Estimation of vertical groundwater fluxes into a streambed through continuous temperature profile monitoring and the relationship of groundwater fluxes to coaster brook trout spawning habitat

We hypothesized that the spatial distribution of groundwater inflows through river bottom sediments is a critical factor associated with the selection of coaster brook trout (a life history variant of Salvelinus fontinalis,) spawning sites. An 80-m reach of the Salmon Trout River, in the Huron Mountains of the upper peninsula of Michigan, was selected to test the hypothesis based on long-term documentation of coaster brook trout spawning at this site. Throughout this site, the river is relatively similar along its length with regard to stream channel and substrate features. A monitoring well system consisting of an array of 27 wells was installed to measure subsurface temperatures underneath the riverbed over a 13-month period. The monitoring well locations were separated into areas where spawning has and has not been observed. Over 200,000 total temperature measurements were collected from 5 depths within each of the 27 monitoring wells. Temperatures within the substrate at the spawning area were generally cooler and less variable than river temperatures. Substrate temperatures in the non-spawning area were generally warmer, more variable, and closely tracked temporal variations in river temperatures. Temperature data were inverted to obtain subsurface groundwater velocities using a numerical approximation of the heat transfer equation. Approximately 45,000 estimates of groundwater velocities were obtained. Estimated velocities in the spawning and non-spawning areas confirmed that groundwater velocities in the spawning area were primarily in the upward direction, and were generally greater in magnitude than velocities in the non-spawning area. In the non-spawning area there was a greater occurrence of velocities in the downward direction, and velocity estimates were generally lesser in magnitude than in the spawning area. Both the temperature and velocity results confirm the hypothesis that spawning sites correspond to areas of significant groundwater influx to the river bed.

The Effects of Smolt Stocking Strategies on Migratory Path Selection of Adult Atlantic Salmon in the Penobscot River, Maine

Understanding the homing behavior of Atlantic salmon Salmo salar is vital to the restoration program employed on the Penobscot River, Maine. To produce significant adult returns, managers currently stock hatchery-raised smolts in specific river sections, providing smolts the opportunity to imprint on chemical signals and enabling their return to productive spawning and rearing habitat as adults. In this study, we used observational evidence from passive integrated transponder telemetry to determine whether adults returning from smolt stockings behaved in a way that suggested strong homing to smolt stocking locations. Adults returning from smolt stocking locations located in or at the mouth of the Piscataquis River were more likely to be detected as entering the Piscataquis River than were adults returning from the upper Penobscot River smolt stocking locations. In general, returning adult Atlantic salmon that had been stocked near or in tributaries as smolts chose a path more quickly than those that had been stocked in more downstream or main-stem locations. These results suggest that Atlantic salmon smolts should be stocked at specific sites with superior habitat for spawning kind juvenile survival to capitalize on the strong homing tendency in adults. This technique call also be utilized to allow for natural selection and the development of localized stocks.

Evolution of the Riparian forest corridor in a large Mediterranean river system

The well-documented re-colonisation of the French large river basins of Loire and Rhone by European otter and beaver allowed the analysis of explanatory factors and threats to species movement in the river corridor. To what extent anthropogenic disturbance of the riparian zone influences the corridor functioning is a central question in the understanding of ecological networks and the definition of restoration goals for river networks. The generalist or specialist nature of target species might be determining for the responses to habitat quality and barriers in the riparian corridor. Detailed datasets of land use, human stressors and hydro-morphological characteristics of river segments for the entire river basins allowed identifying the habitat requirements of the two species for the riparian zone. The identified critical factors were entered in a network analysis based on the ecological niche factor approach. Significant responses to riparian corridor quality for forest cover, alterations of channel straightening and urbanisation and infrastructure in the riparian zone are observed for both species, so they may well serve as indicators for corridor functioning. The hypothesis for generalists being less sensitive to human disturbance was withdrawn, since the otter as generalist species responded strongest to hydro-morphological alterations and human presence in general. The beaver responded the strongest to the physical environment as expected for this specialist species. The difference in responses for generalist and specialist species is clearly present and the two species have a strong complementary indicator value. The interpretation of the network analysis outcomes stresses the need for an estimation of ecological requirements of more species in the evaluation of riparian corridor functioning and in conservation planning.

Brown trout redd superimposition in relation to spawning habitat availability

The relationship between redd superimposition and spawning habitat availability was investigated in the brown trout (Salmo trutta L.) population inhabiting the river Castril (Granada, Spain). Redd surveys were conducted in 24 river sections to estimate the rate of redd superimposition. Used and available microhabitat was evaluated to compute the suitable spawning habitat (SSH) for brown trout. After analysing the microhabitat characteristics positively selected by females, SSH was defined as an area that met all the following five requirements: water depth between 10 and 50 cm, mean water velocity between 30 and 60 cm s)1, bottom water velocity between 15 and 60 cm s)1, substrate size between 4 and 30 mm and no embeddedness. Simple regression analyses showed that redd superimposition was not correlated with redd numbers, SSH or redd density. A simulation-based analysis was performed to estimate the superimposition rate if redds were randomly placed inside the SSH. This analysis revealed that the observed superimposition rate was higher than expected in 23 of 24 instances, this difference being significant (P menor que 0.05) in eight instances and right at the limit of statistical significance (P = 0.05) in another eight instances. Redd superimposition was high in sections with high redd density. High superimposition however was not exclusive to sections with high redd density and was found in moderate- and low-redd-density sections. This suggests that factors other than habitat availability are also responsible for redd superimposition. We argue that female preference for spawning over previously excavated redds may be the most likely explanation for high superimposition at lower densities.

Spawning and habitat management in salmonid populations at the southern edge of their natural ranges = Reproducción y gestión del hábitat en poblaciones de salmónidos en el extremo meridional de sus distribuciones naturales

Las poblaciones de salmónidos en la Península Ibérica (trucha común, Salmo trutta; y salmón atlántico, Salmo salar) se encuentran cerca del límite meridional de sus distribuciones naturales, y por tanto tienen una gran importancia para la conservación de estas especies. En la presente Tesis se han investigado algunos aspectos de la reproducción y de la gestión del hábitat, con el objeto de mejorar el conocimiento acerca de estas poblaciones meridionales de salmónidos. Se ha estudiado la reproducción de la trucha común en el río Castril (Andalucía, sur de España), donde se ha observado que la freza ocurre desde diciembre hasta abril con el máximo de actividad en febrero. Este hecho representa uno de los periodos reproductivos más tardíos y con mayor duración de toda la distribución natural de la especie. Además, actualmente se sabe que el resto de poblaciones andaluzas tienen periodos de reproducción similares (retrasados y extendidos). Análisis en la escala de la distribución natural de la trucha común, han mostrado que la latitud explica parcialmente tanto la fecha media de reproducción (R2 = 62.8%) como la duración del periodo de freza (R2 = 24.4%) mediante relaciones negativas: a menor latitud, la freza ocurre más tarde y durante más tiempo. Es verosímil que un periodo de freza largo suponga una ventaja para la supervivencia de las poblaciones de trucha en hábitats impredecibles, y por tanto se ha propuesto la siguiente hipótesis, que deberá ser comprobada en el futuro: la duración de la freza es mayor en hábitats impredecibles que en aquellos más predecibles. La elevada tasa de solapamiento de frezaderos observada en el río Castril no se explica únicamente por una excesiva densidad de reproductores. Las hembras de trucha eligieron lugares específicos para construir sus frezaderos en vez de dispersarse aleatoriamente dentro del hábitat adecuado para la freza que tenían disponible. Estas observaciones sugieren que las hembras tienen algún tipo de preferencia por solapar sus frezaderos. Además, en ríos calizos como el Castril, las gravas pueden ser muy cohesivas y difíciles de excavar, por lo que el solapamiento de frezaderos puede suponer una ventaja para la hembra, porque la excavación en sustratos que han sido previamente removidos por frezas anteriores requerirá menos gasto de energía que en sustratos con gravas cohesivas que no han sido alteradas. Por tanto, se ha propuesto la siguiente hipótesis, que deberá ser comprobada en el futuro: las hembras tienen una mayor preferencia por solapar sus frezaderos en ríos con sustratos cohesivos que en ríos con sustratos de gravas sueltas. En el marco de la gestión del hábitat, se han empleado dos enfoques diferentes para la evaluación del hábitat físico, con el objeto de cuantificar los cambios potenciales en la disponibilidad de hábitat, antes de la implementación real de determinadas medidas sobre el hábitat. En primer lugar, se ha evaluado el hábitat físico del salmón atlántico en el río Pas (Cantabria, norte de España), en la escala del microhábitat, empleando la metodología IFIM junto con un modelo hidráulico bidimensional (River2D). Se han simulado una serie de acciones de mejora del hábitat y se han cuantificado los cambios en el hábitat bajo estas acciones. Los resultados mostraron un aumento muy pequeño en la disponibilidad de hábitat, por lo que no sería efectivo implementar estas acciones en este tramo fluvial. En segundo lugar, se ha evaluado el hábitat físico de la trucha común en el río Tajuña (Guadalajara, centro de España), en la escala del mesohábitat, empleando la metodología MesoHABSIM. Actualmente, el río Tajuña está alterado por los usos agrícolas de sus riberas, y por tanto se ha diseñado una restauración para mitigar estos impactos y para llevar al río a un estado más natural. Se ha cuantificado la disponibilidad de hábitat tras la restauración planteada, y los resultados han permitido identificar los tramos en los que la restauración resultaría más eficaz. ABSTRACT Salmonid populations in the Iberian Peninsula (brown trout, Salmo trutta; and Atlantic salmon, Salmo salar) are close to the southern limit of their natural ranges, and therefore they are of great importance for the conservation of the species. In the present dissertation, some aspects of spawning and habitat management have been investigated, in order to improve the knowledge on these southern salmonid populations. Brown trout spawning have been studied in the river Castril (Andalusia, southern Spain), and it has been observed that spawning occurs from December until April with the maximum activity in February. This finding represents one of the most belated and protracted spawning periods within the natural range of the species. Furthermore, it is now known that the rest of Andalusian populations show similar (belated and extended) spawning periods. Broad-scale analyses throughout the brown trout natural range showed that latitude partly explained both spawning mean time (R2 = 62.8%) and spawning duration (R2 = 24.4%) by negative relationships: the lower the latitude, the later the spawning time and the longer the spawning period. It is plausible that a long spawning period would be an advantage for survival of trout populations in unpredictable habitats, and thus the following hypothesis has been proposed, which is yet to be tested: spawning duration is longer in unpredictable than in predictable habitats. High rate of redd superimposition observed in the river Castril was not only caused by high density of spawners. Trout females chose specific sites for redd construction instead of randomly dispersing over the suitable spawning habitat. These observations suggest that female spawners have some kind of preference for superimposing redds. Moreover, in limestone streams such as Castril, unused gravels can be very cohesive and hard to dig, and thus redd superimposition may be an advantage for female, because digging may require less energy expenditure in already used redd sites than in cohesive and embedded unused sites. Hence, the following hypothesis has been proposed, which is yet to be tested: females have a higher preference for superimposing redds in streambeds with cohesive and embedded substrates than in rivers with loose gravels. Within the topic of habitat management, two different approaches have been used for physical habitat assessment, in order to quantify the potential change in habitat availability, prior to the actual implementation of proposed habitat measures. Firstly, physical habitat for Atlantic salmon in the river Pas (Cantabria, northern Spain) has been assessed at the microhabitat scale, using the IFIM approach along with a two dimensional hydraulic model (River2D). Proposed habitat enhancement actions have been simulated and potential habitat change has been quantified. Results showed a very small increasing in habitat availability and therefore it is not worth to implement these measures in this stream reach. Secondly, physical habitat for brown trout in the river Tajuña (Guadalajara, central Spain) has been assessed at the mesohabitat scale, using the MesoHABSIM approach. The river Tajuña is currently impacted by surrounding agricultural uses, and thus restoration was designed to mitigate these impacts and to drive the river to a more natural state. Habitat availability after the planned restoration has been quantified, and the results have permitted to identify in which sites the restoration will be more effective.

The Rio Salado Riparian Habitat Restoration Area: Managing the Southwestern Willow Flycatcher

The following document identifies the impact to the current management plan of the Rio Salado Riparian Habitat Restoration Area in the event the endangered Southwestern Willow Flycatcher is found nesting at the project site. Rio Salado is managed by the City of Phoenix Parks and Recreation Department, and consists of a low-flow channel with native vegetation and wildlife along the Salt River. This paper analyzes the regulatory responsibilities of project site management and discusses the necessary adjustments to the management plan. Despite the current absence of the Southwestern Willow Flycatcher from Rio Salado, management should enter into a Safe Harbor Agreement with the U.S. Fish and Wildlife Service to legally protect themselves from the regulations stipulated in the Endangered Species Act.

Sustainability in the Upper Colorado River Basin: A Struggle Between Water Resource Use and Remnants of the Natural Ecosystem

This study evaluated whether development of the Colorado River system has exceeded sustainability by comparing the trends in water use in the Colorado River. Two sustainable areas were identified in the upper basin and one in the lower-- the mainstream Colorado River, Green and Yampa rivers, and the Little Colorado River. These areas are also high priority recovery areas for four endangered fishes and protected by critical habitat provisions of the ESA. Unfortunately, the endangered fishes are declining because of habitat destruction and non-native species. If increasing water demand causes the fishes to go extinct the few sustainable areas will be lost. It will take careful management of the endangered fishes and water users to ensure these areas are maintained.

Quantifying riparian habitat for wildlife in the Vermilion Basin : an evaluation of the Illinois stream information system and other geographic data for statewide classification of riparian habitat /

"This one-year project was designed to assess the feasibility of using the information contained in the Illinois Stream Information System (ISIS), in conjunction with the Illinois Geographic Information System (IGIS), to evaluate the riparian habitat for wildlife in the Vermilion River Basin." -- pg. 4.

Surface Elevation Change Processes in the Snohomish River Estuary, Washington

Estuaries provide crucial ecosystem functions and contain significant socio-economic value. Within Washington State, estuaries supply rearing habitat for juvenile salmon during their transition period from freshwater to open sea. In order to properly manage wetland resources and restore salmon habitat, the mechanisms through which estuaries evolve and adapt to pressures from climate change, most notably eustatic sea level rise, must be understood. Estuaries maintain elevation relative to sea level rise through vertical accretion of sediment. This report investigates the processes that contribute to local surface elevation change in the Snohomish Estuary, conveys preliminary surface elevation change results from RTK GPS monitoring, and describes how surface elevation change will be monitored with a network of RSET-MH’s. Part of the tidal wetlands within the Snohomish River Estuary were converted for agricultural and industrial purposes in the 1800’s, which resulted in subsidence of organic soils and loss of habitat. The Tulalip Tribes, the National Oceanic and Atmospheric Administration (NOAA), Northwest Indian Fisheries Commission (NWIFC), and the Environmental Protection Agency (EPA) are conducting a large-scale restoration project to improve ecosystem health and restore juvenile salmon habitat. A study by Crooks et al. (2014) used 210Pb and carbon densities within sediment cores to estimate wetland re-building capacities, sediment accretion rates, and carbon sequestration potential within the Snohomish Estuary. This report uses the aforementioned study in combination with research on crustal movement, tidal patterns, sediment supply, and sea level rise predictions in the Puget Sound to project how surface elevation will change in the Snohomish Estuary with respect to sea level rise. Anthropogenic modification of the floodplain has reduced the quantity of vegetation and functional connectivity within the Snohomish Estuary. There have been losses up to 99% in vegetation coverage from historic extents within the estuary in both freshwater and mesohaline environments. Hydrographic monitoring conducted by NOAA and the Tulalip Tribe shows that 85% of the historic wetland area is not connected to the main stem of the Snohomish (Jason Hall 2014, unpublished data, NOAA). As vegetation colonization and functional connectivity of the floodplains of the Snohomish estuary is re-established through passive and active restoration, sediment transport and accretion is expected to increase. Under the Intergovernmental Panel on Climate Change (IPCC) “medium- probability” scenario sea level is projected to rise at a rate of 4.28 mm/year in the Puget Sound. Sea level rise in the Snohomish Estuary will be exacerbated from crustal deformation from subsidence and post-glacial rebound, which are measured to be -1.4 mm/year and -0.02 mm/year, respectively. Sediment accretion rates calculated by Crooks et al. (2014) and RTK GPS monitoring of surface elevation change of the Marysville Mitigation site from 2011-2014 measured vertical accretion rates that range from -48-19 mm/year and have high spatial variability. Sediment supply is estimated at 490 thousand tons/year, which may be an under-estimate because of the exclusion of tidal transport in this value. The higher rates of sediment accretion measured in the Snohomish Estuary suggest that the Snohomish will likely match or exceed the pace of sea level rise under “medium-probability” projections. The network of RSET-MH instruments will track surface elevation change within the estuary, and provide a more robust dataset on rates of surface elevation change to quantify how vertical accretion and subsidence are contributing to surface elevation change on a landscape scale.

A comparative study of three river systems leading into Nootka Sound, British Columbia: implications for winter salmon populations

Senior thesis written for Oceanography 445

Resource partitioning in sympatric delphinids: Space use and habitat preferences of Australian snubfin and Indo-Pacific humpback dolphins

1. Many species of delphinids co-occur in space and time. However, little is known of their ecological interactions and the underlying mechanisms that mediate their coexistence. 2. Snubfin Orcaella heinsohni, and Indo-Pacific humpback dolphins Sousa chinensis, live in sympatry throughout most of their range in Australian waters. I conducted boat-based surveys in Cleveland Bay, north-east Queensland, to collect data on the space and habitat use of both species. Using Geographic Information Systems, kernel methods and Euclidean distances I investigated interspecific differences in their space use patterns, behaviour and habitat preferences. 3. Core areas of use (50% kernel range) for both species were located close to river mouths and modified habitat such as dredged channels and breakwaters close to the Port of Townsville. Foraging and travelling activities were the dominant behavioural activities of snubfin and humpback dolphins within and outside their core areas. 4. Their representative ranges (95% kernel range) overlapped considerably, with shared areas showing strong concordance in the space use by both species. Nevertheless, snubfin dolphins preferred slightly shallower (1-2 m) waters than humpback dolphins (2-5 m). Additionally, shallow areas with seagrass ranked high in the habitat preferences of snubfin dolphins, whereas humpback dolphins favoured dredged channels. 5. Slight differences in habitat preferences appear to be one of the principal factors maintaining the coexistence of snubfin and humpback dolphins. I suggest diet partitioning and interspecific aggression as the major forces determining habitat selection in these sympatric species.

Does landscape context affect habitat value? The importance of seascape ecology in back-reef systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Comparison of Ba/Ca and d18OWATER as freshwater proxies: a multi-species core-top study on planktonic foraminifera from the vicinity of the Orinoco River mouth

Past river run-off is an important measure for the continental hydrological cycle and the as-sessment of freshwater input into the ocean. However, paleosalinity reconstructions applying different proxies in parallel often show offsets between the respective methods. Here, we compare the established foraminiferal Ba/Ca and d18OWATER salinity proxies for their capability to record the highly seasonal Orinoco freshwater plume in the eastern Caribbean. For this purpose we obtained a data set comprising Ba/Ca and d18OWATER determined on multiple spe-cies of planktonic foraminifera from core tops distributed around the Orinoco river mouth. Our findings indicate that interpretations based on either proxy could lead to different conclu-sions. In particular, Ba/Ca and d18OWATER diverge in their spatial distribution due to different governing factors. Apparently, the Orinoco freshwater plume is best tracked by Ba/Ca ratios of G. ruber (pink and sensu lato morphotypes), while d18OWATER based on the same species is more related to the local precipitation-evaporation balance overprinting the riverine freshwater contribution. Other shallow dwelling species (G. sacculifer, O. universa) show a muted response to the freshwater discharge, most likely due to their ecological and habitat prefer-ences. Extremely high Ba/Ca ratios recorded by G. ruber are attributed to Ba2+-desorption from suspended matter derived from the Orinoco. Samples taken most proximal to the freshwater source do not show pronounced Ba/Ca or d18OWATER anomalies. Here, the suspension loaded freshwater lid developing during maximum discharge suppresses foraminiferal populations. Both proxies are therefore biased towards dry season conditions at these sites, when surface salinity is only minimally reduced.

Macroinvertebrate communities and habitat structure in least-impacted hill streams of central Portugal

We surveyed macroinvertebrate communities in 31 hill streams in the Vouga River and Mondego River catchments in central Portugal. Despite applying a "least-impacted" criterion, channel and bank management was common, with 38% of streams demonstrating channel modification (damming) and 80% with evidence of bank modification. Principal component analysis (PCA) at the family and species level related the macroinvertebrates to habitat variables derived at three spatial scales -- site (20 m), reach (200 m), and catchment. Variation in community structure between sites was similar at the species and family level and was statistically related to pH, conductivity, temperature, flow, shade, and substrate size at the site scale; channel and bank habitat and riparian vegetation and land-use at the reach scale; and altitude and slope at the catchment scale. While the effects of river management were apparent in various ecologically important habitat features at the site and reach scale, a direct relationship with macroinvertebrate assemblages was only apparent between the extent of walled banks and the secondary PCA axis described by species data. The strong relationship between catchment scale variables and descriptors of physical structure at the reach and site scale suggests that catchment-scale parameters are valuable predicators of macroinvertebrate community structure in these streams despite the anthropogenic modifications of the natural habitat.

Stakeholder perceptions of ecosystem services of the Wami River and Estuary

Management of riverine and coastal ecosystems warrants enhanced understanding of how different stakeholders perceive and depend upon different kinds of ecosystem services. Employing a mixed methods approach, this study compares and contrasts the use and perceptions of upstream residents, downstream residents, tourism officials, and conservation organizations regarding the value of 30 ecosystem services provided by the Wami River and its estuary in Tanzania, and investigates their perceptions of the main threats to this system. Our findings reveal that all of the stakeholder groups place a high value on the provision of domestic water, habitat for wild plants and animals, tourism, and erosion control, and a relatively low value on the prevention of saltwater intrusion, refuge from predators, spiritual fulfillment, nonrecreational hunting, and the provision of traditional medications and inorganic materials for construction. Differences emerge, however, between the groups in the value assigned to the conservation of riverine and estuarine fauna and the provision of raw materials for building and handicrafts. Declining fish populations and an increasing human population are identified by the residents and conservation employees, respectively, as their prime concerns regarding the future conditions of the Wami River and its estuary. These groups also acknowledge increasing salinity levels and the loss of mangroves as other key concerns. The identification of these mutual interests and shared concerns can help build common ground among stakeholders while the recognition of potential tensions can assist managers in balancing and reconciling the multiple needs and values of these different groups.