Exotic species often invade new areas and displace native species. The problems associated with such invasions are well known, but for many exotic species, experimental work has not yet been done to predict which, and under what conditions they may become a problem. Two greenhouse experiments were devised to investigate the plasticity, shade tolerance, and phenotypic differences of full-siblings from 3 populations of Cardamine impatiens, a Eurasian species potentially invasive in North America. Potted plants were subjected to 0, 54, 76, or 91% shade created by neutral density shade cloth application. In addition, the impact of a cold pre-treatment of seedlings on the growth and reproductive output of C. impatiens plants was examined. In our first experiment, we subjected Cardamine impatiens to non-shaded cages, 54%, or 76% shade intensity. Plants died very quickly, so LD50 data were used as a relative measure of fitness, and relative growth indices were calculated over time. Other relative measures of fitness included canopy area, leaf area, number of leaves, number of leaves per canopy area, and final plant weight. Plants in cages with no shade treatment grew faster than those in cages with shade cloth and final plant weight decreased as shade treatment percentage increased. In each population, the number of leaves increased over time and the number of leaves per canopy area decreased over time under shade treatments. Our second experiment involved the application of 54%, 76%, and 91% shade intensity. The additional shade treatment of 91% was applied to determine the extent of plant tolerance and plasticity in response to light reduction. Due to high plant mortality in our first experiment, we treated Cardamine impatiens with a 4 week cold period prior to treatment, which simulates its biennial growth form in its natural western Virginia region habitat. Since this second experiment took place later in the year, day length was extended to more accurately duplicate the conditions during the first experiment. LD50 calculations were not necessary, and 7 of the 135 plants produced seed. Relative measures of fitness included canopy area, leaf area, number of leaves, number of leaves per canopy area, and final plant weights. As in experiment one, the number of leaves per plant increased over time, final plant weight decreased as shade treatment increased, and the number of leaves per canopy area decreased as shade treatment increased. From these two experiments, we determined that Cardamine impatiens is a species that exhibits phenotypic plasticity and therefore may pose a threat as an invasive species. C. impatiens is able to grow and exhibit plasticity of plant architecture under the conditions of very low light. The number of leaves per canopy area decreased as shade increased, suggesting that C. impatiens is highly adaptable to low light conditions, and therefore may be exhibiting phenotypic plasticity by reallocating its resources by producing fewer leaves while maintaining canopy area. This data along with other C. impatiens traits such as high levels needed for seed production, its persistence in seed banks, along with a lack of known major enemies, indicates that they have a great capacity to invade a wide variety of habitats. We also determined that a cold treatment is necessary in order for C. impatiens to obtain optimal growth and reproduction. / Master of Science

Background: Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. Results: From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. Conclusions: ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study.

The Extended Evolutionary Synthesis (EES) is currently emerging as a theoretical alternative to the Modern Synthesis (MS) in which to frame evolutionary observations and interpretations. These alternative frameworks differ fundamentally in their understanding of the relative roles of the genotype, phenotype, development and environment in evolutionary processes and patterns. While the MS represents a gene-centred view of evolution, the EES instead emphasizes the interactions between organism, development and environment. This novel theoretical framework has generated a number of evolutionary predictions that are mutually incompatible with the equivalent of the MS. While research and empirical testing has begun on a number of these in a neontological context, the field of palaeontology has yet to contribute meaningfully to this endeavour. One of the reasons for this is a lack of methodological approaches capable of investigating relevant evolutionary patterns in the fossil record. In this thesis morphometric methods capable of providing relevant data are developed and employed in the analysis of Cambrian fossils. Results of these analyses provide empirical support for the process of evolution through phenotypic plasticity and genetic assimilation hypothesized by the EES. Furthermore, theoretical revision to the species concept in a palaeontological context is suggested. Finally, predictions of the EES specific to the fossil record are made explicit and promising directions of future research are outlined.

[Truncated abstract] In south-western Australia a rare plant community occurs on shallow soils overlaying massive ironstone rock. These 'ironstone communities' are open shrublands, which are subject to extremes in drought and solar radiation and support many rare and endemic species. The restricted distribution of many of these species may be related to their high degree of specialisation to this harsh habitat and their inability to respond plastically to different environmental conditions. Indeed, earlier work has shown that ironstone Hakea species (Proteaceae) have a specialist root-system morphology investing mainly in deep roots, thereby increasing their chance of accessing cracks in the rock surface and obtaining water before the onset of summer drought. In this thesis I further examine aspects of specialisation and its possible consequences for species rarity using two ironstone Hakea species and comparing them with two of their widely distributed congeners. In the first experiment (Chapter 2) I explore inherent drought tolerance, independent of root-system morphology, as a further specialisation to the ironstone environment. All species were grown in sand in pots in a glasshouse for 7 months and then droughted for 5 weeks. There was no evidence that the ironstone species had a greater inherent drought tolerance than their common congeners. During drought all species maintained leaf water content of mature leaves by reducing stomatal conductance and osmotically adjusting, though ironstone species tended to OA (osmotic adjustment) more than common species. ... This suboptimal investment of resources may result in a lower competitive ability in shadier environments, and thus could partially explain their restricted distribution. In Chapter 4, I investigated the plasticity of root traits in response to levels of phosphorus supply. South-western Australian soils are phosphorus impoverished and phosphorus is well known to elicit plastic responses in root allocation and architecture. Ironstone species showed less plasticity in total root length, producing similar root length across P treatments, while common species showed an increase in root length with increasing [P]. Other root characteristics were similarly plastic in response to P treatment between species. However, when supplied with increasing [P], ironstone species invested an increasing proportion of roots in the bottom of pots while common species invested more in the top. This differential response in root allocation in response to P may reflect a fundamental trade-off between nutrient and water acquisition, with the ironstone species mainly foraging for water and investing in deeper roots, while the common species invest more in superficial roots to obtain nutrients. In conclusion, the rarity and restricted distribution of the ironstone Hakea species may be related to their specialist root-system morphology as well as a lowered phenotypic plasticity of functional traits. A reduction in plasticity may reduce their competitive ability outside their ironstone habitats, and thus contribute to the restricted distribution of these species. This may also be the case for other rock-outcrop endemics and more generally, for other rare plant species restricted to particular habitats where a lowered phenotypic plasticity in traits relevant to their particular habitat may contribute to their restricted distribution.

Phenotypic plasticity is the ability of an organism to express different phenotypes in response to biotic or abiotic environmental cues. The ability of an organism to make changes during development to adjust to changes in its environment is a key to survival. Sexually reproducing organisms that have short life cycles and that are easy to raise in the laboratory are more conducive for developmental phenotypic plasticity. Considerable research has already been carried out on the brine shrimp, Artemia franciscana, regarding its morphology due to changing salinities. There is, however, little research considering subsequent generations and how there morphology might be affected by parental experiences. This study has examined: 1) the morphological effects of different rearing regimes of different salinity levels, and 2) the epigenetic transgenerational transfer of these morphological traits in A. franciscana. Measurements included rate of growth (as measured by instar), body size, body length, and other morphological traits. A gradual increase to more hyperosmotic conditions during development produced brine shrimp that were larger in size and also more developmentally advanced. Salinity stress experienced by adults had increased the growth rate in the F1 offspring of A. franciscana. Collectively, these data indicate that Artemia franciscana is a tractable model for investigating phenotypic plasticity. These findings have added to the ever-growing field of developmental phenotypic plasticity while also providing more information on the natural history and adaptive abilities of A. franciscana.

Le succès écologique des organismes dépend principalement de leur phénotype. Une composante important du phénotype est la morphologie fonctionnelle car elle influence la performance d’un organisme donné dans un milieu donné et donc reflète son écologie. Des disparités dans la morphologie fonctionnelle ou dans le développement entre espèces peuvent donc mener à des différences écologiques. Ce projet évalue le rôle des mécanismes de variation morphologique dans la production de différences écologiques entre espèces au sein des poissons hybrides du complexe Chrosomus eos-neogaeus. En utilisant la microtomodensitométrie à rayons X et la morphométrie géométrique 3D, la forme des éléments des mâchoires est décrite pour comparer la variation morphologique et les différences développementales entre les membres du complexe C. eos neogaeus. Les hybrides présentent autant de variation phénotypique que les espèces parentales et présentent des phénotypes nouveaux, dit transgressifs. Les hybrides présentent aussi des différences marquées avec les espèces parentales dans leur allométrie et dans leur intégration phénotypique. Finalement, ceux-ci semblent être plastiques et en mesure de modifier leur phénotype pour occuper plusieurs environnements. L’entièreté de ces résultats suggère que des changements dans le développement des hybrides entraînent une différenciation phénotypique et écologique avec les espèces parentales. / An organism’s success is highly dependent on its phenotype. A major component of the phenotype is functional morphology because of its role in determining performance in a given environment clues as to their ecology. Morphological disparity and developmental differences between species can thus lead to ecological differences. This project assesses the role that mechanisms capable of generating morphological variation have in producing ecological differences between species within the hybrid fishes of the Chrosomus eos-neogaeus complex. Using X-ray based computer-aided micro-tomography and 3D geometric morphometrics, the shape of bones composing the jaws was described to measure morphological variation and developmental differences in the C. eos-neogaeus complex. Chrosomus eos-neogaeus hybrids displayed as much variation as parental species and novel, deemed transgressive, phenotypes. Hybrids were also markedly different from parental species in their patterns of allometric scaling and phenotypic integration. Finally, hybrids appeared to be plastic and able to acclimate to different environments. The results of this study indicate that changes in the development of hybrids could lead to phenotypic and, in turn, ecological differences with parental species.

My dissertation research investigates the genetic architecture and evolutionary significance of physiological variation in two wildflower species, Ipomopsis aggregata and Arabidopsis thaliana. In particular, my work focuses on water use efficiency (WUE), a critical physiological trait that dictates plant growth and performance in resource-limited environments. I used a combination of quantitative trait loci (QTL) mapping, field selection experiments, and classic quantitative genetics to investigate 1) the genetic architecture of water use efficiency and flowering time, 2) patterns of natural selection on water use efficiency, flowering time, and other ecological traits in I. aggregata, and 3) additive genetic variation, genetic correlations, and selection on water use efficiency, flowering time, and plasticity to drought in Arabidopsis thaliana. Using an Ipomopsis aggregata genetic mapping population, I identified four QTL underlying WUE, three QTL-QTL epistatic interactions, and evidence for a possible QTL x cytoplasmic interaction affecting WUE. I found a similar genetic architecture underlying flowering time, with four main effect QTLs that all adjacently localized to the same linkage groups as WUE, and three QTL-QTL epistatic interactions, which occur between the same chromosome pairs as the WUE interactions. The combined main and interactive effects explain 35% and 40% of the phenotypic variation in WUE and flowering time, respectively. The adjacent localization suggests a possible role for the evolution of co-inheritance or, if the true QTL positions actually overlap, a possible role for pleiotropy underlying the phenotypic correlation between WUE and flowering time. Additionally, these results suggest epistasis is a significant factor affecting phenotypic variation in nature. In a reciprocal transplant and water addition experiment, I demonstrated variable natural selection on WUE, flowering time, and nectar production in I. aggregata across elevation/habitat and differential water availability. At low elevation in the water addition treatment, natural selection favors early flowering and greater nectar sugar concentration, while dry conditions favor high WUE and early flowering time. At high elevation, where the growing season is shorter and drier, selection favors early flowering regardless of water addition. These results suggest natural selection on ecophysiological and floral traits varies with resource availability (e.g. water availability and pollinator visitation). Using data from a glasshouse experiment involving a global panel of accessions of Arabidopsis thaliana, I demonstrated strong positive genetic correlation between WUE and flowering time, as well as selection for low WUE and early flowering under experimental season-ending drought. Finally, I found significant genetic variation in plasticity as well as selection favoring greater WUE plasticity under drought, indicating plasticity to drought is adaptive in A. thaliana. / text

BACKGROUND:A hub protein is one that interacts with many functional partners. The annotation of hub proteins, or more generally the protein-protein interaction "degree" of each gene, requires quality genome-wide data. Data obtained using yeast two-hybrid methods contain many false positive interactions between proteins that rarely encounter each other in living cells, and such data have fallen out of favor.RESULTS:We find that protein "stickiness", measured as network degree in ostensibly low quality yeast two-hybrid data, is a more predictive genomic metric than the number of functional protein-protein interactions, as assessed by supposedly higher quality high throughput affinity capture mass spectrometry data. In the yeast Saccharomyces cerevisiae, a protein's high stickiness, but not its high number of functional interactions, predicts low stochastic noise in gene expression, low plasticity of gene expression across different environments, and high probability of forming a homo-oligomer. Our results are robust to a multiple regression analysis correcting for other known predictors including protein abundance, presence of a TATA box and whether a gene is essential. Once the higher stickiness of homo-oligomers is controlled for, we find that homo-oligomers have noisier and more plastic gene expression than other proteins, consistent with a role for homo-oligomerization in mediating robustness.CONCLUSIONS:Our work validates use of the number of yeast two-hybrid interactions as a metric for protein stickiness. Sticky proteins exhibit low stochastic noise in gene expression, and low plasticity in expression across different environments.

For vector-borne parasites such as malaria, how within- and between-host processes interact to shape transmission is poorly understood. In the host, malaria parasites replicate asexually but for transmission via mosquitoes to occur, specialized sexual stages (gametocytes) must be produced. Once inside the mosquito vector, gametocytes immediately differentiate into male and female gametes, and motile male gametes must swim through the hostile environment of the bloodmeal to find and fertilise female gametes. Despite the central role that gametocytes play in disease transmission, explanations of why parasites adjust gametocyte production in response to in-host factors remain controversial. Furthermore, surprisingly little is known about the mating behaviour of malaria parasites once inside the mosquito. Developing drugs and/or vaccines that prevent transmission by disrupting sexual stages are major goals of biomedicine, but understanding variation in gametocyte investment and male gamete behaviour is key to the success of any intervention. First, I propose that the evolutionary theory developed to explain variation in reproductive effort in multicellular organisms provides a framework to understand gametocyte investment strategies in malaria parasites. I then demonstrate that parasites appear to change their reproductive strategies in response to environmental cues and in a manner consistent with our predictions. Next, I show how digital holographic microscopy can be used to characterise the morphology and motility of male gametes. I then provide evidence for non-random movement of male gametes and that gamete interactions with red blood cells appear to hinder mating success in a bloodmeal. Finally, I discuss the variation in gametocyte differentiation and fertilisation success when exposed to a number of factors implicated in gametocyte activation. The data presented here provides important information on the basic biology of malaria parasite reproductive stages and demonstrates considerable variation in parasite traits and behaviours in response environmental changes; both in the host and in the mosquito vector.

Earth mean surface temperature has increased by 1 °C since the industrial revolution, and this has already had considerable effects on animal and plant species. Ecological responses to the warming climate – often facilitated via phenotypic plasticity – are ubiquitous. However, even though evolution can occur rapidly there are only few examples of genetic adaptation to climate change. In my thesis, I used a near-natural system to study if and how organisms have adapted to 30 years of warming, and how this has affected competitive species interactions. I investigated Baltic Sea populations of the aquatic snails Galba truncatula and Theodoxus fluviatilis, which had been subjected to cooling water discharge from power plants, resulting in water temperatures 4 to 10 °C higher than in the surrounding sea. G. truncatula had high upper thermal limits and large acclimation potential. This plasticity may have helped the species to survive under the new conditions, allowing evolution through natural selection to take place. I found that the populations of the two thermal origins had diverged in SNP markers associated with warmer temperature, whereas divergence in selectively neutral markers was mainly related to geographical distance. Adaptation occurred from standing genetic variation, emphasizing the importance of genetic diversity and population size in enabling the persistence of populations. Changes in thermal sensitivity of growth and survival were subtle yet significant, and complied with theoretical models of thermal adaptation in ectotherms. At the community level, pre-adaptation to warmer conditions aided the native T. fluviatilis when competing with the alien Potamopyrgus antipodarum. However, interspecific competition limited the snails most in those traits favored under warming, highlighting the challenge of adapting to different selecting forces during global change. The persistence of species and populations under climate change depends on several factors - plasticity allowing for initial survival, evolvability in allowing the genetic changes, and species interactions affecting the new ecological niches. The results of my thesis indicate that persistence under climate change is possible when these factors align, but the relative roles of ecology and plasticity may explain why there are so few observed instances of evolution in response to climate change.