Bull trout are a fish species listed as threatened under the Endangered Species Act.Historically, they ranged from Northern California at the southernmost extent, into Canada at the northern most extent, and east into Nevada and Montana. Bull trout are highly migratory and require large, unfragmented habitats to persist and are thus highly susceptible to human induced land-use practices. The goal of my thesis was to obtain a better understanding of bull trout movement patterns in the Walla Walla River, Washington using complimentary techniques; Passive Integrated Transponder (PIT)technology and otolith microchemistry. PIT tags can be injected into a fish body cavity, similar to how pets are “chipped”, and as the fish swim through antennas placed in the river, their location and movements are be documented.Otolith microchemistry is a technique that is similar to analysis of tree rings. The otolith, a hard bony structure of a fish’s ear, develops over a lifetime and as the rings of the otolith are created the chemical signature in the water in which they live is recorded and can be compared to chemical makeup of water samples collected through the river system. Using these two techniques, I found that the age or size of a fish and the season are important factors to explain both a fish’s movements and where in the river a fish might be located at a given time. Knowing at what size, age and season a fish is attempting to migrate allows managers to provide the best possible river conditions (e.g., temperatures, flow) to allow for unimpeded migrations to occur and to foster conservation and recovery of bull trout populations.

Freshwater mussels have played an important role in the history of human culture and also in ecosystem functioning. But during the past several decades, the abundance and diversity of mussel species has declined all over the world. To address the urgent need to maintain and restore populations of endangered freshwater mussels, quantitative population dynamics modeling is needed to evaluate population status and guide the management of endangered freshwater mussels. One endangered mussel species, the oyster mussel (Epioblasma capsaeformis), was selected to study its population dynamics for my research. The analysis was based on two datasets, length frequency data from annual surveys conducted at three sites in Clinch River: Wallen Bend (Clinch River Mile 192) from 2004-2010, Frost Ford (CRM 182) from 2005 to 2010 and Swan Island (CRM 172) from 2005 to 2010, and age-length data based on shell thin-sections. Three hypothetical scenarios were assumed in model estimations: (1) constant natural mortality; (2) one constant natural mortality rate for young mussels and another one for adult mussels; (3) age-specific natural mortality. A Bayesian approach was used to analyze the age-structured models and a Bayesian model averaging approach was applied to average the results by weighting each model using the deviance information criterion (DIC). A risk assessment was conducted to evaluate alternative restoration strategies for E. capsaeformis. The results indicated that releasing adult mussels was the quickest way to increase mussel population size and increasing survival and fertility of young mussels was a suitable way to restore mussel populations in the long term. The population of E. capsaeformis at Frost Ford had a lower risk of decline compared with the populations at Wallen Bend and Swan Island. Passive integrated transponder (PIT) tags were applied in my fieldwork to monitor the translocation efficiency of E. capsaeformis and Actinonaias pectorosa at Cleveland Islands (CRM 270.8). Hierarchical Bayesian models were developed to address the individual variability and sex-related differences in growth. In model selection, the model considering individual variability and sex-related differences (if a species has sexual dimorphism) yielded the lowest DIC value. The results from the best model showed that the mean asymptotic length and mean growth rate of female E. capsaeformis were 45.34 mm and 0.279, which were higher than values estimated for males (42.09 mm and 0.216). The mean asymptotic length and mean growth rate for A. pectorosa were 104.2 mm and 0.063, respectively. To test for the existence of individual and sex-related variability in survival and recapture rates, Bayesian models were developed to address the variability in the analysis of the mark-recapture data of E. capsaeformis and A. pectorosa. DIC was used to compare different models. The median survival rates of male E. capsaeformis, female E. capsaeformis and A. pectorosa were high (>87%, >74% and >91%), indicating that the habitat at Cleveland Islands was suitable for these two mussel species within this survey duration. In addition, the median recapture rates for E. capsaeformis and A. pectorosa were >93% and >96%, indicating that the PIT tag technique provided an efficient monitoring approach. According to model comparison results, the non-hierarchical model or the model with sex--related differences (if a species is sexually dimorphic) in survival rate was suggested for analyzing mark-recapture data when sample sizes are small. / Master of Science

Doctor of Philosophy / Department of Biology / Donald W. Kaufman / Glennis A. Kaufman / Little is known about nightly activity patterns of nocturnal small mammals under natural conditions, and how these activity patterns might be affected by photoperiod, season, and sex, age, and reproductive status of individuals. The main objectives of this research were: 1) to find an appropriate method for marking individual deer mice (Peromyscus maniculatus) so that their activity could be monitored remotely; 2) to design a portable activity-monitoring system to investigate temporal patterns of shelter use by deer mice under natural conditions; 3) to determine the influence of environmental conditions such as photoperiod and season on nightly activity of deer mice; and 4) to compare effects of demographic or physiological factors such as sex, age, and reproductive status on nightly activity of deer mice at artificial burrows in tallgrass prairie. In general, commencement of activity was correlated positively with timing of sunset, and time of retirement to the burrow was correlated positively with sunrise. Among adults, males first emerged from the burrow earlier and made more trips of shorter duration in a night than did females, although total duration of trips was similar. Return visits and subsequent stays typically were shorter for males than females, but total time spent in the burrow and retirement time relative to sunrise were similar for both sexes. Young deer mice emerged significantly later, made more trips of shorter duration, spent less total time outside, and retired to their burrow earlier than adults. Reproductive females emerged later, made fewer trips of generally longer duration, and spent shorter total amounts of time away from the burrow each night than non-reproductive females. Return visits of reproductive females were of longer duration than non-reproductives, but total time spent inside and time of retirement for the night did not differ relative to reproductive status. From parturition through lactation, activity of females showed a number of directional trends. Results suggest that under natural conditions, activity patterns of deer mice are highly variable but responsive to both the changing physical environment and internal conditions related to sex-specific maximization of fitness.

The freshwater pearl mussel Margaritifera margaritifera is an endangered bivalve which is usually regarded as sedentary, although individual movement has been observed both vertically and horizontally. Little is known about the causes and rates of mussel movement. The objective of this study was to test the effect of microhabitat characteristics on the horizontal movement distance and rates of freshwater pearl mussels. A total of 120 mussels (length range 40–59 mm) were marked individually with passive integrated transponder tags, placed in stream microhabitats differing in their sediment composition and monitored biweekly over a period of 10 weeks. Mussels situated in sand-dominated habitats had a significantly higher mean movement rate (3.2 ± 4.2 cm/day, mean ± SD) than mussels situated in gravel-dominated (1.9 ± 2.7 cm/day) or stone-dominated habitats (1.8 ± 3.2 cm/day). The direction of the movements appeared random; however, an emigration from sandy habitats was observed, probably to avoid dislodgment from these hydraulically unstable habitats. This study demonstrates that freshwater pearl mussels can actively emigrate from unsuitable microhabitats. Once suitable streams with respect to physical, chemical, and biological quality were identified, it is therefore only necessary to identify suitable mesohabitats (area of 10–30 m²) when reintroducing or relocating mussels.

Submitted by Edineia Teixeira (edineia.teixeira@unioeste.br) on 2018-04-13T14:51:51Z No. of bitstreams: 2 Carola_Gutfreund2017.pdf: 2632451 bytes, checksum: 73a0a3864936cf1f3347866fcda5f49f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-04-13T14:51:51Z (GMT). No. of bitstreams: 2 Carola_Gutfreund2017.pdf: 2632451 bytes, checksum: 73a0a3864936cf1f3347866fcda5f49f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-04-18 / Large hydroelectric dams along the Paraná River have caused severe impacts on fish communities as they represent obstacles to long-range migratory species that need to migrate to complete their life cycle. Dams can bring numerous problems through the interception of migratory routes and reduction of spawning areas. The most common measures used to mitigate the effect of these physical obstacles is the implementation of fish ladders. It is not only important to implement these structures, but also to monitor them. This study was performed at the Engenheiro Sergio Motta Hydroelectric Power plant in the Upper Paraná River during December/2012 and March/2016. The aim of it was to evaluate the effectiveness of this structure in relation to the attractiveness rate and passage efficiency of to two Neotropical fish species in the fish ladder. In total, 563 fish of genus Leporinus (447 Leporinus obtusidens and 116 Leoporinus piavussu) were tagged and released with the implementation of 32-mm programmable transponders (PIT-tags). Radio Frequency Identification (RFID) was used to monitor the system. The attractiveness of the ladder was 8.7%. The minimum time to find it was 1.49 days for the fish released upstream and the maximum time was 449.86 days for the individuals released downstream. The release site had a significant influence on the entry rate of fish released on the other side of the river. No detection was observed for fish released downstream and upstream on the right bank of the river. Only the fish released on the same site where the fish ladder is located were detected, suggesting low attractiveness of the ladder in relation to the studied species. In the course of this study it was verified that for the two species studied it would be extremely important to increase the attractiveness at the entrance of the ladder, as well as to build a second ladder for fish on the right side of the river. / As grandes hidrelétricas ao longo do Rio Paraná têm causado impactos severos nas comunidades de peixes, pois representam obstáculos para as espécies migradoras de longa distância, que precisam migrar para completar seu ciclo de vida. As barragens podem trazer inúmeros problemas por meio da intercepção das rotas migratórias e redução das áreas de desova. As medidas mais comuns utilizadas para mitigar o efeito desses obstáculos físicos é a implementação de escadas para peixes. Não é somente importante a implementação dessas estruturas, como também o monitoramento. Esse estudo realizado na escada para peixes da Usina Hidrelétrica Engenheiro Sérgio Motta no alto Rio Paraná no período de dezembro/2012 a março/2016 teve como objetivo avaliar a efetividade dessa estrutura em relação a taxa de atratividade e eficiência de passagem para duas espécies de peixes migradores neotropicais. No total, foram marcados e liberados 563 peixes do gênero Leporinus (447 Leporinus obtusidens e 116 Leoporinus piavussu) com a implantação de transponders com códigos programáveis (PIT-tags) de 32 mm. Foi utilizado o sistema de rádio frequência (RFID Radio Frequency Identification) para o monitoramento do sistema. A atratividade da escada foi de 8,7%. O tempo mínimo para encontrar a escada correspondeu a 1,49 dias para os peixes liberados a montante e o tempo máximo foi de 449,86 dias para os indivíduos liberados a jusante. O local de liberação influenciou significativamente a taxa de entrada dos peixes liberados na margem oposta do rio, sendo que nenhuma detecção foi observada para peixes liberados na margem direita, tanto a jusante como a montante. Foram detectados apenas os peixes liberados na mesma margem onde a escada para peixes está localizada, sugerindo baixa atratividade da escada para as espécies analisadas. No decorrer deste estudo verificou-se que para as duas espécies estudadas seria extremamente importante aumentar a atratividade na entrada da escada, como também a construção de uma segunda escada para peixes no lado direito do rio.

Freshwater mussels (Unionidae) in the United States have experienced dramatic declines, and 25% species are listed as federally endangered. Hence, recovery plans for endangered species proposed a strategy of propagation of young mussels for release to natal rivers to augment declining populations. In this study, I conducted laboratory experiments, assessed site suitability for mussel restoration, and evaluated survival and growth rates of released mussels to meet the requirements of recovery plan. I conducted multiple experiments to develop an improved protocol for juvenile mussel propagation and culture. Significantly greater survival and growth rates were found in newly metamorphosed juveniles of the rainbow mussel (Villosa iris) reared in a substrate of fine sediment and one-month-old juveniles of wavy-rayed lampmussel (Lampsilis fasciola) fed on natural food in pond water. Bio-filter media greatly increased water quality by reducing the concentration of ammonia and nitrite. The negative impacts of flatworm predation and filamentous algae in juvenile culture were controlled, and juvenile escapement was prevented. Juvenile mussels were successfully produced and cultured to stockable size (>15 mm) for release. I released laboratory-propagated mussels at three historically important sites in Clinch and Powell rivers for the assessment of site suitability. Use of cages was the most effective method to determine site suitability because the free-released mussels (untagged, tagged) had low catchability. Mussels released at Horton Ford, Clinch River, exhibited significantly faster growth. Horton Ford is the most suitable site, while environmental conditions at Fugate Ford, Powell River, are deemed unsuitable for mussel restoration and recovery. To facilitate the detection of released mussels, I applied Passive Integrated Transponder tags to laboratory-produced juveniles of the endangered Cumberlandian combshell (Epioblasma brevidens) and released them near Brooks Bridge, Powell River. The detection probability increased above 98%. I developed a set of hierarchical Bayesian models incorporating individual variations, seasonal variations, periodic growth stages and growth cessation to estimate survival, detection probability and growth of released mussels in a changing environment. Mussels of E. brevidens exhibited great survival (> 99% per month) and growth, indicating suitable conditions for recovery of this endangered species at this site. / Ph. D.

The Staunton River is a high gradient, second order stream approximately 6 km in length located on the eastern slope of the Blue Ridge Mountains in Shenandoah National Park, VA. In June 1995, a catastrophic flood and debris flow altered the instream habitat and <i>Salvelinus fontinalis</i> population of the Staunton River. The debris flow scoured the streambed, deposited new substrate materials, removed trees from the riparian zone, and eliminated fish from a 1.9km section of the stream. By June 1998, both young-of-year (YOY) and age 1+ <i>S. fontinalis</i> had recolonized the debris flow affected area. The event provided a rare opportunity to examine recovery of the <i>S. fontinalis</i> population and instream habitat in addition to addressing potential effects of the debris flow on movement, activity, and growth of fish in the debris flow affected and unaffected areas of the stream. Post-recolonization movement and activity were monitored using two-way fish traps (weirs), mark-recapture techniques, and radio telemetry. The weirs failed to produce any movement data. Most fish (91%) in the mark-recapture study had range sizes less than 100m, however biases common to mark-recapture study designs (low recapture rate, flawed logic, etc.) hampered interpretation of results. For example, subsequent recapture of individually marked fish indicated that as many as 54% of marked fish confirmed to have been alive at the time of a recapture session were not recaptured. Radio telemetry provided information on <i>S. fontinalis</i> movement and activity at seasonal and diel scales during summer and fall. Differences in movement and activity between the debris flow affected and unaffected areas were minimal when compared to seasonal variations. During summer, range sizes were near 0m and crepuscular activity patterns were observed. During the fall range size increased and diel activity was concentrated in the mid-afternoon with a much higher peak than during summer. Basin-wide visual estimation technique (BVET) fish population surveys performed each spring and fall from 1993 = 1999 provided pre- and post-event fish population abundance and density estimates. Post-event fish growth in the debris flow affected and unaffected areas was monitored using mark-recapture techniques. Abundance and density of both YOY and age 1+ <i>S. fontinalis</i> exceeded pre-event levels within 2-3 years. Growth of YOY and age 1+ fish was significantly greater in the debris flow affected area until spring 1999. Population density appeared to have a strong negative influence on growth. The observed changes in fish growth and differences in fish size associated with population density would be of minimal importance to the typical angler but may suggest a mechanism by which <i>S. fontinalis</i> populations can quickly recover from catastrophic events. BVET habitat surveys provided information on total stream area, number of pools and riffles, pool and riffle surface area and depth, substrate composition, and large woody debris (LWD) before (1993), immediately following (1995), and four years post-event (1999). Immediately following the debris flow, the stream channel was highly disordered which resulted in an increase in the total number of habitat units and a decrease in average habitat unit surface area, total stream area, and average depth when compared with pre-event conditions. In addition, substrate composition had shifted from small to large diameter particles and LWD loading had increased in both debris flow affected and unaffected areas. Four years after the event, the total number of habitat units, average habitat unit surface area, total stream area, and average depth had all returned to near pre-debris flow levels and substrate composition had begun to shift towards smaller particle sizes. Changes in LWD loading from 1995-1999 reflected changes in the riparian zone following the debris flow. In the unaffected area, where riparian trees remained intact, LWD loading increased, whereas in the debris flow affected area, where riparian trees were eliminated, LWD loading decreased. For the most part the effects of the debris flow, although immediately dramatic, were in the long term minimal. The debris flow affected area was recolonized rapidly and abundance and density quickly rebounded past pre-event levels. Differences in fish growth between the affected and unaffected area were short lived. Any effect the debris flow affected area may have had on movement or activity was minimal when compared with seasonal variations. Most habitat characteristics reverted to near pre-event levels just four years after the flood and debris flow. Although a number of factors will influence recovery time from such events, these results indicate that immediate management action, such as stocking or habitat modifications, are not necessary in all cases. / Master of Science

Migration occurs among many animal species for the purpose of, among other things, finding food or to reproduce. Spawning migration is a form of migration that occurs among many fish species where they move to another site for reproduction. The movement can be obstructed by migration barriers like road culverts. Barriers to migration pose one of the greatest threats to biodiversity and ecosystem functions in freshwater. They impair the connectivity of watercourses and may prevent fish from improving reproductive success or completing their life histories altogether. There are both benefits and costs with migration, benefits such as increased survival for the adults and offspring, and costs such as increased energy consumption and increased mortality. The costs are often dependent on the morphological traits of the individual, like body shape and size. In this study, the spawning migration of two species of fish of the family Cyprinidae, ide (Leuciscus idus) and roach (Rutilus rutilus) was investigated. Few studies have been made on ide or on roach compared to other cyprinids and salmonids. This study might therefore enhance the overall knowledge of these two species. The overall aims of this project are to study and compare phenotypic correlates of spawning migration behaviour of ide and roach. The field studies were performed in Oknebäcken, Mönsterås (SE632310-152985), Sweden in March and April 2020. To describe the watercourse and define the location and characteristics of different potential migration barriers, a simplified biotope mapping method was used. The fish were caught in a hoop net and then measured, weighted, sexed, and injected with passive integrated transponder using the bevel down method. In order to register in stream movement of fish, reading stations with antennas were placed, at two locations upstream from the marking station and one downstream at the estuary. The sex ratio differed from the expected 1:1 with a majority of females for both species. This might be a result of fluctuations in survival of spawn coupled with different age-at-maturity between sexes. We found that individuals that arrived early to the stream were larger for both study species, as other studies also reported. Also, male ide was both larger and arrived before female ide. There might be an energy cost associated with early arrival to the stream and therefore, larger individuals arrive first. For roach, there was no difference in arrival time between the sexes although female roach were larger. There was no difference in the time spent in the stream between the species. For ide, females stayed for a longer period of time in the stream than males. However, the opposite was true for roach. This may be because male roach might benefit from more fertilization events when staying longer. There might therefore be a trade-off between the energy cost in staying in the stream and the increased fitness advantage in fertilization events. We found no correlation between any of the morphological traits and migration distance. However, since very few individuals were registered at the upstream reading stations, there might be an effect of migration barriers on the spawning migration. The mortality after spawning was higher for roach than for ide. For ide, a larger proportion of females than males died. For roach, individuals that arrived early was classified as alive to a greater extent than those who arrived late. Both similarities and differences between the species were discovered in this study which concludes that even closely related species might differ substantially from each other.

Thesis by publication -- 8 co-authored articles. / Thesis (PhD)--Macquarie University, Division of Environmental and Life Sciences, Department of Biological Sciences. / Includes bibliographical references. / Preface -- Management issues of urban common brushtail possums (Trichosurus vulpecula): a loved or hated neighbour -- Effects of deslorelin implants on reproduction in the common brushtail possum (Trichosurus vulpecula) -- Brushtail possums (Trichosurus vulpecula) in metropolotan Sydney: population biology and response to contraceptive implants -- Strategic survey for Toxoplasma gondii and Neospora caninum in the common brushtail possum (Trichosurus vulpecula) from urban Sydney, Australia -- Leptospirosis serology in the common brushtail possum (Trichosurus vulpecula) from urban Sydney, Australia -- Conclusions. / The common brushtail possum (Trichosurus vulpecula) is indeed a common inhabitant of many Australian citites, and one of the few marsupials that has adapted well to the urban environment. Their close proximity to people provides a great opportunity to experience native wildlife in the backyard, however, their utilization of house roofs, bold behaviour and appetite for garden plants often leads to conflict with householders. Population numbers are sufficiently high to require ongoing management to minimise negative impacts for humans and brushtail possums alike in a socially acceptable manner. The aim of this thesis was to identify current management issues and address the need for improved and novel management strategies. The potential of slow-release implants, containing the GnRH agonist deslorelin, as a contraceptive agent for brushtail possums was tested on a captive population. Males appeared resistant to treatment, but deslorelin was found to inhibit reproduction in female brushtail possums for at least one breeding season, making it a promising tool to control fertility in some wild populations. A further aim was to trial deslorelin implants on a wild urban population, to collect more information about the urban biology of this species and to point out issues which have previously not been addressed. Close proximity and interaction of urban brushtail possums with humans and their domestic animals can increase the risk of disease exposure and transmission and influence the health of wild populations. Serosurveys showed that animals were readily exposed to Leptospira spp. and Toxoplasma gondii. This thesis also provides the first data on brushtail possum dispersal in urban areas, knowledge which is highly relevant to the development of management strategies such as fertility control. The findings from this research broaden our knowledge about urban brushtail possums and should assist wildlife authorities in developing alternative or improved management procedures. / Mode of access: World Wide Web. / xxv, 287 p. ill., maps