Abundance trends and environmental habitat usage patterns of bottlenose dolphins (Tursiops truncatus) in lower Barataria and Caminada Bays, Louisiana

The paucity of research into the environmental requirements, stock membership, abundance and residency patterns of bottlenose dolphins (Tursiops truncatus) in coastal Louisiana creates difficulty in understanding how local ecosystems and threats (such as fishery interactions, habitat degradation and pollution) affect populations. This study combined fine-scale environmental measurements and photo-identification techniques to describe patterns of habitat usage and abundance of bottlenose dolphins in lower Barataria Basin from June 1999 to May 2002. In addition I investigated the validity and limitations of using mark-recapture models to estimate abundance from cetacean photo-identification data. Bottlenose dolphins were present year-round in a wide range of water temperatures (10.9 – 33.9 ºC), dissolved oxygen levels (3.7 – 16.6 mg/L), salinities (11.7 – 31.5 psu), turbidity levels (1.4 – 34.0 NTU), distances from shore (3 – 800 m), and water depths (0.4 - 12.5 m). However, feeding activity was concentrated in a narrower range of conditions, 20 – 24 ºC water temperature, 6 – 9 mg/L of dissolved oxygen, turbidity values between 20 – 28 NTU, 200 – 500 m from shore, and depths of 4 – 6 m. Spatial mapping showed differences in the seasonal distribution of individuals and a tendency for feeding activity and larger group sizes to be concentrated in passes. Using distinctive natural markings present on dorsal fins, I identified 133 individual dolphins. Closed-population models were improved by inclusion of temporal and individual heterogeneity as sources of sighting variability and produced estimates of between 138 and 238 (95% CL range = 128 – 297) bottlenose dolphins for the study area. Analysis of Jolly-Seber model assumptions demonstrated the importance of ensuring cetacean surveys accurately represent temporal, geographic and demographic properties of a study population. In addition such factors as non-preferential image acquisition, group size, gender, behavior, stability and distinctiveness of natural markings, weather conditions and boat traffic must be considered. Evidence of a relatively closed Barataria Basin population agrees with current assumptions that bay bottlenose dolphin stocks are distinct from those found in deeper, offshore waters. Furthermore, the characterization of environmental usage patterns for this bay population strengthens adequate description and management of this relatively discrete Gulf of Mexico bottlenose dolphin stock

The Drivers and Consequences of Change to the Physical Character of Waterholes on an Australian Dryland River

Waterholes are a critical feature of dryland rivers globally, providing geomorphic and ecohydrological complexity. Waterholes typically develop as a series of deep pools that can retain water for extended periods in the absence of surface water connectivity or groundwater inputs. They are often the only source of water in an otherwise arid environment and as such have high ecological, social, and cultural value. From an ecological perspective, waterholes provide refuge to aquatic biota in a drying environment ensuring both their immediate survival and their subsequent recolonisation of the broader river system once flows recommence. Waterholes provide an important water supply to local communities for stock and domestic use and recreation. They are also pivotal to the cultural practise and spiritual beliefs of Indigenous Australians. This study has shown that despite their significance in the landscape, waterholes are increasingly threatened by anthropogenic landscape change. The Barwon-Darling River, an alluvial, dryland river in south-east Australia, is a river where the impact of human activity on waterholes is of concern. This thesis is aimed at understanding (1) if and how the physical character of waterholes on the Barwon-Darling has changed since European colonisation and (2) understanding the drivers and consequences of change to waterholes on the Barwon-Darling River. In this study, a comparison of historical (1890s) and contemporary (2015) riverbed profiles revealed a substantial change to the depth and spatial distribution of waterholes post European colonisation. The trajectory and magnitude of change is spatially variable and closely aligned with the presence or absence of low-level weirs. These structures create artificially high-water levels immediately upstream of the weir structure, which has increased waterhole depths for approximately 40 % of the river. In contrast, waterholes located outside of the weir pool influence have experienced a significant decline in maximum waterhole depths (median decline of 1.6m). This has resulted in fewer deep waterholes, which is also associated with an increase in the distance between the remaining deep waterholes (i.e., those deeper than 4m). In some cases, those distance have more than doubled. A change to the depth of waterholes and their spatial distribution has serious implications for hydrological connectivity, water quality, habitat availability and for the long-term presence and persistence of waterholes in the landscape. The decline in waterhole depths observed on the Barwon-Darling has been attributed to an increase in the rate of sedimentation associated with anthropogenic landscape change. Anthropogenic landscape change has increased the delivery of sediment to the river whilst reducing the capacity of the river system to transport sediment. Although sediment can originate from a range of sources, this study focused on the potential contribution from alluvial floodplain gullies. Floodplain gullies were found to be a prevalent feature within the catchment, with their presence increasing over the past 50 years. Over 4000 gullies were recorded, impacting an area of floodplain of approximately 148 million m2 and with a combined gully length of 2364 km. The total volume of sediment originating from these gullies is approximately 168 million m3, which is magnitudes higher than previous estimates for gully erosion in the Barwon-Darling catchment. However, given the gullies in this study have been cut into floodplain alluvium it was assumed that a sizable proportion of the fine sediment exported from the gullies would have remained in suspension and therefore transported some distance from the original source gullies. This was supported through statistical analysis that showed no predictive relationship between the total volume of gully derived sediment delivered to a reach and the magnitude of change to waterhole depth in that reach. The less mobile coarse sediment fraction would, however, be more likely to contribute to the shallowing of waterholes and to the expansion of in-channel feature such as bars and benches. Like many dryland rivers, the flow regime of the Barwon-Darling River has been modified as a result of water resource development. The abstraction of water, interception of floodplain flows and storage of water within in-stream impoundments has substantially altered the frequency, magnitude, and duration of flows. These changes have compromised the capacity of in-channel flows to entrain and transport sediment, reducing opportunities for sediment to be conveyed throughout the system. The number of events capable of entraining sediment has declined from 23 to 48 % across all sediment calibres (i.e., coarse sand, coarse silt/fine sand, fine silt/clay), whilst the frequency and duration of flows conducive to sediment deposition have increased considerably. Overbank flooding has halved, limiting the opportunities for lateral sediment exchange with the floodplain. During periods of low flow, the longitudinal transport of sediment is limited by low-level weirs. Collectively, these modifications increase the likelihood of sediment being retained within the river channel and, as such, increases the opportunity for within-channel sedimentation and the in-filling of ecologically important waterholes. Fish populations were used to examine the influence of waterhole depth on dryland river ecology. In particular, the focus was on determining if access to deep water habitat within the broader waterhole setting would influence fish assemblage patterns. Waterhole depth is an ecologically important variable as it influences habitat availability, water quality, density-dependent biotic interactions, and waterhole persistence. As such, waterhole depth was expected to shape fish assemblage patterns in the Darling River, however, its affect was thought to be difficult to isolate given the association that water depth has on creating habitat complexity through the inundation of in-stream wood and other habitat features. As a result, this study investigated the independent and interactive effects of both waterhole depth and habitat complexity on fish assemblage patterns. The presence and size of instream wood was used as a surrogate for habitat complexity. The results suggest that waterhole depth does not directly influence fish assemblage patterns, nor does it have an interactive effect with habitat complexity. A significant relationship with in-stream wood was observed, but only when native fish assemblages were considered. The inclusion of exotic species had a homogenising influence due to the relatively even distribution of common carp across sites of varying complexity. Despite this outcome, depth remains a critical factor in dryland rivers as it ensures the presence and persistence of waterholes within the landscape and creates important fish habitat through the inundation of instream wood and other habitat features. The findings in this thesis enhance our understanding of the trajectory and magnitude of geomorphic adjustment that can occur on a dryland river as a consequence of anthropogenic landscape change. This study has shown that the threat to dryland river waterholes is not limited to any one issue but is instead the culmination of a broad range of disturbances within the catchment (i.e., land use on the adjacent floodplain, modifications to the flow regime, in-stream infrastructure, climate change). Often though, it is difficult to isolate the impact of individual activities given the large spatial and temporal scale at which human disturbance has occurred. As such, it is imperative to establish an integrated approach to managing sediment on dryland rivers, which could include landscape management through gully remediation and grazing management, the provision of environmental flows and the removal of redundant in-stream infrastructure. The results from this study have relevance to dryland rivers globally, highlighting the significance of these important and widespread rivers

Ecosystem Structure and Function in a Hydrogeomorphically Complex Riverine Landscape

Dynamic patterns and processes underlie the physical templates that house ecological communities. These patterns and process operate over various scales to create spatial and temporal variability within the landscape, resulting in heterogeneous systems that support diverse communities. The physical template is important to biota because it is the foundation on which communities establish and persist in the landscape. The template governs composition of communities as well as ecosystem processes that support the structure and function of communities in space and through time. In riverine landscapes the physical template is created by the interaction of hydrology, geomorphology and ecology operating over multiple spatial and temporal scales. Understanding the hydrogeomorphic character underpinning ecosystems in riverine landscapes, and the mechanisms that elicit biological responses, is essential to understanding the processes by which freshwater ecosystems maintain patterns of biodiversity and ecosystem function. The aim of this thesis was to investigate how ecosystem structure and function are influenced by the hydrogeomorphic character of the riverine landscape. A literature review was first undertaken to identify work currently available to inform on the hierarchical way in which riverine ecosystems operate. Review of the literature highlighted the need for further work to investigate habitat-biota relationships through an interdisciplinary lens that incorporates hydrology, geomorphology and ecology. Added to this interdisciplinary approach is the application of scale, whereby the spatial and temporal context of variables and ecological response are considered. From review of the literature, four objectives were developed to address current deficiencies identified in the literature: 1) describe the hydrogeomorphic character of the physical template of the Upper Mississippi river-floodplain across multiple spatial and temporal scales; 2) investigate the influence this character has on fish community structure; 3) determine if the same hydrogeomorphic variables responsible for describing the physical template also influences fish community structure and food-web dynamics; and 4) describe the response of fish communities and food webs to temporal variability over a connection event. This work demonstrated that hydrogeomorphic variables from multiple spatial and temporal scales contribute to the heterogeneous nature of patches of the Upper Mississippi river floodplain. Variables included patch-scale descriptors of entry morphology and depth, short-term hydrology variables describing the duration and magnitude of connection events 2-years prior to sampling, long-term duration and magnitude of connections and the nature of rises and falls over the historical record, and finally, landscape scale variables of where a patch was located in a pool and its proximity to neighbouring patches. Five hydrogeomorphically distinct habitat patches were identified, including four different types of backwater habitats not previously described in the Upper Mississippi river-floodplain, and a floodplain lake group. Three hydrogeomorphically distinct off-channel habitats, namely floodplain lakes and two types of backwaters supported distinct fish communities in the 2012 sampling season. In general, differences were driven by black crappie (Pomoxis nigromaculatus) dominating floodplain lakes, Group 2 backwaters having a high abundance of gizzard shad (Dorosoma cepedianum) and bluegill (Lepomis macrochirus) dominating Group 5 backwaters. Fish community structure and food web structure changed temporally over the connection event sampled in 2013 in response to decreasing connectivity and associated changes in conditions, although the change in food web structure was strongest. Structural changes to fish assemblages were influenced by the functional response of breeding events among common species such as bluegill (Lepomis macrochirus), black crappie (Pomoxis nigromaculatus) and largemouth bass (Micropterus salmoides). Functional changes in food web structure were seen through shifts in trophic assemblages (represented by the interaction of species present and their trophic position in each community), a decrease in mean trophic position, food chain length and average consumer δ15N, and broadening of the consumer carbon base as connectivity decreased. Consumers also expanded their carbon food source earlier in some patch types than other (i.e. floodplain lakes compared to backwaters). A spatial pattern was also reflected in food webs with trophic assemblages varying between patch types with rheophilic species dominating channels and a greater diversity of macroinvertebrate taxa in off-channel patches. Mean trophic position was lower in floodplain lakes, intermediate in backwaters and highest in channels. Fish community structure did not vary spatially. Hydrogeomorphic variables responsible for differentiating the physical character of the Upper Mississippi river-floodplain were not the same set of variables influencing fish communities and food-web structure, although there was some overlap. The mixture and importance of variables associated with fish assemblages in space were different among patch types (i.e. floodplain lakes and sub-groups of backwaters) and included patch-scale characteristics and long-term hydrology, and in the case of backwaters, which pool they were located in. The mixture and influence of variables associated with changes in fish assemblage and trophic assemblage through the connection event also changed over time. In conclusion, an interdisciplinary, multi-scale approach is critical for describing the hydrogeomorphic character of riverine landscapes. Characterisation of the physical template should be done prior to biological sampling so patches can be targeted based on their physical character in order to draw out key habitat-community relationships. Added to this should be the tendency to move way from broad classifications of habitats (e.g. floodplain lake vs backwater) since such classifications could be too simplistic and may miss biota-relevant patterns in the landscape. Instead, individual characteristics defining the physical nature of a habitat need to be linked to biological responses across scales. This need is reinforced by the finding that the suite of variables responsible for describing the physical template is not necessarily the same as the suite found to be important to biota. A hierarchical framework and interdisciplinary approach enable a holistic view of the spatiotemporal heterogeneity of a system and provides a firm basis for investigating how the physical template influences and helps to maintain ecosystem structure and function through space and time. Understanding the mechanisms that elicit these responses in riverine landscapes is essential in our quest to improve and maintain the biostructure of communities and thus functioning ecosystems