Suspension-feeding bivalves produce biodeposits (faeces and pseudofaeces) that have much higher sinking velocities than their constituent particles. Consequently they cause sedimentation of material that might otherwise not be deposited. The benthic remineralisation of biodeposits increases sediment oxygen demand and nutrient regeneration, thus enhancing the benthic-pelagic coupling of nearshore ecosystems. In New Zealand the mussel Perna canaliculus has a high natural abundance and is also intensively cultured. This thesis examines the dispersal and remineralisation characteristics of mussel P. canaliculus biodeposits and the impacts of sedimentation from a mussel farm in the Firth of Thames on sediment biogeochemistry by combining laboratory, field and modelling studies. Dispersal characteristics were examined in the laboratory by measuring sinking velocities and erosion thresholds of biodeposits produced by mussels of a wide size range fed three experimental diets. The results show that biodeposit dispersal is a function of mussel diet and size and thus could differ significantly between locations and seasons. Estimates of dispersal distances based on these results demonstrated that the initial dispersal of biodeposits produced by cultured mussels is not far. Depending on the hydrodynamic conditions, secondary dispersal via resuspension potentially plays a more important role in the dispersal of biodeposits from mussel farms than initial dispersal and almost certainly serves as the major means of transport of biodeposits from natural mussel beds. Biodeposit mineralisation was studied by incubating coastal sediments with added biodeposits and measuring oxygen and nutrient fluxes as well as sediment characteristics over an 11 d period. Sediment oxygen consumption and ammonium release increased immediately after biodeposit addition and remained elevated compared to control cores without additions for the incubation period. A biodeposit decay rate (0.16 d-1) was calculated by fitting a first-order G model to the observed increase in oxygen consumption. This rate is 1 - 2 orders of magnitude higher than published decay rates of coastal sediments without organic enrichment or plant material. Nutrient fluxes during the incubation period illustrated that biodeposit remineralisation alters the stoichiometry of the nutrients released from the sediments which may potentially be more significant than the changes of the individual fluxes. To determine the impact of a mussel farm in the Firth of Thames I measured sediment oxygen and nutrient fluxes by deploying benthic chambers, sediment characteristics by collecting sediment cores and sedimentation rates by deploying sediment traps in four seasons. Oxygen consumption and sediment nutrient release rates were generally higher under the farm compared to a reference site, demonstrating the typical response to increased organic input. Unusually low nitrogen release rates measured in summer may indicate enhanced denitrification under the farm. A simple budget demonstrated the importance of benthic nutrient regeneration in maintaining primary production in this region and that mussel culture can lead to a redistribution of nutrients. This study showed that site-specific hydrodynamic and biogeochemical conditions have to be taken into account when planning new mussel farms to prevent excessive modifications of nutrient dynamics. Results of the laboratory and field studies conducted in this thesis were used to parameterise, calibrate and validate models of mussel biodeposit dispersal and remineralisation. A particle tracking model showed that the maximum initial dispersal of faecal pellets from the mussel farm is approximately 300 m and that pellets can be transported several times this distance via resuspension. The remineralisation model was able to simulate the increased nitrogen fluxes from the sediments well and highlighted the need for thorough calibration and parameterisation of the model. This thesis contributed to the current understanding of the ecosystem impacts of mussel culture and provided numerical models and model parameters that will assist in the assessment of mussel culture sustainability and the contribution of mussels to the nutrient cycling in nearshore ecosystems.

The entrainment of microbes from agricultural land into overland flow during rainfall events is recognised as an important source of pathogenic microbes to surface water bodies and yet this transport process is poorly understood. In this study, a method has been developed to separate bacteria into the forms in which they have been postulated to exist in overland flow. Then Escherichia coli was used as a model organism to investigate the transported state of bacteria eroded from cowpats and their subsequent transport in overland flow. Simulated rainfall experiments were used to generate runoff direct from cowpats. Concentrations of E. coli in the runoff direct from cowpats were found to be directly proportional to the concentration in the cowpat, regardless of the age of the cowpat. It was also observed that E. coli were predominantly eroded from cowpats as individual cells. The interactions between E. coli and soil particles in overland flow were then examined in a small laboratory scale model system and showed that E. coli attached to large (>45 [mu]m) soil particles were transported significantly less than unattached cells. However, in the runoff from the model system, E. coli were found to be attached mainly to clay particles that were similar in size to the bacterial cells. Furthermore, the transport of E. coli through the model system appeared to follow the transport of a conservative chemical tracer implying that (a) the cells were being transported as a solute with the bulk of the water flow, and (b) that E. coli attached to small clay particles were as mobile in the overland flow as unattached cells. These observations imply that E. coli predominantly interact with small clay particles that are also being carried along in the overland flow. The transport of E. coli at a larger scale was then investigated using 5-metre long, 1-metre wide buffer strips operated under saturation excess conditions. In buffer strips using intact soils and existing pasture cover, E. coli removal was very poor (26 % removal) at the low flow rate of 2 L min⁻� with no removal observed at the higher flow rates of 6 and 20 L min⁻�. E. coli removal rates were increased to 41 % removal at 2 L min⁻� by cultivating the soils, with the removal rate again decreasing with increasing flow rate. E. coli in the overland flow from the buffer strips did not form into large flocs or attach to large soil particles, but were transported in small neutrally buoyant particles that remain entrained in the overland flow. Under saturation excess runoff conditions, E. coli in overland flow were not effectively removed by buffer strips as the small particles are transported either over the soil surface or, through large pores in the soil. This Thesis has shown that E. coli is transported in overland flow in small particle sizes that are difficult to trap or remove from overland flow thereby explaining the high fluxes of faecal bacteria observed in overland flow from agricultural land.

The Moehau Kiwi Sanctuary is one of five sanctuaries established in 2000 and managed by the Department of Conservation. The objective of the sanctuaries is to protect the most endangered kiwi taxa, and increase kiwi survivorship. Operation Nest Egg (ONE) is a programme utilised by the Moehau Kiwi Sanctuary for artificially incubating abandoned Kiwi eggs and captive rearing chicks until they begin to show a gain in weight. ONE chicks were then released back onto Moehau or adjacent protected areas. Kiwi populations are declining on the mainland at an average of about 3% per year in areas where predators of kiwi are not controlled. The main cause for this decline is chick mortality due to predation by stoats (Mustela erminea). During natal dispersal kiwi are known to disperse significant distances of between 5–20 km, and this has influenced the size of management areas needed for the protection of kiwi (10,000 hectares). The type of forest-cover is an important element in determining where management areas are located, as kiwi has preferences for certain forest types over others. This study conducted at Moehau, Coromandel, on the North Island Brown Kiwi advances our knowledge of kiwi by examining differences in rates and distances of dispersal among chicks, sub-adults, non-territorial and territorial adults, as well as between genders. This study investigates kiwi selective use of roost site types, ground-cover types, forest types and physiographical features. Addressed in this study are differences in dispersal, habitat selection and mortality among age-classes and between genders over the months of the year, and across elevations. Comparisons between ONE and wild-reared kiwi dispersal and mortality are included. Data were collected between 2001 and 2008 from observations of kiwi located during daytime hours. The data recorded included the grid reference, elevation, ground-cover type, forest type, physiography, and the type of roost site. The sample size for this study was significantly larger than for any previous studies thus enabling a greater confidence in estimated dispersal rates and dispersal distances, habitat selection and factors relating to mortality. All wild-reared kiwi displayed dispersal and were not philopatric to their natal area. Dispersal distances were found to be further than previously estimated, with the net distance of natal dispersal differing among age-classes, from an average of 834m (SE +/- 131) for kiwi chicks to 7,553m (SE = +/- 1167) for non-territorial adults. Female sub-adult kiwi dispersed further (7,215m) than male sub-adult kiwi (4,226m) (p = 0.04). The time taken to travel one km during natal dispersal ranged from an average of 131days/km (SE = +/- 9) for chicks to 89 days/km (SE = +/- 13) for sub-adults. Habitat selection has been observed in other studies on kiwi but not specifically for Coromandel North Island Brown Kiwi, and selection for ground-cover types by kiwi when roosting on the surface has never been previously studied. Roost site selection of kiwi differed among age-classes (p <0.001), between gender (p <0.001), and across elevations (p <0.001). Female kiwi were found more often in surface roosts (64%) than hole roosts (32%), and male kiwi were found at similar frequencies in holes (46%) and on the surface (47%). Sub-adults used holes to a greater extent as elevation increased, and selected for sub-alpine forest over broadleaf forest (p <0.001). This study is the first to recognise that selection of ground-cover types by kiwi differs among age-classes (p <0.001). Kiwi chicks were more often found on the surface under dead fern fronds and debris (39%) than other ground-cover types. The mortality rate was highest in chicks (33%), with predation responsible for 60% of these deaths; conservation management techniques were responsible for a further 20% of deaths; the remaining 20% of deaths were due to natural or unknown causes. Summer (December-February) was the season in which 81% of kiwi chick deaths occurred. The high proportion of deaths from monitoring techniques and the use of radio-transmitters (22%) indicates improvements need to be made to current management practices. ONE chicks were found to disperse shorter distances and had a greater mortality rate than wild-reared chicks. Therefore, recommendations are made for changes to ONE management practices. Further recommendations are made for the enhancement of kiwi habitat that could reduce kiwi mortality, and for increasing the habitat available to kiwi, thereby potentially increasing population sizes and/or densities.

Specialist and generalist phytoseiid mites are widely used for biological control of spider mites. Understanding dispersal attributes of these mites is important to implementing more stable, cost-efficient integrated pest management. In this regard, we studied dispersal of phytoseiid mites from a local ambulatory phase of movement within a prey patch to a longer-range phase that includes emigration (aerial take-off and dispersal distance) and immigration to a new plant. Specialist phytoseiids showed higher ambulatory and aerial dispersal than generalist species. Somewhat different dispersal strategies were seen between Neoseiulus fallacis (more specialized predator) and N. calfornicus (more generalized predator): The most important difference was earlier and continuous dispersal of N. californicus from a prey patch. Cues from spider mite infestation suppressed the dispersal rates for specialists, but either increased or did not change the dispersal rates for generalist phytoseiids. Aerodynamic calculations support the hypothesis that Phytoseiulus persimilis may not require a standing take-off behavior to become airborne. However, with less vertical profile, a mite may become airborne more by standing erect (N. fallacis), than a species that does not show standing take-off (N. calfornicus). Jumping behavior by P. persimilis was observed for the first time among Phytoseiidae. Falling speed ranged from 0.4 to 0.73 m/s for 13 phytoseiid species and 0.79 to 0.81 for two-spotted spider mite. These values were quite similar to theoretical estimates for specialist phytoseiids, but less for generalists. From falling speed estimates and other morphological data, it was possible to predict aerial dispersal distance of phytoseiids using analytical models. After landing on bare soil following aerial dispersal, high mortality of N. fallacis was observed in the field during summer. Distance from the landing point to target plants showed negative log linear relationships. Soil surfaces and management actions influenced survival and recovery. Environmental conditions greatly affected survival of the predator. We speculated that phytoseiids that fell on ground were moving to the target plants via both ambulatory and aerial means. / Graduation date: 2001

Managing cattle to disseminate seeds of desirable plants, or alternatively, to restrict weed seed contamination on rangelands is of interest to managers. Four experiments were conducted to determine effects of ruminant digestion on germination of ingested seeds. A number of plant species representing a variety of seed size and seed coat hardness were subjected to in vitro digestion. Experiment one was conducted to determine effect of varying lengths of digestion time on seed germination. Seed germination varied by plant species in response to length of digestion. Germination of large soft-coated seeds, such as bluebunch wheatgrass (Agropyron spicatum (Pursh) Scribn. & Smith Goldar) and basin wildrye (Elymus cinereus Scribn & Merril Magnar), was reduced to 0%. Smaller grass seeds, such as Sherman big bluegrass (Poa secunda Presl. Sherman), survived but germination declined following 24-hour, 48-hour, and 72-hour digestion. Experiment two examined effect of different stages of ruminant digestion on seed germination. The combination of Stage I (rumen-simulated digestion) and Stage II (abomasal-simulated digestion) resulted in greatest seed mortality. Two water treatments were included to evaluate the effects of high temperatures (39��C), moisture uptake, and lack of oxygen. Water + O��� and Water + CO��� reduced germination, however not as much as Stage I and Stage II treatments. The third experiment determined effects of diet quality on seed germination. Seeds digested in rumen fluid collected from steers fed a 72% corn concentrate diet resulted in 0% germination for all species. Grass seed germination was low for seeds digested in rumen fluid collected from steers fed a forage diet. Whitetop (Cardaria draba (L.) Hand.) germination was 24% and 28% for 35-hour and 59-hour roughage treatment, respectively, and germination was 0% for 35-hour and 59-hour concentrate treatments. Germination of water-only treatments for most species was reduced in comparison to the control treatment, but was greater than remaining treatments. Experiment four evaluated germination of seeds exposed to in situ versus in vitro digestion. In situ digestion resulted in lower seed germination than in vitro digestion for all species examined. Large, soft grass seeds may not be suitable candidates for reseeding rangelands. However, it is important for managers to recognize that cattle may distribute viable weed seeds in feces. Confining cattle or supplementing with high concentrate diets may help prevent spread of weedy species. / Graduation date: 1997

Gene flow dictates a broad range of ecological and evolutionary processes. Understanding the factors mediating magnitude and direction of gene flow is crucial for interpreting patterns of genetic diversity and for answering many kinds of biological questions. Recent advances at the interface of population genetics and GIS technology have expanded our perspective of the geographic and physical features influencing gene flow and, in turn, shaping genetic structure of populations. I investigated the effect of surface-level trade winds on genetic structure and gene flow in two species of phyllostomid bats in the Bahamas and Greater Antilles: Erophylla sezekorni (the buffy flower bat) and Macrotus waterhousii (Waterhouse's leaf-nosed bat). Bayesian Clustering Analysis revealed that all islands sampled represent independent genetic populations for M. waterhousii but not for E. sezekorni. Samples from 13 islands (spanning E. sezekorni?s range) clustered into five genetic populations and revealed the existence of two main clades (eastern: Hispaniola and Puerto Rico; western: Cuba, Jamaica, and Bahamas). To test the hypothesis that surface-level trade winds mediate gene flow in this system, I generated measures of effective distance between islands using anisotropic cost modeling based on wind data from the National Climactic Data Center. Both species exhibited significant isolation by distance with geographical distance and some of the measures of effective distance, but effective distance did not provide increased explanatory power in predicting distribution of genetic diversity. The IBDGEO slope was steeper for E. sezekorni than M. waterhousii, suggesting greater dispersal ability in the former species. According to Maximum Likelihood analysis, a majority (80%) of gene flow between genetic populations was asymmetric in both species. The degree of asymmetric gene flow between populations was not explained by the degree of asymmetry in effective distance or island area, indicating an unknown mechanism driving asymmetric gene flow. More information about the ecology of these taxa is required to understand the incidence of asymmetric gene flow in this system. The results of this study suggest that gene flow among islands is highly restricted for M. waterhousii and that this species deserves greater taxonomic attention and conservation concern.

This thesis focuses on the spatial structure and methods to identify spatial structure in plants. Methods that investigate genetic structure can mainly be divided into equilibrium methods that reveal summed dispersal over many generations, and cluster methods, that reveal more recent dispersal events. Depending on the spatial level, local or global, suitable methods are different. The thesis consists of four papers. The first explores the spatial genetic structure in two epiphytic bryophytes that have different dispersal strategies (Orthotrichum speciosum and O. obtusifolium) using three different approaches based on pairwise kinship coefficients assessed from AFLP data. The spatial kinship structure was detected with both autocorrelation analysis and generalized additive models, but linear regression failed to detect any structure in O. speciosum. In the second paper the spatial genetic structure in marginal populations of the forest tree Quercus robur is investigated at both local and regional scales. At the local scale, dispersal kernels as estimated using maximum likelihood parentage methods showed to be comparable to results acquired in central located populations. At the regional scale the degree of isolation at the margin of the distribution is shown. The third paper compares a number of sibship clustering methods. It was found that the performances of the sibship reconstruction algorithms are strongly dependent on fulfilling the assumptions of the model and that using an overly simple model produced very unreliable results. The amount of information included in the model affected the results; models including all the available information outperformed the models using only a subset of the information. In the last paper we show that the number of clusters as estimated by the software Structurama depends on sample size. At high number of subpopulations, the estimated number of clusters tends to be grossly underestimated when the number of sampled individuals per subpopulation is low.

I investigated the population attributes and habitat selection of mountain beaver (Aplodontia rufa) recolonizing clearcuts in the Coast Range mountains of Polk and Lincoln counties, Oregon between June 1989 and August 1990. The population characteristics of colonizing mountain beaver were evaluated in 12 stands of 3 types: 1-year-old clearcuts assumed to be inhabited entirely by immigrants, 4- to 5-year-old clearcuts inhabited by immigrants and their descendants, and 40- to 60-year-old forest stands assumed to support stable mountain beaver populations. Mountain beaver rapidly recolonized vacant habitat created by previous trapping efforts; after only 1 year, densities in clearcuts were statistically indistinguishable from forest sites (P = 0.7). Populations in 1-year-old clearcuts had more juveniles (P = 0.03) and had a female bias (P = 0.02) when compared with the predominantly adult male populations in the other two stand types. Individuals from clearcuts were heavier than those from forest sites (P < 0.05). Approximately half of the juvenile females in clearcuts reproduced; no juvenile females were found to be reproductively active in forest stands. Among juvenile females that conceived, those in 1-year-old clearcuts had larger litter sizes than those in 4- to 5-year-old clearcuts (P < 0.05). The 8 clearcuts were used to identify habitat features selected by recolonizing mountain beaver. Clearcuts were colonized irrespective of distances < 400 m from edge (R² = 0.01). Six habitat variables were selected by stepwise logistic regression model colonized versus non-colonized habitat. Mountain beaver selected areas with high amounts (<25-cm) and large (>25-cm) woody debris, forage plants, and uprooted stumps; they were likely to colonize areas that had highly penetrable (soft) soils and areas near drainages. The logistic function that included these 6 variables had a correct classification rate of 85% based on a jackknife procedure. Forest managers may find these habitat features useful in predicting mountain beaver recolonization and damage. / Graduation date: 1992

An improved ability to assess whether individuals have been added through immigration or natality and lost through emigration or mortality could alleviate several problems in population ecology. Fortunately, advances in stable isotope techniques now allow the movements of individuals to be retraced from tissue values and provide an opportunity to link information about the origins of individuals with demographic rates so that questions about the significance of dispersal can be assessed. I used such an approach by combining feather isotope information with demographic rates derived from capture-mark-recapture of individual mallards (Anas platyrhynchos) breeding in the Canadian aspen parklands, at multiple spatiotemporal scales, to answer questions about population persistence, settling patterns by dispersers, and the fitness of immigrant birds relative to residents.<p> Feather isotope (ä34S, äD, ä15N, and ä13C) values from an independent sample of flightless mallard ducklings sampled from across the mid-continent breeding range was used to validate an existing model used for origin assignments. Spatial resolution analysis within the mid-continent mallard breeding range generally showed a loss in prediction when attempting to assign individuals to more narrowly separated geographic origins among boreal, aspen parkland and prairie regions. For feather äD, spatial resolution may be limited by temporal patterns of local climatic events that produce variability in consumer tissue values. Thus, the use of multiple feather isotope signals would provide more reliable information about the origin of individuals for addressing questions about long-distance dispersal in yearling mallards.<p> Demographic rescue in an apparent population sink near Minnedosa, Manitoba, Canada, was due to elevated survival rates from a highly productive group of nesting female mallards using nest tunnels (i.e., an artificial nesting structure) and recruitment of yearling females having natal origins within the aspen parklands. There was little evidence that immigration by yearling females dispersing long-distances was important to annual population growth rates. Consistently high annual survival rates of adult females using nest tunnels lowered the recruitment rates needed for population stability. While tunnel-origin and within-region recruitment of yearling females were nearly equally important to local population growth rate, fine-scale limitations of isotopic origin assignments prevented further assessment of where recruits originated from within the aspen parkland region.<p> Factors related to breeding area settling patterns of yearling females are not well understood despite implications to local population dynamics. The likelihood that immigrant yearling females would settle in a parkland breeding area was positively correlated with local breeding-pair density and the amount of perennial nest cover, but was negatively correlated with the amount of wetlands. Although these relationships were not well estimated, they are most consistent a hypothesis that females were attracted to breeding sites by conspecific cues rather than avoidance. Immigrants comprised an average of 9% (range: 0 39% over 22 sites) of yearling recruits; most had natal origins in the U.S. prairie pothole region but a non-trivial number originated from the boreal forest, indicating a high degree of connectedness among breeding regions resulting from long-distance natal dispersal.<p> One of the most frequent explanations for strong site fidelity in breeding female ducks is that females benefit from site familiarity. However, evidence for differential reproductive success between immigrant and resident yearling females was weak, On sites with favourable wetland conditions and low breeding-pair densities immigrant females were more likely to breed and nest successfully than were residents whereas under opposite wetland and pair conditions, resident females were favoured. Thus, the costs and benefits of a natal dispersal decision seemed to vary with social context and environmental conditions, and further work is needed to clarify these processes.

An improved ability to assess whether individuals have been added through immigration or natality and lost through emigration or mortality could alleviate several problems in population ecology. Fortunately, advances in stable isotope techniques now allow the movements of individuals to be retraced from tissue values and provide an opportunity to link information about the origins of individuals with demographic rates so that questions about the significance of dispersal can be assessed. I used such an approach by combining feather isotope information with demographic rates derived from capture-mark-recapture of individual mallards (Anas platyrhynchos) breeding in the Canadian aspen parklands, at multiple spatiotemporal scales, to answer questions about population persistence, settling patterns by dispersers, and the fitness of immigrant birds relative to residents.<p> Feather isotope (ä34S, äD, ä15N, and ä13C) values from an independent sample of flightless mallard ducklings sampled from across the mid-continent breeding range was used to validate an existing model used for origin assignments. Spatial resolution analysis within the mid-continent mallard breeding range generally showed a loss in prediction when attempting to assign individuals to more narrowly separated geographic origins among boreal, aspen parkland and prairie regions. For feather äD, spatial resolution may be limited by temporal patterns of local climatic events that produce variability in consumer tissue values. Thus, the use of multiple feather isotope signals would provide more reliable information about the origin of individuals for addressing questions about long-distance dispersal in yearling mallards.<p> Demographic rescue in an apparent population sink near Minnedosa, Manitoba, Canada, was due to elevated survival rates from a highly productive group of nesting female mallards using nest tunnels (i.e., an artificial nesting structure) and recruitment of yearling females having natal origins within the aspen parklands. There was little evidence that immigration by yearling females dispersing long-distances was important to annual population growth rates. Consistently high annual survival rates of adult females using nest tunnels lowered the recruitment rates needed for population stability. While tunnel-origin and within-region recruitment of yearling females were nearly equally important to local population growth rate, fine-scale limitations of isotopic origin assignments prevented further assessment of where recruits originated from within the aspen parkland region.<p> Factors related to breeding area settling patterns of yearling females are not well understood despite implications to local population dynamics. The likelihood that immigrant yearling females would settle in a parkland breeding area was positively correlated with local breeding-pair density and the amount of perennial nest cover, but was negatively correlated with the amount of wetlands. Although these relationships were not well estimated, they are most consistent a hypothesis that females were attracted to breeding sites by conspecific cues rather than avoidance. Immigrants comprised an average of 9% (range: 0 39% over 22 sites) of yearling recruits; most had natal origins in the U.S. prairie pothole region but a non-trivial number originated from the boreal forest, indicating a high degree of connectedness among breeding regions resulting from long-distance natal dispersal.<p> One of the most frequent explanations for strong site fidelity in breeding female ducks is that females benefit from site familiarity. However, evidence for differential reproductive success between immigrant and resident yearling females was weak, On sites with favourable wetland conditions and low breeding-pair densities immigrant females were more likely to breed and nest successfully than were residents whereas under opposite wetland and pair conditions, resident females were favoured. Thus, the costs and benefits of a natal dispersal decision seemed to vary with social context and environmental conditions, and further work is needed to clarify these processes.