Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08

Temporal and spatial variation in temperature experienced by macrofauna at main endeavour Hydrothermal vent field

A significant focus of hydrothermal vent ecological studies has been to understand how species cope with various stressors through physiological tolerance and biochemical resistance. Yet, the environmental conditions experienced by vent species have not been well characterized. This objective requires continuous observations over time intervals that can capture environmental variability at scales that are relevant to animals. We used autonomous temperature logger arrays (four roughly parallel linear arrays of 12 loggers spaced every 10–12 cm) to study spatial and temporal variations in the thermal regime experienced by hydrothermal vent macrofauna at a diffuse flow vent. Hourly temperatures were recorded over eight months from 2010 to 2011 at Grotto vent in the Main Endeavour vent field on the Juan de Fuca Ridge, a focus area of the Ocean Networks Canada cabled observatory. The conspicuous animal assemblages in video footage contained Ridgeia piscesae tubeworms, gastropods (primarily Lepetodrilus fucensis), and polychaetes (polynoid scaleworms and the palm worm Paralvinella palmiformis). Two dimensional spatial gradients in temperature were generally stable over the deployment period. The average temperature recorded by all arrays, and in some individual loggers, revealed distinctive fluctuations in temperature that often corresponded with the tidal cycle. We postulate that this may be related to changes in bottom currents or fluctuations in vent discharge. A marked transient temperature increase lasting over a period of days was observed in April 2011. While the distributions and behavior of Juan de Fuca Ridge vent invertebrates may be partially constrained by environmental temperature and temperature tolerance, except for the one transient high-temperature event, observed fluid temperatures were generally similar to the thermal preferences for some species, and typically well below lethal temperatures for all species. Average temperatures of the four arrays ranged from 4.1 to 11.0 °C during the deployment, indicating that on an hourly timescale the temperature conditions in this tubeworm community were fairly moderate and stable. The generality of these findings and behavioural responses of vent organisms to predictable rhythmicity and non-periodic temperature shifts are areas for further investigation

Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific .1. Influence of vent site distribution, bottom currents, and biological patterns

Deep-sea hydrothermal-vent habitats are typically linear, discontinuous, and short-lived. Some of the vent fauna such as the endemic polychaete family Alvinellidae are thought to lack a planktotrophic larval stage and therefore not to broadcast-release their offspring. The genetic evidence points to exchanges on a scale that seems to contradict this type of reproductive pattern. However, the rift valley may topographically rectify the bottom currents, thereby facilitating the dispersal of propagules between active vent sites separated in some cases by 10s of kilometers or more along the ridge axis. A propagule flux model based on a matrix of intersite distances, long-term current-meter data, and information on the biology and ecology of Alvinellidae was developed to test this hypothesis. Calculations of the number of migrants exchanged between two populations per generation (N-m) allowed comparisons with estimates obtained from genetic studies. N, displays a logarithmic decrease with increasing dispersal duration and reaches the critical value of 1 after 8 d when the propagule Aux model was run in standard conditions. At most, propagule traveling time cannot reasonably exceed 15-30 d, according to the model, whereas reported distances between sites would require longer lasting dispersal abilities. Two nonexclusive explanations are proposed. First, some aspects of the biology of Alvinellidae have been overlooked and long-distance dispersal does occur. Second, such dispersal never occurs in Alvinellidae, but the spatial-temporal dynamics of vent sites over geological timescales allows short-range dispersal processes to maintain gene flow.

Recruitment patterns and processes of coastal fish species in a temperate rocky reef

Tese de Doutoramento, Ciências do Mar, da Terra e do Ambiente, Ramo: Ciências do Mar, Especialização em Ecologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Spatial and depth-associated distribution patterns of shallow gorgonians in the Algarve coast (Portugal, NE Atlantic)

The ecological role of gorgonians for marine rocky bottoms is worldwide recognized, but the information on the distribution patterns of NE Atlantic temperate species is insufficient, considering current global, regional and local threats. To overcome the lack of information on the spatial distribution patterns of gorgonians in south Portugal, in 2009/2010, the occurrence and abundance of gorgonian species in rocky bottoms were quantified over more than 25 km of coast (37.1N/8.6W) down to 30 m depth. Eunicella labiata, Eunicella gazella, Eunicella verrucosa and Leptogorgia sarmentosa were abundant and frequent in the studied area, while Leptogorgia lusitanica was less abundant. All species evidenced a similar depth pattern, that is abundance significantly increased with depth below 15 m. At shallower waters (up to 15 m), the distribution of gorgonians may be constrained by abiotic factors and competition with algae. Indeed, the abundance of gorgonians was negatively correlated with the percentage cover of algae along the depth gradient, but gorgonians and sponges coexist. Competition among gorgonian species also seems to be low in this area because of the similarity in the abundance pattern observed for the most abundant species and also their high association. In NE Atlantic shallow temperate rocky bottoms, the distribution of gorgonians seems to be influenced by environmental factors and biological interactions, namely competition (algae) and coexistence (sponges and other gorgonians).

The influence of habitat heterogeneity on patterns of connectivity among rabbit populations in southern Queensland

Patterns of connectivity among local populations influence the dynamics of regional systems, but most ecological models have concentrated on explaining the effect of connectivity on local population structure using dynamic processes covering short spatial and temporal scales. In this study, a model was developed in an extended spatial system to examine the hypothesis that long term connectivity levels among local populations are influenced by the spatial distribution of resources and other habitat factors. The habitat heterogeneity model was applied to local wild rabbit populations in the semi-arid Mitchell region of southern central Queensland (the Eastern system). Species' specific population parameters which were appropriate for the rabbit in this region were used. The model predicted a wide range of long term connectivity levels among sites, ranging from the extreme isolation of some sites to relatively high interaction probabilities for others. The validity of model assumptions was assessed by regressing model output against independent population genetic data, and explained over 80% of the variation in the highly structured genetic data set. Furthermore, the model was robust, explaining a significant proportion of the variation in the genetic data over a wide range of parameters. The performance of the habitat heterogeneity model was further assessed by simulating the widely reported recent range expansion of the wild rabbit into the Mitchell region from the adjacent, panmictic Western rabbit population system. The model explained well the independently determined genetic characteristics of the Eastern system at different hierarchic levels, from site specific differences (for example, fixation of a single allele in the population at one site), to differences between population systems (absence of an allele in the Eastern system which is present in all Western system sites). The model therefore explained the past and long term processes which have led to the formation and maintenance of the highly structured Eastern rabbit population system. Most animals exhibit sex biased dispersal which may influence long term connectivity levels among local populations, and thus the dynamics of regional systems. When appropriate sex specific dispersal characteristics were used, the habitat heterogeneity model predicted substantially different interaction patterns between female-only and combined male and female dispersal scenarios. In the latter case, model output was validated using data from a bi-parentally inherited genetic marker. Again, the model explained over 80% of the variation in the genetic data. The fact that such a large proportion of variability is explained in two genetic data sets provides very good evidence that habitat heterogeneity influences long term connectivity levels among local rabbit populations in the Mitchell region for both males and females. The habitat heterogeneity model thus provides a powerful approach for understanding the large scale processes that shape regional population systems in general. Therefore the model has the potential to be useful as a tool to aid in the management of those systems, whether it be for pest management or conservation purposes.

A versatile and reliable two-component system for tissue-specific gene induction in Arabidopsis

Developmental progression and differentiation of distinct cell types depend on the regulation of gene expression in space and time. Tools that allow spatial and temporal control of gene expression are crucial for the accurate elucidation of gene function. Most systems to manipulate gene expression allow control of only one factor, space or time, and currently available systems that control both temporal and spatial expression of genes have their limitations. We have developed a versatile two-component system that overcomes these limitations, providing reliable, conditional gene activation in restricted tissues or cell types. This system allows conditional tissue-specific ectopic gene expression and provides a tool for conditional cell type- or tissue-specific complementation of mutants. The chimeric transcription factor XVE, in conjunction with Gateway recombination cloning technology, was used to generate a tractable system that can efficiently and faithfully activate target genes in a variety of cell types. Six promoters/enhancers, each with different tissue specificities (including vascular tissue, trichomes, root, and reproductive cell types), were used in activation constructs to generate different expression patterns of XVE. Conditional transactivation of reporter genes was achieved in a predictable, tissue-specific pattern of expression, following the insertion of the activator or the responder T-DNA in a wide variety of positions in the genome. Expression patterns were faithfully replicated in independent transgenic plant lines. Results demonstrate that we can also induce mutant phenotypes using conditional ectopic gene expression. One of these mutant phenotypes could not have been identified using noninducible ectopic gene expression approaches.

Shoot growth dynamics and photosynthetic response to increased nitrogen availability in the alpine willow salix-glauca

Plants subjected to increases in the supply of resource(s) limiting growth may allocate more of those resources to existing leaves, increasing photosynthetic capacity, and/or to production of more leaves, increasing whole-plant photosynthesis. The responses of three populations of the alpine willow, Salix glauca, growing along an alpine topographic sequence representing a gradient in soil moisture and organic matter, and thus potential N supply, to N amendments, were measured over two growing seasons, to elucidate patterns of leaf versus shoot photosynthetic responses. Leaf-(foliar N, photosynthesis rates, photosynthetic N-use efficiency) and shoot-(leaf area per shoot, number of leaves per shoot, stem weight, N resorption efficiency) level measurements were made to examine the spatial and temporal variation in these potential responses to increased N availability. The predominant response of the willows to N fertilization was at the shoot-level, by production of greater leaf area per shoot. Greater leaf area occurred due to production of larger leaves in both years of the experiment and to production of more leaves during the second year of fertilization treatment. Significant leaf-level photosynthetic response occurred only during the first year of treatment, and only in the dry meadow population. Variation in photosynthesis rates was related more to variation in stomatal conductance than to foliar N concentration. Stomatal conductance in turn was significantly related to N fertilization. Differences among the populations in photosynthesis, foliar N, leaf production, and responses to N fertilization indicate N availability may be lowest in the dry meadow population, and highest in the ridge population. This result is contrary to the hypothesis that a gradient of plant available N corresponds with a snowpack/topographic gradient.

Diagnostic and treatment pathways for men with prostate cancer in Queensland : investigating spatial and demographic inequalities

Background: Patterns of diagnosis and management for men diagnosed with prostate cancer in Queensland, Australia, have not yet been systematically documented and so assumptions of equity are untested. This longitudinal study investigates the association between prostate cancer diagnostic and treatment outcomes and key area-level characteristics and individual-level demographic, clinical and psychosocial factors.---------- Methods/Design: A total of 1064 men diagnosed with prostate cancer between February 2005 and July 2007 were recruited through hospital-based urology outpatient clinics and private practices in the centres of Brisbane, Townsville and Mackay (82% of those referred). Additional clinical and diagnostic information for all 6609 men diagnosed with prostate cancer in Queensland during the study period was obtained via the population-based Queensland Cancer Registry. Respondent data are collected using telephone and self-administered questionnaires at pre-treatment and at 2 months, 6 months, 12 months, 24 months, 36 months, 48 months and 60 months post-treatment. Assessments include demographics, medical history, patterns of care, disease and treatment characteristics together with outcomes associated with prostate cancer, as well as information about quality of life and psychological adjustment. Complementary detailed treatment information is abstracted from participants’ medical records held in hospitals and private treatment facilities and collated with health service utilisation data obtained from Medicare Australia. Information about the characteristics of geographical areas is being obtained from data custodians such as the Australian Bureau of Statistics. Geo-coding and spatial technology will be used to calculate road travel distances from patients’ residences to treatment centres. Analyses will be conducted using standard statistical methods along with multilevel regression models including individual and area-level components.---------- Conclusions: Information about the diagnostic and treatment patterns of men diagnosed with prostate cancer is crucial for rational planning and development of health delivery and supportive care services to ensure equitable access to health services, regardless of geographical location and individual characteristics. This study is a secondary outcome of the randomised controlled trial registered with the Australian New Zealand Clinical Trials Registry (ACTRN12607000233426)

New variational Bayesian approaches for statistical data mining : with applications to profiling and differentiating habitual consumption behaviour of customers in the wireless telecommunication industry

This thesis investigates profiling and differentiating customers through the use of statistical data mining techniques. The business application of our work centres on examining individuals’ seldomly studied yet critical consumption behaviour over an extensive time period within the context of the wireless telecommunication industry; consumption behaviour (as oppose to purchasing behaviour) is behaviour that has been performed so frequently that it become habitual and involves minimal intentions or decision making. Key variables investigated are the activity initialised timestamp and cell tower location as well as the activity type and usage quantity (e.g., voice call with duration in seconds); and the research focuses are on customers’ spatial and temporal usage behaviour. The main methodological emphasis is on the development of clustering models based on Gaussian mixture models (GMMs) which are fitted with the use of the recently developed variational Bayesian (VB) method. VB is an efficient deterministic alternative to the popular but computationally demandingMarkov chainMonte Carlo (MCMC) methods. The standard VBGMMalgorithm is extended by allowing component splitting such that it is robust to initial parameter choices and can automatically and efficiently determine the number of components. The new algorithm we propose allows more effective modelling of individuals’ highly heterogeneous and spiky spatial usage behaviour, or more generally human mobility patterns; the term spiky describes data patterns with large areas of low probability mixed with small areas of high probability. Customers are then characterised and segmented based on the fitted GMM which corresponds to how each of them uses the products/services spatially in their daily lives; this is essentially their likely lifestyle and occupational traits. Other significant research contributions include fitting GMMs using VB to circular data i.e., the temporal usage behaviour, and developing clustering algorithms suitable for high dimensional data based on the use of VB-GMM.

Weather variability and influenza A (H7N9) transmission in Shanghai, China: A Bayesian spatial analysis

Abstract Background A novel avian influenza A (H7N9) virus was first found in humans in Shanghai, and infected over 433 patients in China. To date, very little is known about the spatiotemporal variability or environmental drivers of the risk of H7N9 infection. This study explored the spatial and temporal variation of H7N9 infection and assessed the effects of temperature and rainfall on H7N9 incidence. Methods A Bayesian spatial conditional autoregressive (CAR) model was used to assess the spatiotemporal distribution of the risk of H7N9 infection in Shanghai, by district and fortnight for the period 19th February–14th April 2013. Data on daily laboratory-confirmed H7N9 cases, and weather variability including temperature (°C) and rainfall (mm) were obtained from the Chinese Information System for Diseases Control and Prevention and Chinese Meteorological Data Sharing Service System, respectively, and aggregated by fortnight. Results High spatial variations in the H7N9 risk were mainly observed in the east and centre of Shanghai municipality. H7N9 incidence rate was significantly associated with fortnightly mean temperature (Relative Risk (RR): 1.54; 95% credible interval (CI): 1.22–1.94) and fortnightly mean rainfall (RR: 2.86; 95% CI: 1.47–5.56). Conclusion There was a substantial variation in the spatiotemporal distribution of H7N9 infection across different districts in Shanghai. Optimal temperature and rainfall may be one of the driving forces for H7N9.

Imagined Landscapes: Geovisualizing Australian Spatial Narratives

Imagined Landscapes teams geocritical analysis with digital visualization techniques to map and interrogate films, novels, and plays in which space and place figure prominently. Drawing upon A Cultural Atlas of Australia, a database-driven interactive digital map that can be used to identify patterns of representation in Australia’s cultural landscape, the book presents an integrated perspective on the translation of space across narrative forms and pioneers new ways of seeing and understanding landscape. It offers fresh insights on cultural topography and spatial history by examining the technical and conceptual challenges of georeferencing fictional and fictionalized places in narratives. Among the items discussed are Wake in Fright, a novel by Kenneth Cook, adapted iconically to the screen and recently onto the stage; the Australian North as a mythic space; spatial and temporal narrative shifts in retellings of the story of Alexander Pearce, a convict who gained notoriety for resorting to cannibalism after escaping from a remote Tasmanian penal colony; travel narratives and road movies set in Western Australia; and the challenges and spatial politics of mapping spaces for which there are no coordinates.

Hot spot detection and spatio-temporal dynamics of dengue in Queensland, Australia

Dengue has been a major public health concern in Australia since it re-emerged in Queensland in 1992-1993. This study explored spatio-temporal distribution and clustering of locally-acquired dengue cases in Queensland State, Australia and identified target areas for effective interventions. A computerised locally-acquired dengue case dataset was collected from Queensland Health for Queensland from 1993 to 2012. Descriptive spatial and temporal analyses were conducted using geographic information system tools and geostatistical techniques. Dengue hot spots were detected using SatScan method. Descriptive spatial analysis showed that a total of 2,398 locally-acquired dengue cases were recorded in central and northern regions of tropical Queensland. A seasonal pattern was observed with most of the cases occurring in autumn. Spatial and temporal variation of dengue cases was observed in the geographic areas affected by dengue over time. Tropical areas are potential high-risk areas for mosquito-borne diseases such as dengue. This study demonstrated that the locally-acquired dengue cases have exhibited a spatial and temporal variation over the past twenty years in tropical Queensland, Australia. There is a clear evidence for the existence of statistically significant clusters of dengue and these clusters varied over time. These findings enabled us to detect and target dengue clusters suggesting that the use of geospatial information can assist the health authority in planning dengue control activities and it would allow for better design and implementation of dengue management programs.

Searching for common threads in threadfins: phylogeography of Australian polynemids in space and time

Proper management of marine fisheries requires an understanding of the spatial and temporal dynamics of marine populations, which can be obtained from genetic data. While numerous fisheries species have been surveyed for spatial genetic patterns, temporally sampled genetic data is not available for many species. We present a phylogeographic survey of the king threadfin Polydactylus macrochir across its species range in northern Australia and at a temporal scale of 1 and 10 yr. Spatially, the overall AMOVA fixation index was Omega(st) = 0.306 (F-st' = 0.838), p < 0.0001 and isolation by distance was strong and significant (r(2) = 0.45, p < 0.001). Temporally, genetic patterns were stable at a time scale of 10 yr. However, this did not hold true for samples from the eastern Gulf of Carpentaria, where populations showed a greater degree of temporal instability and lacked spatial genetic structure. Temporal but not spatial genetic structure in the Gulf indicates demographic interdependence but also indicates that fishing pressure may be high in this area. Generally, genetic patterns were similar to another co-distributed threadfin species Eleutheronema tetradactylum, which is ecologically similar. However, the historical demography of both species, evaluated herein, differed, with populations of P. macrochir being much younger. The data are consistent with an acute population bottleneck at the last glacio-eustatic low in sea level and indicate that the king threadfin may be sensitive to habitat disturbances.

The Miocene of Western Asia; Fossil mammals at the crossroads of faunal provinces and climate regimes

Being at the crossroads of the Old World continents, Western Asia has a unique position through which the dispersal and migration of mammals and the interaction of faunal bioprovinces occurred. Despite its critical position, the record of Miocene mammals in Western Asia is sporadic and there are large spatial and temporal gaps between the known fossil localities. Although the development of the mammalian faunas in the Miocene of the Old World is well known and there is ample evidence for environmental shifts in this epoch, efforts toward quantification of habitat changes and development of chronofaunas based on faunal compositions were mostly neglected. Advancement of chronological, paleoclimatological, and paleogeographical reconstruction tools and techniques and increased numbers of new discoveries in recent decades have brought the need for updating and modification of our level of understanding. We under took fieldwork and systematic study of mammalian trace and body fossils from the northwestern parts of Iran along with analysis of large mammal data from the NOW database. The data analysis was used to study the provinciality, relative abundance, and distribution history of the closed- and open-adapted taxa and chronofaunas in the Miocene of the Old World and Western Asia. The provinciality analysis was carried out, using locality clustering, and the relative abundance of the closed- and open-adapted taxa was surveyed at the family level. The distribution history of the chronofaunas was studied, using faunal resemblance indices and new mapping techniques, together with humidity analysis based on mean ordinated hypsodonty. Paleoichnological studies revealed the abundance of mammalian footprints in several parts of the basins studied, which are normally not fossiliferous in terms of body fossils. The systematic study and biochronology of the newly discovered mammalian fossils in northwestern Iran indicates their close affinities with middle Turolian faunas. Large cranial remains of hipparionine horses, previously unknown in Iran and Western Asia, are among the material studied. The initiation of a new field project in the famous Maragheh locality also brings new opportunities to address questions regarding the chronology and paleoenvironment of this classical site. Provinciality analysis modified our previous level of understandings, indicating the interaction of four provinces in Western Asia. The development of these provinces was apparently due to the presence of high mountain ranges in the area, which affected the dispersal of mammals and also climatic patterns. Higher temperatures and possibly higher co2 levels in the Middle Miocene Climatic Optimum apparently favored the development of the closed forested environments that supported the dominance of the closed-adapted taxa. The increased seasonality and the progressive cooling and drying of the midlatitudes toward the Late Miocene maintained the dominance of open-adapted faunas. It appears that the late Middle Miocene was the time of transition from a more forested to a less forested world. The distribution history of the closed- and open-adapted chronofaunas shows the presence of cosmopolitan and endemic faunas in Western Asia. The closed-adapted faunas, such as the Arabian chronofauna of the late Early‒early Middle Miocene, demonstrated a rapid buildup and gradual decline. The open-adapted chronofaunas, such as the Late Miocene Maraghean fauna, climaxed gradually by filling the opening environments and moving in response to changes in humidity patterns. They abruptly declined due to demise of their favored environments. The Siwalikan chronofauna of the early Late Miocene remained endemic and restricted through all its history. This study highlights the importance of field investigations and indicates that new surveys in the vast areas of Western Asia, which are poorly sampled in terms of fossil mammal localities, can still be promising. Clustering of the localities supports the consistency of formerly known patterns and augments them. Although the quantitative approach to relative abundance history of the closed- and open-adapted mammals harks back to more than half a century ago, it is a novel technique providing robust results. Tracking the history of the chronofaunas in space and time by means of new computational and illustration methods is also a new practice that can be expanded to new areas and time spans.