fully explored. Additionally, phenotypic plasticity (changes in morphology resulting from environmental factors influencing the expressed phenotype despite a shared genotype) is prevalent amongst Scleractinia. In order to better understand the nature of these characters and explore their variation, I created a series of aquaria-based experiments designed to test the stability of these new morphological characters in response to differing environmental conditions. Light intensity and temperature were chosen as the environmental factors varied in these experiments on the basis of being a known trigger for environmentally-driven plasticity and their importance in calcification rate. In addition to aquaria-based phenotypic plasticity experiments I also examined a group (Family: Euphylliidae) within Scleractinia that had been divided by molecular phylogeny into two disparate groups. My research focused on morphological features viewed at magnifications observable by scanning electron microscopy (SEM) called micromorphology. Although variation in the skeletal micromorphology is observable, the new morphological characters that are used in taxonomy display only small amounts of variation caused by changing environmental conditions and were found to be stable for use in taxonomic studies. Additionally, I found a few micromorphological features distinguishing the two groups previously assigned to Euphylliidae including the shape of the septal margins and the fine-scale skeletal texture.

Mainstream evolutionary biology lacks a mature theory of phenotype. Following from the Modern Synthesis, researchers tend to assume an unrealistically simple mapping of genotype to phenotype, or else trust that the complexities of developmental architecture can be adequately captured by measuring trait variances and covariances. In contrast, the growing field of evolutionary developmental biology (evo-devo) explicitly examines the relationship between developmental architecture and evolutionary change, but lacks a rigorous quantitative and predictive framework. In my dissertation, I strive to integrate quantitative genetics and evo-devo, using both theoretical and empirical studies of plasticity. My first paper explores the effect of realistic development on the evolution of phenotypic plasticity when there is migration between two discrete environments. The model I use reveals that nonadditive developmental interactions can constrain the evolution of phenotypic plasticity in the presence of stabilizing selection. In my second paper, I examine the manner in which the genetically controlled responsiveness of traits to each other is shaped by selection and can in turn shape the phenotypic response to selection. Here, results indicate that developmental entanglement through plasticity can facilitate rapid multivariate adaptation in response to a novel selective pressure. In my final paper, I examine patterns of gene expression underlying ancestral plasticity and adaptive loss of melanin in Daphnia melanica. My results indicate that the developmental mechanism underlying ancestral plasticity has been co-opted to facilitate rapid adaptation to an introduced predator.

<p>Many prey species are able to develop different morphological structures as defence against</p><p>for example predators. Some of these structures are induced only by individuals exposed to a</p><p>predator. This phenomenon is called phenotypic plasticity. In this paper we examine whether</p><p>cuticle thickness in Leucorrhinia dubia (Odonata) larvae differed between specimens caught</p><p>in fish containing lakes and fish-free lakes respectively. We measured the thickness of the</p><p>cuticle from four different parts of the larvae; profemur, pronotum, ninth segment sternite and</p><p>ninth segment tergite. Our results showed a significantly thicker exocuticle on profemur in</p><p>larvae with a head width bigger than 4.5 mm caught in lakes with fish. The smaller larvae</p><p>showed a tendency to have thinner exocuticle on profemur in presence of fish. We discuss the</p><p>probability that the differences in exocuticle thickness on profemur could be some kind of</p><p>trade-off situation. The results also showed a tendency among the large larvae; the large</p><p>individuals from lakes containing fish had a slightly thicker exocuticle on pronotum than the</p><p>bigger individuals from fish-free lakes.</p>

This study examined the moderating role of motivational tendencies for social approach and avoidance behavior, as measured by anterior EEG asymmetry, on symptom expression. In particular, this study aimed to replicate and extend previous findings that measures of anterior EEG asymmetry provide an important marker of subgroups of HFA children that significantly differ from each other, and controls, on measures of social communication impairment. EEG data were collected across two occasions on 51 HFA and 44 non-HFA children. EEG asymmetry was computed for homologous electrode pairs (e.g., lnF4-lnF3). More positive scores were indicative of relative left frontal asymmetry. Data on social and behavioral functioning were collected via parent- and self-report. Results of this short-term longitudinal study revealed moderate test-retest reliability for midfrontal asymmetry, r (65) = .39, p < .01. Results supported previous research demonstrating the differential relation of EEG asymmetry to symptom impairment among HFA children, such that parents of LFA-HFA children reported lower levels of impairment than RFA-HFA children on the SCQ Total Score, F (3, 47) = 3.58, p = .065, and Social Interaction Domain, F (3, 47) = 4.59, p < .05. Results also indicated that parents of LFA-HFA children reported higher levels of general communicative competence on the CCC-2, GCC, F (3, 47) = 6.83, p = .01, but greater impairment in pragmatic communication when compared to RFA-HFA children, SIDC, F (3, 47) = 4.41, p < .05. Additional analyses indicated that RFA was associated with early and more confident recognition of atypical (and stereotypically autistic) development based on retrospective parent-report (ADI-R #86), while LFA was associated with early, but less unambiguously autistic impairment, X2 (51) = 3.75, p = .05. This study demonstrates that anterior EEG asymmetry subgroups are reliable and useful markers of phenotypic variability that are meaningfully related to the experience and expression of symptoms of core autism impairment.

A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication. In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus). In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken. In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.

Many prey species are able to develop different morphological structures as defence against for example predators. Some of these structures are induced only by individuals exposed to a predator. This phenomenon is called phenotypic plasticity. In this paper we examine whether cuticle thickness in Leucorrhinia dubia (Odonata) larvae differed between specimens caught in fish containing lakes and fish-free lakes respectively. We measured the thickness of the cuticle from four different parts of the larvae; profemur, pronotum, ninth segment sternite and ninth segment tergite. Our results showed a significantly thicker exocuticle on profemur in larvae with a head width bigger than 4.5 mm caught in lakes with fish. The smaller larvae showed a tendency to have thinner exocuticle on profemur in presence of fish. We discuss the probability that the differences in exocuticle thickness on profemur could be some kind of trade-off situation. The results also showed a tendency among the large larvae; the large individuals from lakes containing fish had a slightly thicker exocuticle on pronotum than the bigger individuals from fish-free lakes.

Phenotypic plasticity allows some animals to change their behavioural, morphological, performance, and life history traits in response to changes in environmental conditions such as the presence of predators. These changes can enhance survival, but come at a cost. Some of these phenotypic changes are predator and diet specific. I examined the effects of predator diet on the performance, life-history, and morphology of developing Northern Leopard Frog (Lithobates pipiens) tadpoles. Tadpoles were either exposed to cues from fish free water, cues from Brown Bullhead (Ameiurus nebulosus) fed a diet of trout pellets, or cues from A. nebulosus fed a L. pipiens tadpoles diet. Tadpoles exposed to predatory fish cues had smaller bodies, deeper tail fins, slower growth and development rates, and better rotational performance than tadpoles that were not exposed to predatory fish cues. Moreover, tadpoles appeared to differentiate between predatory fish diet and produced diet-specific responses in tail morphology and activity, although the latter effect was only marginally significant. Hatching, metamorphosis rates, and linear performance were not affected by the treatments. These results suggest that A. nebulosus can induce phenotypic changes in L. pipiens tadpoles, with some of these changes being diet specific.

Growth rates are highly variable, both within and among genotypes and populations. The resolution of the trade-off between size and age at maturity has been the study of extensive research by life historians. The fitness advantages of large body size and rapid development time are well supported, leading to two predictions. First, realized growth rates should be maximized. Second, growth rate will be subject to strong stabilizing or directional selection, and consequently, low genetic variability. In real populations, despite the advantages of rapid growth, animals often, in fact, grow at rates lower than the maximum rate that is physiologically possible, even in the absence of external constraints on growth rate (e.g. resource restriction or risk of predation while foraging). This implies that growth may have direct fitness consequences that are independent of the size and age of maturity, thereby lowering the optimal rate of growth. In addition to inducing plastic declines in growth rate, such costs may also select for lower intrinsic rates of growth. Despite the strong fitness effects arising from attaining a large body size quickly, variation in growth rate persists at both the phenotypic and genetic levels. The evolutionary and ecological factors contributing to this variation in growth rate are the focus of this thesis. Growth rate variation in insect model species was produced by the manipulation of resource levels during development. By comparing fitness-associated traits and body composition of adults from different treatment groups, I identify direct costs of rapid growth that could explain why animals benefit from growth at submaximal rates. In the second part of the thesis, the relationship between environmental variation and genetic variance in growth rate is investigated by quantitative genetic analysis of body size at different ages and in different growth environments. The results of this analysis suggest that environmental stress can lead to increased genetic variance via decanalization. This has consequences for the evolvability of growth rates in changing environments.

Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. The presence and diversity of Pseudomonas spp. in the rhizosphere is important because of their ability to influence plant and soil health. Diversity is generated as the result of mutation, the rearrangement of genes within the genome and the acquisition of genes by horizontal transfer systems, e.g. plasmids, bacteriophages, transposons or integrons. The purpose of this study was to examine the phenotypic and genotypic diversity of a subset of pseudomonads (N=133) isolated from the rhizosphere and root-interior of four cultivars of field-grown canola. Pseudomonads were analyzed according to their 16S rRNA and cpn60 gene sequences and selected phenotypic properties (fatty acid methyl ester (FAME) profiles, antibiotic resistance, extracellular enzyme production and carbon substrate utilization). On the basis of 16S rRNA and cpn60 gene sequences, two major clusters were observed, the Pseudomonas fluorescens complex and the P. putida complex. Phylogenetic analysis of the partial gene sequences suggested that the phylogeny of root-associated pseudomonads had no effect on their associations with different cultivars or root zones (i.e. rhizosphere and root interior). Principal component analysis (PCA) of their phenotypic properties revealed little variation among the pseudomonads associated with different canola cultivars. Importantly, while little difference was observed in isolates from different cultivars significant phenotypic variation was observed in isolates from different root zones. Cluster analysis of their phenotypic properties exhibited little correlation with their phylogenetic relationships. In the majority of situations, the isolates grouped into a phylogenetic cluster had less than 75-80% similarity among their phenotypic traits despite a close evolutionary relationship as determined by 16S rRNA and cpn60 gene sequencing. The results indicated that the genotype of the rhizosphere pseudomonads was not accurately reflected in their phenotype. Analysis of the mobile genetic elements (MGEs) associated with a randomly selected subset of the pseudomonad isolates (N=66) revealed that 58% (N=38) contained plasmids, 50% (N=33) contained inducible prophages, 24% (N=16) contained integrons and 23% (N=15) contained transposons. Examination of the MGEs associated with a subset of rhizosphere pseudomonads revealed that MGEs were present in the isolates independent of the degree of similarity between their phenotypic and phylogenetic relationships. Therefore, mutation and genomic rearrangement appear to be the major influences in the observed incongruence between the phylogenetic and the phenotypic relationships of the bacteria examined.