Do rearing salmonids predictably occupy physical microhabitat?

Microhabitat suitability models are commonly used to estimate salmonid habitat abundance and quality with unknown accuracy or reliability. When tested, the metrics used to evaluate these models are often limited by the methods used to develop them. More generalized bioverification strategies that transcend methodology are therefore needed in ecohydraulics. This study further developed and applied such a generalized bioverification framework to four approximately 1-m-resolution rearing salmonid microhabitat suitability models. Water depth and velocity habitat suitability criteria (HSC) functions were developed for two size classes of rearing Oncorhynchus tshawytscha and O. mykiss using snorkel survey data collected over three years at seven sites along the lower Yuba River in California, USA. An expert-based cover HSC function was modified from previous studies. HSC functions were applied to previously validated, approximately 1-m-resolution two-dimensional hydrodynamic models and cover maps of the river. Mann–Whitney U tests confirmed that suitability values were significantly higher at utilized locations compared to randomly generated, non-utilized locations for all four models. Bootstrapped forage ratios demonstrated that microhabitat suitability models accurately predicted both preferred and avoided habitat beyond the 95% confidence level. This generalized bioverification framework is recommended for evaluating and comparing the accuracy and reliability of ecohydraulic models used in habitat management worldwide

A Multiscale Linkage Between Riverscape and Fish Community Coevolution

Sediment dynamics are foundational to stream and watershed morphology. Yet aquatic ecologists have relied on an oversimplified model of sediment dynamics characterizing sediments as agents of stream bed burial, and which fails to describe many types of aquatic habitat evolution. In this dissertation I employ both fluvial geomorphic and ecological frameworks to gain a deeper understanding of how sediment dynamics shape stream morphology and fish community evolution at multiple scales. Using a paired historic and contemporary approach, I analyzed geomorphic evolution and fish community change in the Bayou Pierre, Mississippi, from the 1980s to recent. Patterns of erosion due to headcutting have advanced considerably, leading to wide, shallow, homogenous channels with coarser substrates, opposite of stable conditions in the Gulf Coastal Plain. Fish communities homogenized, and community change was tied to geomorphic process change over time. Examining the minnows (a taxonomically and ecologically diverse group), species persisting in the highly unstable mainstem and larger tributaries were characterized by traits indicative of mobility and ecological adaptability. Communities in these reaches had spatial patterns suggesting effects processes. Further examination of the Bayou Pierre showed sedimentary process connectivity at the watershed scale, strong ties between geomorphic activity and aquatic habitat conditions, evidence of an increased pulse of erosion and ongoing relaxation corresponding to the floods of 1983, and evidence that this event led to considerable gravel bar consolidation and habitat fragmentation in the mainstem. I then examined patterns of genetic structure for Fundulus olivaceus, a headwater specialist, in seventeen watersheds throughout southern Mississippi and Louisiana in relation to fluvial geomorphic activity. Planform analysis of the watersheds demonstrated a gradient between stable and unstable, and also detected evidence of a pulse of erosion and relaxation. Analysis of genetic structure and heterozygosity suggested fragmentation of dispersal and potential bottlenecks associated with channel instability. STRUCTURE analysis revealed a complicated pattern of population structure, with five of 82 populations being assigned to a neighboring watershed, potentially either from stream capture or altered extinction rates due to fluvial geomorphic activity. This work demonstrates clear linkages between geomorphic processes, altered channel morphology, and altered local and spatial ecological processes

Long‐Term Minnow Community Trait Shifts and Metacommunity Dynamics In a Geomorphically Unstable River

Ecological disturbances may affect both habitat connectivity and heterogeneity, changing the dominant metacommunity processes affecting local communities. Altered fluvial sediment dynamics in rivers experiencing headcutting and accelerated erosion may foster morphologically unstable reaches in which supplies of habitat-forming materials are spatially and temporally unpredictable. We hypothesise such environments will select for species with traits which promote dispersal or rapid resource use. We tested this hypothesis using historical and recent datasets from a biologically and functionally diverse taxonomical group, minnows (Leuciscidae and Cyprinidae) in the Bayou Pierre, Mississippi. Local communities decreased in both α and β-diversity over time. Spatial autocorrelation of communities was consistently high through time, and more strongly related to regional community structure than local habitat variables in contemporary data. Communities shifted towards species with larger body sizes, less parental care, shorter age at maturity and higher fecundity. Communities also shifted towards more generalist species with lower potential trophic positions, and keystone species declined. Our data support the hypothesis of community-level shifts towards species with dispersal trait syndromes and opportunistic resource utilisation. These shifts have led to a decrease in ecological complexity and overall homogenisation of minnow communities in the geomorphically evolving Bayou Pierre mainstem. The Bayou Pierre presents a unique window into ecological dynamics in a watershed characterised by altered sediment dynamics and sediment loss, in contrast to the large body of literature examining systems with increased sedimentation. These insights demonstrate the importance of studying the full range of fluvial sediment dynamics, including how broader processes of loss and transport may affect long-term habitat stability, persistent trait syndromes and metacommunity dynamics

Historical and Contemporary Drivers of Knickpoint Retreat and Morphological Evolution Along Bayou Pierre, Mississippi

Channel incision in rivers can cause marked ecological and economic damages. This phenomenon is abundant and generally well documented along impacted streams in the loess hills adjacent to the Lower Mississippi River valley. Bayou Pierre, an ecologically important small tributary of the Mississippi River, is currently incising but causes are not well understood. In this study, we examine diverse data sources to: (1) reconstruct a history of erosional stimuli and possible origins and (2) examine effects of contemporary controls. Review of long-term planform and land use data for the Mississippi River revealed episodic foreshortening events followed by episodic deforestation and reforestation. Hydrologic data suggest an increase in rainfall over the last few decades. Estimates of knickpoint retreat place origins prior to Mississippi River channel straightening (1929–1944). Planform analysis in three focal reaches of Bayou Pierre demonstrates slow change prior to 1982, but accelerated changes after those periods. Mean rainfall and 3-day storm intensity correlate to some planform changes; however, the storm of 1983 may be a better explanation of sudden planform change. We found some evidence of potential internal feedback loops in patterns of bar growth. Together, our analyses provide a synthesis of stimuli experienced by Bayou Pierre over the last ~200 years and suggest both channel migration events before straightening of the Mississippi River and more recent hydrologic events have influenced patterns of geomorphic change in Bayou Pierre