Thesis (Ph. D.)--Oregon State University, 1998. / Typescript (photocopy). Includes bibliographical references (leaves 111-124). Also available on the World Wide Web.

1. This thesis presents the results of a population ecology study of the Dipper Cinclus cinclus in the western Ochil Hills, Tayside and Central Regions, Scotland between April 1985 and May 1988. 2. Particular attention was given to factors affecting juvenile survival between fledging and recruitment to the breeding population. These included investigation of the variation and significance of body size, plumage colour. dispersal distance, home range acquisition, dominance status and autumn body condition. 3. Overwinter survival was higher in adults than juveniles. Juvenile females had a greater overwinter survival and recruitment rate than juvenile males. Few body size measures were consistently associated with overwinter survival,though juvenile females with longer wings and tarsi tended to survive better. 4. Males had higher plumage brightness scores than females and, within sexes, adults were brighter than juveniles. Overall, survival overwinter and recruitment were not related to plumage brightness. 5. A laboratory test arena was developed for assessing dominance relations in small groups of temporarily captive birds. Social status between age and sex classes was correlated with plumage brightness. Within age classes, plumage brightness was a significant predictor of status in adults, but body size was more important in juveniles. 6. Females settled farther from their natal sites than males; most of this dispersal was completed soon after independence. The relationship between dispersal and dominance is discussed and a model developed. 7. Autumn population density was manipulated locally in a series of experimental juvenile introductions. Numbers rapidly returned to initial levels, though earlier released individuals persisted for longer. About 20% of introduced birds recruited, mainly higher status males. 8. Body composition of a small sample of birds collected between September and April is described. Lipid stores were greatest in winter and least in spring. A method for measuring pectoralis muscle thickness was developed using an ultrasound-based technique. 9. Condition indices derived from "ultrasound" measurements on live birds were used to evaluate the importance of protein reserves in overwinter survival. Males in good condition in autumn were more likely to recruit but no trend was apparent in females. 10. Two periods of high juvenile losses were identified: post-independence and late autumn. Predation could only be implicated in the former. The agent of late autumn losses was not proven but probably involved territorial intolerance and the consequent exclusion of subordinates to fringe habitats. It is concluded that density-dependent changes in mortality, related to dominance and mediated via dispersal, caused Dipper numbers tobe matched to available resources, principally food and breeding territories.

Acidified catchments are known to hold significantly reduced dipper Cinclus cinclus populations throughout the year relative to circum-neutral rivers, although the processes leading to these declines remain unclear. This study considered the population ecology of dippers within the circumneutral River Devon catchment, Central Scotland, and focused primarily on determining the factors influencing survival, breeding probabilities and reproductive success. It aimed to examine the role of spatial variation in 'habitat quality' on the population (and meta-population) dynamics of dippers, based on measures of seasonal and lifetime reproductive success, and the balance between survival and reproduction; in particular, to assess if the reduced reproductive success of dippers on acid rivers is likely to lead to population declines. Within the Devon catchment, approximately 81% of all adults survived from spring (March/April) to autumn (September/October), with 65% of these birds surviving from autumn to the following breeding season. Overall, these estimates predicted annual adult survival rates of c.53%, with no significant differences between years. Population density had no detectable effect on adult mortality rates, although juvenile over-winter survival was significantly lower than the adult rate at between 40 and 58%, and negatively related to the total size of the autumn population. There was no evidence of sex differences in juvenile over-winter survival, or any significant influence of weather or river flows on the rates for adults or juveniles. The local post-fledging survival of females was significantly lower than for males, however, apparently reflecting sex differences in post-natal dispersal. On average, less than 6.5% of all eggs laid, or 10.4-14.5% of male and 6.3-9.2% of female fledglings raised within the Devon catchment survived locally to breeding age. Juvenile, although not adult, recapture rates in spring were significantly lower than for birds known to have bred previously and negatively related to spring river flows. This suggested that with recapture dependent on a breeding attempt that was successful at least until laying, either more first year birds failed during the initial stages of nesting or that full breeding was not achieved at age one. The birds fledging the most young, both within a season and over a lifetime, all bred at 'prime' lowland sites characterised by wide, shallow rivers of intermediate gradient, although with less than 10% of all birds attempting to raise a second brood each year, no significant habitat differences were identified in any component of reproductive output measured until fledging. River width, altitude and gradient were all significantly inter-correlated and related to laying date, however, and post-fledging survival was significantly reduced for late fledged young. On average, lowland birds laid earlier than upland breeders, and were significantly more likely to produce autumn 'recruits' due to the enhanced post-fledging survival prospects of their young. This suggested that broad measures of river structure can provide a biologically appropriate classification of habitat quality. The size of the breeding population of dippers within the Devon catchment appeared to be related to the availability of critical resources, most likely food, roost sites and ultimately breeding territories through density-dependent changes in over-winter mortality and recruitment. The relative importance of resource abundance and recruitment levels in determining autumn population densities on acid streams still remained unclear, although reference to published relationships between acidity and reproductive success suggested that with adult survival at the rate estimated for the Devon catchment, many dipper populations are unlikely to produce sufficient recruits to match all adult losses, and may only persist with continued immigration from more productive (circumneutral) catchments elsewhere.

1. Cost constraints in models of territory size are based on time/activity/laboratory estimates that predict birds using larger territories will incur higher energy costs. The predicted form of the cost constraint may be linear, accelerating or decelerating depending on assumptions inherent in the models. The aim of this study was to assess the reality and form of the cost constraint by making direct measurements of the energy costs of territory use in birds that occupy territories of different size and shape; polygonal territories represented by the robin Erithacus rubecula, and linear by the dipper Cinclus cinclus. Free-living energy expenditure was measured using the doubly-labelled water technique, whilst simultaneously recording patterns of territory use by radio-tracking. 2. Territorial robins concentrated their activity in one or more foraging patches located in bushes. Range polygons containing all the foraging patches used by an individual provided estimates of territory area, and were generally of high eccentricity. A small proportion of robins was classified as non-territorial based on range polygon areas. Furthermore, while territorial robins showed high fidelity to ranges over the short term (days), non-territorial individuals were nomadic. Over the longer term (months), however, some territorial robins showed range drift. Dippers similarly used preferred core regions within ranges, although there was no selection for particular habitat features. 3. Because robins occupied territory polygons which varied from polygonal to highly linear, work was focused on this species to allow intra-specific comparison. Robins tended to commute between foraging patches by flying. It was appropriate, therefore, to describe territories in terms of a number of patches linked by a network of flight paths. This generated two further measures of territory size; the number of patches used and the total flight distance between patches. 4. The robins exploited a renewing food supply. Predictions were tested concerning the temporal scheduling of visits to foraging patches within territories. Patches tended to be separated by flight paths of similar lengths, and were visited in a regular sequence. Although the number of foraging patches used varied, all territories had similar total core areas. Robins using many small foraging patches commuted between patches more often and covered a larger total flight distance during each foraging circuit of the territory. The configurations of foraging patches were used in a highly linear manner. This was true even if the territory containing them was of low eccentricity. 5. Changes in structure and pattern of use varied predictably with territory size, and could be described mathematically. Based on this and published time/activity budgets, a suite of models was developed to predict how energy costs would vary with number of patches used and total flight distance between patches. Models were tested by directly measuring the energy expenditure of robins using different territories. The number of patches used and total flight distance between patches were both significantly correlated with energy expenditure, while territory area was not. One of the models showed a significant fit to the observed data, and suggested that the form of the energy cost constraint on territory size was linear. The effect of territory shape on energy costs was minimal. The implications of these results for models of territory size are discussed. 6. The slope and elevation of the energy cost constraint varied with the morphology of territory occupants. Based on this, an association of morphology with territory size was predicted; robins of lower mass and wing-loading using larger territories. The observed data supported these predictions, and suggested a possible genetic predisposition to particular patterns of territory occupancy in the robin.

In Chapter 2 of this thesis I present my database of molecular absorption cross sections. These were developed using public molecular transition line-lists (from the ExoMol group). I use them to find limitations in the modelling of exoplanet atmospheres due to pressure broadening. Pressure broadening, where collisions between molecules in atmospheres cause a Lorentzian broadening of molecular transitional lines, is little understood in the field. In this chapter I consider its effects on real exoplanet atmosphere observations, both with current and future instruments. I show that pressure broadening may affect future observations of exoplanets in the JWST era. Pressure broadening primarily affects cooler, small exoplanets such as Earth analogues. In Chapter 3 I present the pipeline I have developed to reduce HST WFC3 spectra of exoplanet hosts during transits to create transmission spectra. This code corrects several instrumental systematics, from varying dark signal in the detector to subpixel shifts in the target position over time. By creating a pipeline to process all targets, regardless of observing strategy, systematics are dealt with uniformly and different planets’ spectra can be meaningfully compared. I show that the height of the water feature in 30 unique exoplanets’ transmission spectra is strongly correlated with the most simplistic absorption model. I use this to predict a list of the best future targets for observations with HST WFC3 to find water. In Chapter 4 I discuss my work with the stellar spectra from WFC3, which utilise the sub-pixel shifts in target position to oversample the spectra and increase the resolution. I have compared these exoplanet host stellar spectra with stellar models to investigate how well stellar atmosphere models describe the near IR. I find a small discrepancy in temperature when WFC3 alone is used to assess the stellar temperature, particularly with cooler stars. I attribute this firstly to an error in the WFC3 sensitivity curve and secondly to an inaccuracy in models of cool, small stars due to molecular absorption. In Chapter 5 I present my work on K2 light curve data using machine learning to find young stellar objects that display unusual, transit-like behaviour. These objects are known as dipper stars due to their distinctive occultations with depths of 10-50% in flux and very fast orbital periods of a few hours to a few days. Such large occultations are difficult to explain and are currently attributed to material at the inner edge of the protoplanetary disk. This behaviour is often variable and aperiodic, suggesting that the occulting material is changing in morphology on the time scale of a single orbit. Using python’s scikit-learn I have developed a code that utilises a Random Forest algorithm to classify stars in K2 Campaign Field 2 and distinguish these objects from other types of variables, such as eclipsing binaries and pulsating stars. This method has proved very successful and has allowed me to nearly quadruple the number of known dipper candidates in the Upper Scorpius and Rho Ophiuchus regions.

La théorie de la sélection sexuelle a drastiquement orienté l’effort de recherche sur la communication acoustique chez les oiseaux : les mâles apprennent et produisent des chants élaborés et les femelles choisissent. Par conséquent (1) la production vocale chez les femelles a été négligée, (2) les cris (la majorité de la communication sociale) ont été peu étudiés. Contrairement aux chants, les cris ont été considérés comme innés et aucun effet de l’environnement sur leur structure n’était attendu. J’ai donc posé la question de la flexibilité vocale (court-terme) et de la plasticité vocale (au cours du développement) chez les femelles, en étudiant les cris majoritairement. J’ai étudié deux contextes où les deux sexes vocalisent: la communication dans le couple au nid et la communication parent-jeunes. Les vocalisations produites au nid par les couples montrent-elles de la flexibilité en réponse au bruit? Le développement des cris est-il influencé par l’environnement social ? J’ai travaillé sur deux espèces: le cincle plongeur, Cinclus cinclus et le diamant mandarin, Taeniopygia guttata. Chez les deux espèces, en réponse au bruit, les couples augmentent l’amplitude de leurs vocalisations. Chez le cincle une variation de la structure spectrale est observée dans les notes de chant mais pas dans les cris. Chez le diamant mandarin, les cris montrent des changements de leur structure spectrale: ils peuvent donc être flexibles en réponse au bruit. Les changements sont similaires chez les femelles et les mâles : la flexibilité n’est pas spécifique du sexe. Enfin, j’ai montré que l’environnement social précoce influence le développement des cris de quémande alimentaire chez le diamant mandarin : il existe une plasticité précoce des cris chez les mâles. J’ai montré que les femelles expriment des degrés de flexibilité similaires aux mâles mais que leur développement vocal peut prendre des trajectoires différentes. Les cris sont de bons objets de recherche pour étudier des variations de comportement vocal liées au sexe / The theory of sexual selection has drastically oriented research on acoustic communication in birds: males learn and sing conspicuous songs and females choose. Consequently, (1) female vocal production has been neglected, (2) birdcalls (most bird social communication) have been understudied. Birdcalls were supposed to be non-learned and no effect of the environment was expected on their structure (no flexibility, no learning). I thus focused my thesis on vocal flexibility (short-term) and vocal plasticity (developmental) of female vocalizations (mainly calls). I studied two contexts in which both sexes produce vocalizations: intrapair communication at the nest and parent-offspring communication. Do pairs express vocal flexibility in their calls in response to environmental noise? Is call development influenced by social environment? I studied two species: the white-throated dippers, Cinclus cinclus. (in which both sexes produce calls and songs) and the zebra finch, Taeniopygia guttata, (in which only males sing but both sexes use the same calls). I showed in both species, that in response to environmental noise, pairs increased the amplitude of their calls or song notes. In dippers, spectral flexibility was observed in song notes but not in calls. However, zebra finch calls showed spectral flexibility in response to noise. Both sexes showed similar changes in their calls: call spectral flexibility is not sex specific. Last, I showed that the structure of male begging calls changed in response to the early social environment, bringing evidence of early vocal plasticity in males. No change was found in females, showing that they either differ in their plasticity abilities or do not express plasticity because they receive different social feedbacks. My work showed that females and males show vocal flexibility but their vocal developmental trajectories may differ. Calls are thus good study objects to investigate sexual dimorphism in vocal behaviour