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The presence of triploid individuals, whether hybrids arising from crosses of diploid and tetraploid plants, or spontaneously generated triploid hybrids diploid populations, is increasingly important in plant populations. However, the possible evolutionary role of the triploid hybrids is closely connected to the frequency of their occurrence, to their relative fitness (compared to parental cytotype) and fertility. As a model plant I choosed Tripleurospermum inodorum, in which a relatively frequent occurrence of triploid hybrids was documented in mixed populations of tetraploids and diploids. This annual plant achieves realy quick its reproductive maturity and is easily cultivated, making it an ideal model for cultivation and pollinating experiments. Compared to parental cytotypes, the triploid hybrids of T. inodorum take approximately the same (mostly mediated) fitness values. In vitro conditions were cultivated to measure of germination rates. Germination rate of triploid seeds was comparable to diploid parental cytotype. In the subsequent comparative cultivation, nearly 150 plant individuals (2x, 3x, 4x, and aneuploid cytotype) in the greenhouse showed that the triploids had intermedial values of their parental cytotypes or close to one of the parents. Thus, the vitality of the triploid plants is...

Sterile triploid Atlantic salmon represent a solution to the issues of pre-harvest sexual maturation and mature escapees from open aquaculture systems. Although the initial problems of reduced performance and increased deformities in triploids have been thoroughly researched, there is a continued lack of information on their susceptibility and response to disease and routine on-farm treatments compared to diploids. Thus, the main aim of this thesis was to enhance the current understanding of triploid health and immunity through experimental disease challenges and treatments, and aid in determining their robustness and, therefore, suitability for aquaculture. A commercial furunculosis vaccine equally protected diploids and triploids against challenge with Aeromonas salmonicida, and adhesion scores were similar between ploidy (Chapter 2). Interestingly, triploids had lower white blood cell counts but increased cellular activity, e.g. respiratory burst, compared to diploids. Following experimental cohabitation infection with Neoparamoeba perurans, causative agent of Amoebic Gill Disease (AGD), ploidy did not affect the manifestation or severity of AGD-associated gill pathology, or the serum innate immune response (Chapter 3). Hydrogen peroxide, used to treat against parasitic diseases, elicited similar primary and secondary stress responses in both ploidy, but led to differences in the expression of stress (cat, gpx1, gr, hsp70, sod1, sod2) and immune (saa5, crp/sap1a, crp/sap1b, il1β) genes (Chapter 4). Finally, vaccination with different vaccine treatments (4 commercial vaccines, 6 different vaccine combinations and a sham-vaccinated control) showed no ploidy differences in adhesion score or antibody response, although vertebral deformities remained higher in triploids (Chapter 5). Increasing severity of vaccine treatments negatively affected weight, length and thermal growth coefficient in both ploidy. Triploids were heavier than diploids at smolt (+ 14 %) and post smolt (+ 32 %). Overall, this research shows that triploid Atlantic salmon respond as well as diploids to disease and treatment challenges, and supports their application into full-scale commercial aquaculture.

Triploid (sterile) trout potentially offer a more risk-averse option for stocking popular non-native sport fish; however the relative performance (e.g., survival and growth) of triploid versus diploid fish in natural settings is not well understood. I evaluated the relative performance of triploid versus diploid brook trout (Salvelinus fontinalis) stocked in high mountain Uinta lakes in response to food availability and lake morphology. I chose a set of 9 lakes that included a range of elevation and lake morphology. I observed no difference in CPUE or relative weight (Wr) of both types of trout in all lakes. Food availability (e.g., zooplankton and macroinvertebrates) varied substantially among lakes; however I observed no discernible difference between diploid and triploid diets, diet preference, or isotopic trophic signatures. Physical lake characteristics (e.g., dissolved oxygen [DO, mg/L] and temperature [°C]) were within or near optimal brook trout conditions (metabolically beneficial range) during the summer, but over-winter DO reached near lethal levels under the ice. In sum, between the two strains, I did not observe any significant differences in relative performance measured across a number of indices; however the size distribution of diploid fish was marginally (20 mm) skewed towards larger fish (a difference likely not great enough to be detectable by the average angler). In contrast to the similarity in performance between strains, I did observe considerable variability in performance of brook trout across lakes as a function of lake productivity, food availability, and most importantly fish density. Fish performance was greater in lakes with a lower density of stocked fish. Overall, the results from this study indicate triploid brook trout offer a viable and risk-averse alternative to stocking diploid fish in Uinta mountain lakes. Stocking triploid fish should decrease the threat of uncontrolled expansion into adjacent water bodies, while still allowing managers to maintain a popular non-native sport fishery.

Over the last century, flowering rush (Butomus umbellatus L.: Butomaceae) has escaped its native Eurasian range and has become a problematic species in North America. As an aquatic invasive species, flowering rush has degraded native wetlands and has interfered with human water usage. Although experimental work has been done regarding the reproductive biology of the species, few empirical studies regarding the ecology of the species have been conducted. The research reported here demonstrates that flowering rush is capable of aggressive clonal growth and propagation, and can perform well along a depth gradient from zero to 132cm. Proper management and control of invasive species relies on sound ecological knowledge of the target species, and this work aims to help gather that information.

Salinity is a critical challenge facing productivity of crops around the world, causing major reduction in growth, yield, and quality. It is necessary to produce varieties with the ability to tolerate salinity. However, the lack of genetic variation among H. vulgare genotypes prevents progress in developing salt tolerant varieties. H. bulbosum is a source of tolerance to stress conditions. Consequently, five accessions of domestic barley and six of wild barley were used in this study. Accessions were screened for salinity tolerance. Genotypes 7, 9, and 10 germinated at 2% NaCl. Lines of H. vulgare showed reduction of root and shoot length greater than H. bulbosum. Crosses were made between diploid and tetraploid H. vulgare ♀ and tetraploid H. bulbosum ♂. Immature embryos were rescued. Murashige and Skoog medium was found to be generally better for most crosses. Number of successful crosses varied among families. Female 5, for diploid crosses, and female 2, for tetraploid crosses, have high GCA and compatibility with bulbosum males, and 17.9% and 17.6% of their progeny exceeding the mean grain yield, respectively. Parent 9 had also high GCA and compatibility with vulgare parents (2x), and its progeny seem to exceed the mean in many cases with most families. During germination screening, progeny of diploid females 1 and 2 were found to be highly desirable for saline tolerance. Among the tetraploid crosses, Family 1 had greatest percentage of superior progeny (18.8%), while Families 2 and 3 had greatest number of superior individuals (8 and 7, respectively). For seedling growth, diploid Families 2 and 3 crosses had the greatest shoot dry weight and tolerant saline index (SSI<1). Families 2 and 4 of tetraploid crosses had 12 of 39 and eight of 26 crosses show greatest shoot dry weight and tolerance as measured by SSI, respectively. Final germination percentage (FG%) showed positive association with plant height, while associating negatively with tiller number, fertility, cSW, and grain yield. In diploid crosses, FG% associated positively with tiller number. Shoot dry weight showed negative association with plant height, while it associated positively with tiller number, fertility, cSW, and grain yield.

Freshwater sport fisheries contribute substantially to the economies of England and Wales. However, many trout fisheries rely partly or entirely on stocking farmed trout to maintain catches within freshwater fisheries. Farmed trout often differ genetically from their wild counterparts and wild trout could be at risk of reduced fitness due to interbreeding or competition with farmed fish. Therefore, to protect remaining wild brown trout (Salmo trutta L) populations and as a conservation measure, stocking policy has changed. Legislation introduced by the Environment Agency (EA, 2009) will now only give consent to stocking of rivers and some stillwaters with sterile, all-female triploid brown trout. There are reliable triploidy induction protocols for some other commercially important salmonid species however; there is limited knowledge on triploid induction in brown trout. Previously, triploid brown trout have been produced by heat shocks although reduced survivals were obtained suggesting that an optimised heat shock had not been identified, or that heat shock gives less consistent success than hydrostatic pressure shock (HP), which is now recognised as a more reliable technique to produce triploid fish. Thus the overall aim of this thesis was to conduct novel research to support the aquaculture and freshwater fisheries sector within the United Kingdom by optimising the production and furthering the knowledge of triploid brown trout. Firstly, this PhD project investigated an optimised triploidy induction protocol using hydrostatic pressure (Chapter 2). In order to produce an optimised hydrostatic pressure induction protocol three experiments were conducted to (1) determine the optimal timing of HP shock application post-fertilisation, (2) define optimal pressure intensity and duration of the HP shock and (3) study the effect of temperature (6-12 °C) on triploid yields. Results indicated high survival to yolk sac absorption stage (69.2 - 93.6 %) and high triploid yields (82.5 - 100 %) from the range of treatments applied. Furthermore, no significant differences in triploid rates were shown when shock timings and durations were adjusted according to the temperature used. In all treatments deformity prevalence remained low during incubation (<1.8 %) up to yolk sac absorption (~550 degree days post hatch). Overall, this study indicated that the optimised pressure shock for the induction of triploidy in brown trout delivering high survival and 100 % triploid rate (a prerequisite to brown trout restocking) is a shock with a magnitude of 689 Bar applied at 300 Centigrade Temperature Minutes (CTM) for 50 CTM duration. Regarding the assessment of triploid status, the second experimental chapter tested the accuracy and efficacy of three ploidy verification techniques (Chapter 3). Techniques studied were erythrocyte nuclei measurements (Image analysis), flow cytometry (Becton Dickinson Facscalibur flow cytometer) and DNA profiling (22 polymorphic microsatellite loci) to assess the effectiveness of triploidy induction in brown trout. Results indicated the validity of using erythrocyte indices major nuclear axis measurements, flow cytometric DNA distributions expressed as relative fluorescence (FL2-Area), and polymorphic microsatellite loci (Ssa410UOS, SSa197, Str2 and SsaD48) for assessing ploidy status in brown trout. Accuracy of each technique was assessed and indicated that all techniques correctly identified ploidy level indicating 100 % triploid rate for that commercial batch of brown trout. These techniques may be utilised within aquaculture and freshwater fisheries to ensure compliance with the legislation introduced by the EA. As a result of the legislation introduced by the Environment Agency triploid brown trout will freely interact with diploid trout therefore there is a need to assess feeding response and behavioural differences between diploid and triploid trout prior to release. Therefore, in the third experimental chapter (Chapter 4) diploid and triploid brown trout were acclimated for six weeks on two feeding regimes (floating/sinking pellet). Thereafter, aggression and surface feeding response was compared between pairs of all diploid, diploid and triploid and all triploid brown trout in a semi natural stream (flume). In each pairwise matching, fish of similar size were placed in allopatry and rank determined by the total number of aggressive interactions initiated. Dominant individuals initiated more aggression than subordinates, spent more time defending a territory and positioned themselves closer to the food source (Gammarus pulex) whereas subordinates occupied the peripheries. When ploidy was considered, diploid trout were more aggressive than triploid, and dominated their siblings when placed in pairwise matchings. However, surface feeding did not differ statistically between ploidy irrespective of feeding regime. Triploids adopted a sneak feeding strategy while diploids expended more time defending a territory. In addition, an assessment of whether triploids exhibited a similar social dominance to diploids when placed in allopatry was conducted. Although aggression was lower in triploid pairs than in the diploid/triploid pairs, a dominance hierarchy was observed between individuals of the same ploidy. Dominant triploid fish were more aggressive and consumed more feed items than subordinate individuals. Subordinate fish displayed a darker colour index than dominant fish suggesting increased stress levels. However, dominant triploid fish seemed more tolerant of subordinate individuals and did not display the same degree of invasive aggression as observed in the diploid/diploid or diploid/triploid matchings. These novel findings suggest that sterile triploid brown trout feed similarly but are less aggressive than diploid trout and therefore may provide freshwater fishery managers an alternative to stocking diploid brown trout. In addition to research at the applied level in triploid brown trout, this thesis also examined the fundamental physiological effects of ploidy in response to temperature regime. Triploid salmonids have been shown to differ in their tolerance to environmental temperature. Therefore the fourth experimental chapter (Chapter 5) investigated whether temperature tolerance affected feed intake and exercise recovery. Diploid and triploid brown trout were exposed to an incremental temperature challenge (10 and 19 °C) and subsequent survival and feed intake rates were monitored. Triploids took longer to acclimate to the increase in temperature however feed intake were significantly greater in triploids at high temperature. In a follow on study, we investigated post-exercise recovery processes under each temperature regime (10 and 19 °C). Exhaustion was induced by 10 minutes of forced swimming, with subsequent haematological responses measured to determine the magnitude of recovery from exercise. Plasma parameters (alkaline phosphatase, aspartate aminotransferase, calcium, cholesterol, triglycerides, phosphorous, total protein, lactate, glucose, pH, magnesium, osmolality, potassium, sodium, chloride, lactate dehydrogenase) were measured for each ploidy. Basal samples were taken prior to exercise and then at: 1; 4, and 24 hours post-exercise. Contrary to previous studies, there was no triploid mortality during or after the exercise at either temperature. Although diploid and triploid brown trout responded metabolically to the exercise, the magnitude of the response was affected by ploidy and temperature. In particular, triploids had higher levels of plasma lactate, osmolality, and lower pH than diploids at 1 hour post exhaustive exercise. By 4 hours post-exercise plasma parameters analysed had returned to near basal levels. It was evident that the magnitude of the physiological disturbance post-exercise was greater in triploids than diploids at 19 °C. This may have implications where catch and release is practiced on freshwater fisheries. Overall, this work aimed to develop and/or refine current industry induction and assessment protocols while better understand the behaviour and physiology of diploid and triploid brown trout. The knowledge gained from this work provides aquaculture and freshwater fisheries with an optimised protocol, which delivers 100 % triploid rates and profitability without compromising farmed trout welfare, thus ultimately leading towards a more sustainable brown trout industry within the United Kingdom.

Hieracium lepidulum is an invasive weed in New Zealand. It colonises a wide range of habitats including pine plantations, scrubland, native Nothofagus forest, and mid-altitude to alpine tussock grassland, where it is competing with indigenous species. Understanding the breeding systems and population genetic structure of H. lepidulum is important for biocontrol, and aids in the understanding of evolutionary colonisation processes. H. lepidulum is a triploid, diplosporous, obligate apomict. This type of reproduction through clonal seed does not involve meiosis or fertilisation, and theoretically populations should contain very low levels of genetic variation, the only source being somatic mutation. Common garden experiments and microsatellite markers were used to determine the population genetic structure of H. lepidulum populations in the Craigieburn Range, Canterbury. Both experiments revealed that populations, sampled from three replicate altitudes within three geographically-separated locations, contained no genetic variation; individuals all possessed the same microsatellite genotype. These results strongly suggest that the Craigieburn Range H. lepidulum individuals reproduce solely by apomixis and populations belong to the same clonal lineage. Populations were also examined for their response to two abiotic environmental ‘stresses’, drought and shade. H. lepidulum populations’ exhibited high drought tolerance, yet appeared to be shade-intolerant. Low levels of reproduction in light-limiting habitats will prevent the invasion of H. lepidulum into closed-canopy forest habitats. H. lepidulum appears to have overcome the reduction in fitness associated with apomictic reproduction by phenotypic plasticity, fixed heterozygosity and polyploidy – all associated with increased vigour, fitness, and the ability to occupy broader ecological niches. This study’s results are hopeful for the development of biocontrol programs involving genotype-specific pathogens but suggest that grazing management may not succeed. The data will be useful for future comparisons of genetic structure during the course of H. lepidulum invasions and will contribute to the management of this invasive weed.

The objective of the work described in the current thesis was to provide a better understanding of some of the key factors associated with sea louse, Lepeophtheirus salmonis, infection of farmed Atlantic salmon. In Chapter 2, initial work focused on establishing the vertical and horizontal distribution of sea lice copepodids and spatial patterns of on-farm infections. The louse distribution was investigated along the main current gradient across adjacent salmon production pens at three commercial sites. A depth profile for the distribution of larval lice was also established for the top 12 m of the water column at three different locations in close proximity to commercial salmon farms. Within all multi-pen sites there were clear patterns of distribution and infection along the main water current gradient with the abundance of lice in end pens at each site appearing to be different from the central pens. The vertical distribution pattern of free swimming L. salmonis larvae (nauplii and copepodids) showed that the surface 6 m harboured 85.5 ± 1.6 % of the lice present in the water body analysed (0 – 12 m depth), irrespective of sampling date and location. In Chapter 3, further environmental effects / influences on attachment success of the copepodids were analysed using controlled infection challenges. A flume with adjustable flow rates, and controlled light conditions was designed for this study. Flume current velocity was observed to be a significant factor in infection success, with higher infection levels observed at lower current velocities, while higher current velocities were demonstrated to reduce settlement success. At fixed velocity, higher copepodid exposure levels gave rise to higher infection levels, this having a linear relationship suggestive of a lack of competitive effects for space on the fish. Light was also shown to play an important role in host settlement. A positive correlation between increasing light intensity and higher louse attachment success was found for all tested light spectra / wavelengths (white - Halogen, blue 455 nm, green 530 nm and red 640 nm). Observation of an infecting cohort of copepodids showed maximal infection at four days post-moulting with a tail-off of infection by six days post-moulting. However, even under the optimal conditions represented by a flume challenge, including linear water flow, the constraint of copepodids to pass close to the salmon host and the very high exposure levels of copepodids per fish, louse attachment success was still relatively low. Chapter 4 examined implementation of a possible management approach based upon some of the environmental influences observed. This chapter described a study in which environmental manipulation of salmon swimming depth was employed on-site in an attempt to reduce farm infection of Atlantic salmon. The effects of submerged artificial lighting in combination with submerged feeding were tested with respect to salmon swimming depth and sea lice infection, following the hypothesis that L. salmonis infection in a commercial salmon population could be reduced through exposure to deep lighting and feeding. The results of the study suggest that swimming depth manipulation can indeed be used at a commercial scale to reduce salmon lice burdens on Atlantic salmon by physically minimising spatial interactions between the two animals. In the final research chapter (Chapter 5), this thesis examines the question of whether ploidy of the host impacts on sea louse infection levels and whether susceptibility of individual fish is consistent between replicate infections. Results showed that triploid salmon are not subject to higher sea louse infection levels under experimental challenge and farm infection conditions compared to diploid hosts. In addition, triploid fish subject to initial infection, did not become more or less resistant to infection compared to diploids when comparing repeated sea louse infections. In summary, this thesis describes work conducted to analyse key infection pathways and factors influencing infection of Atlantic salmon by sea lice and suggestions made as to how findings may be exploited to reduce louse burdens in Atlantic salmon farming. The practical solutions presented to exploit the results found in this work are currently under consideration by the Scottish salmon industry.

Background: Over the relatively short period of its evolutionary history, Boechera (Brassicaceae) has undergone rapid radiation that has produced 70+ morphologically distinct, sexual diploids. However, reproductive isolation has moved more slowly than morphological divergence in this group and the diploids appear to hybridize frequently where they coexist. Boechera duchesnensis appears to be the result of hybridization between its putative parents Boechera thompsonii and Boechera formosa. Objectives: The objectives of this study are to (i) analyze and document genetic diversity patterns in the population structure, - including allelic and heterozygosity frequencies - of B. thompsonii and B. formosa in concert with their geographic distribution to determine clustering relationships within these populations, (ii) confirm and expand the morphological characteristics of B. thompsonii and B. formosa, as initially proposed in the literature, including pollen and trichome structure using Scanning Electron Microscopy (SEM) to confirm ploidy level and to determine whether both putative parent species share morphological characteristics with their apomictic diploid offspring, and (iii) use genetic and morphologic evidence to show that B. thompsoii and B. formosa are, in fact, the parents of B. duchesnensis by comparing the genetic diversity patterns, population structure, and morphological characteristics of B. duchesnensis, to those of its proposed putative parents (B. thompsonii and B. formosa) and to confirm that B. duchesnensis shares characteristics of Boechera. Methods: Microsatellite data from 14 loci previously identified in Boechera were used to reexamine the current classifications and taxonomic foundations of three Boechera spp. GenAlEx 6.501 (Peakall and Smouse, 2006, 2012) was used to analyze genetic population structures of two divergent sexual diploids in the genus Boechera: B. thompsonii and B. formosa and to later compare those with the population structure of B. duchesnensis. Geographicaldata were plotted using ArcGIS 10.1 (Esri, 2012) to map heterozygosity distribution. Cluster analysis was run with STRUCTURE 2.3.3 (Pritchard et al., 2000; Falush et al., 2003, 2007) and distribution of allelic diversity and heterozygosity was subsequently compared within each taxon and correlated with geographic distribution characteristics. Resultant data were then compared with B. duchesnensis data to document genetic diversity patterns, population structure, and morphological characteristics. Key Results: Analysis of genetic diversity patterns, allelic distribution of the populations, and heterozygosity of B. thompsonii and B. formosa across their geographic range identified four genetically distinct clusters within B. thompsonii, and one genetically distinct cluster in B. formosa. Allelic frequencies in all four discrete population clusters of B. thompsonii and in one discrete population cluster of B. formosa were close to values found in species on the decline. Reproductive isolation, genetic variability, and allelic frequencies were determined, specimen elevations reported, and morphological characteristics reported in the literature were confirmed and expanded. A codominant genetic analysis performed for 14 different loci for B. duchesnensis against those of its parents showed that B. duchesnensis inherits alleles from both putative parents and confirms B. thompsonii and B. formosa as the parents of B. duchesnensis. Observed levels of heterozygosity of B. thompsonii and B. formosa were lower than expected levels and lower than those of other outcrossing diploids. The mean overall observed heterozygosities for each cluster were determined and documented by geographic location. A substantially higher level of observed heterozygosity in B. duchesnensis (Ho = 0.908) consistent with genetic fixation of a heterozygote and apomixis, supports hybridization as a speciation mechanism and apomixis as a mode of reproduction accounting for genotypic and phenotypic diversity. Morphological characteristics, especially those of pollen and trichomes were confirmed, expanded, and documented with SEM imagery. Discussion: This study provides an analysis of the genetic diversity patterns inherent in the population structure, allelic frequencies, allelic variation among individuals of the rare sexual diploids B. thompsonii, B. formosa, and the apomictic diploid B. duchesnensis in correlation with their geographic distribution. There is an implication of a reproductive barrier, within populations of the same species, that contributes to genetic isolation between clusters. I analyze the tendency of reduced heterozygosity to lead to genetic fixation, reproductive isolation, and how the heightened heterozygosity supports the classification of B. duchesnensis as an apomict. Assessing potential populations that might exist based on similar characteristics could possibly provide inferences about where future research might find similar examples of this hybridization. Reproductive isolation is hypothesized to limit gene flow between identified clusters of B. thompsonii and B. formosa exacerbating low observed heterozygosity levels and low allelic frequency levels. Population studies and cluster analysis have implications for offering future conservation strategies for both taxa.