Physical Habitat Model Research Articles

A physical habitat model for predicting the effects of flow fluctuations in nursery habitats of the endangered Colorado pikeminnow (Ptychocheilus lucius)

Larval and juvenile Colorado pikeminnow (Ptychocheilus lucius) use shallow, low-velocity, channel-margin areas (backwaters) as nursery habitats. It is hypothesized that within-day flow fluctuations caused by hydropower operations can directly affect the suitability of such habitats by altering water temperature and habitat geometry. Despite the importance of backwaters to juvenile fishes, there is a lack of established approaches for modelling how river management affects these habitats. Here, we describe a physical habitat model that predicts the effects of mainstem flow variation on backwater temperature, geometry and invertebrate availability. We specifically modelled these effects on habitat in a portion of the Green River in Utah below Flaming Gorge Dam. The overall model combines a cell-based model of backwater geometry, a pond-based temperature model and a model of invertebrate production. Results from a series of simulations suggest that the most important biological effects of within-day flow fluctuations are likely to be those associated with the availability of invertebrate prey including (1) minimum wetted area, (2) the proportion of the backwater's volume exchanged with the mainstem, and, to a lesser degree, (3) backwater temperature. Taken together, such effects could have important implications for the growth and survival of juvenile fish when flow fluctuations are sufficiently large. Copyright © 2006 John Wiley & Sons, Ltd.

An application of physical habitat modelling to quantify ecological flow for the Rheinau hydropower plant, River Rhine

The meander of the River Rhine at the Swiss-German hydropower plant Rheinau suffers from residual flow (5 m 3 /s vs. 372 m 3 /s mean flow). As a consequence, fish and benthic communities have shifted from lotic to lentic, and ubiquous species are more abundant. The simulation model CASiMiR, linking hydraulic and morphological conditions (water depth, flow velocity, near-bottom hydraulic forces) with ecological requirements of fish and benthos, was applied to assess habitat suitability for lotic species. Various scenarios of discharge and changes in the operation of two additional weirs located within the residual water stretch were considered. Model calculations showed that good quality habitats can be achieved either by significantly increasing residual flow and unchanged weir position (90-130 m 3 /s) or by lowering the weirs and moderately increasing discharge (20-70 m 3 /s). Seasonal variation in discharge and additional ecomorphological restoration are further options to optimize the living conditions for aquatic fauna. The suggested technical operation of the weirs allows an additional 60-70 m 3 /s to the turbines without lowering the habitat availability for fish indicator species. Hence, it can reduce the loss of energy production from about 30 to 6 % (other feasible measures such as additional turbines using the provided residual discharge are. not implied). In conclusion, such hydraulic habitat simulations can quantify the ecological impacts of technical alternatives and enable an objective, appropriate balance of ecological and economic benefits. Therefore, this kind of investigation may mitigate the controversy among stakeholders.

PHYSICAL HABITAT ASSESSMENT IN URBAN RIVERS UNDER FUTURE FLOW SCENARIOS

ABSTRACTRiver corridors in urban environments provide areas of biodiversity which are important for both aesthetic and economic reasons. A physical habitat model, which was used to assess urban rivers in Birmingham, UK, was applied to pairs of selected reaches to represent differing levels of habitat diversity on three rivers. The results for different life‐stages of dace, roach and chub suggest that the worst physical habitat occurs in highly modified channels and at the highest flows. Four scenarios, which were designed to represent alterations in flow regime caused by changes in management practices, were calculated using the hydrological model. Changes in physical habitat created by changes to the flow regime were assessed using a consistent, replicable method. It was shown that an increase in runoff would have detrimental effects in all cases, and that less engineered sites would benefit more from flow reductions. The lack of a suitable habitat for fry is shown to be a limiting factor for fish at all sites.

Automated segmentation of seafloor bathymetry from multibeam echosounder data using local Fourier histogram texture features

Patterns of seafloor topography represent regions of geomorphological feature types and the physiography governing the spatial distributions of benthic habitats. Topographic variability can be considered seafloor texture and can be remotely sensed by acoustic and optical devices. Benthic habitat delineations often involve distinctions based upon seafloor morphology and composition based upon acoustic data maps that are ground-truthed by optical imaging tools. Habitat delineations can be done manually, however, automation of the procedure could provide more objectivity and reproducible map products. Recently a technique using Fourier transforms (FT) to produce texture features called local Fourier histograms (LFH) has been used successfully to classify standard textures in grayscale images and automatically retrieve digital images from archives according to texture content [Zhou, F., Feng, J., Shi, Q., 2001. Texture feature based on local Fourier transform, ICIP Conference Proceedings, IEEE 0-7803-6725-1/01.]. We implemented a modified form of that approach by varying the spatial scales at which local Fourier histograms were calculated. A modified LFH texture feature classification technique was applied to multibeam echosounder (MBES) data from Piscataqua River, New Hampshire, USA, for automatic delineation of a seafloor topographic map into regions of distinct geomorphology and apparent benthic habitats. Automated segmentations were done by the LFH method on 1-m gridded MBES data, applying the local Fourier transform, used to generate the LFH, at spatial scales from 1 to 5 m. Seven seafloor texture classes were identified, corresponding to the primary substrate types and configurations in the study area as well as some previously unidentified regions and transitional zones. The texture regions serve as a physical habitat model for the seafloor, a basis for predicting benthic faunal inhabitants, their areal distributions, and serving as sampling strata for ground-truthing efforts.

Upscaling: Integrating Habitat Model into River Management

Physical habitat modelling has been developed at the scale best applicable to short river stretches and selected species of fish. The integration of these models into management practices at the river and watershed scale would therefore require corresponding modifications in both the models and results. Such procedures fall into three major categories: biological, spatial and temporal upscaling. Biological upscaling develops methods for applying habitat models to aquatic communities, as opposed to individual indicator species. Spatial upscaling creates a hierarchical framework through which to translate habitat observations from the species to management scale. Temporal upscaling incorporates biological and hydro-morphological dynamics into the static model. In the following paper the upscaling concept will be described in greater detail, illustrating its application with the example of the Quinebaug River in New England.

Instream Flow Assessment Modelling: Combining Physical and Behavioural-Based Approaches

Most state-of-the-art applications of habitat modelling rely on three-dimensional channel topography and two-dimensional hydrodynamic models that have centered on the simple extension of one-dimensional physical habitat-based concepts (i.e., extension of the Physical Habitat Modelling System - PHABSIM). However, as demonstrated in this paper, these approaches can be extended to more realistically incorporate both the physical habitat-based metrics of streamflow and behavioural decision rules that can incorporate fish community structure and dynamics. This approach evaluates the spatial suitability of physical habitat-based on the incorporation of behavioural rule sets, such as the association with escape cover type and distance, exclusion zones associated with predators or linear dominance hierarchies, and lag-time dependence of macroinvertebrate re-colonization of habitats associated with varial zones induced by peaking/load following operations of hydropower facilities. In the paper we lay the foundation between field data collection strategies for characterization of the physical domain, and modelling the hydraulic properties of flow using two- or three-dimensional hydraulic models. We then describe the use of GIS for the integration of additional factors such as substrate, cover, distance to cover and distance to water’s edge factors. We then demonstrate how GIS, in conjunction with decision based habitat algorithms, can be used with classical-based physical habitat modelling to incorporate behavioural-based rules to evaluate escape cover, exclusion zones and lag-time dependence for macroinvertebrate under variai zone induced impacts. These examples are based on results from studies in regulated river systems in which these techniques have been shown to improve the assessment of impacts/benefits associated with altered flow regimes.

Small mammals: consequences of stochastic data variation for modeling indicators of habitat suitability for a well-studied resource

Abstract Increasingly, models of physical habitat variables (i.e. vegetation, soil) are utilized as indicators of small mammal habitat suitability or quality. Presumably, use of physical habitat models indicating habitat suitability or quality would be improved and enhanced by the extensive amount of research that has been conducted for these species. However, current knowledge of small mammal habitat associations is based mostly upon site specific empirical observation, not the quantitative data that are the foundation of habitat modeling. Small mammal data are affected by technique-related capture variability. Existing data do not demonstrate that fine spatial and temporal variability associated with technique substantially affects habitat models. Small mammal abundance also exhibits ecologically important high spatial and temporal variability. Microhabitat spatial variability is a poor predictor of trap use compared to larger spatial scale phenomena in mesic and xeric biomes. Habitat suitability has been modeled with accuracy ranging between 80 and 93% for 14 species. This accuracy is achieved by filtering out stochastic temporal variability that was not related to physical habitat indicators. Inclusion of stochastic temporal variability degrades model performance, especially in ecosystems where predictive vegetation and substrate variables are essentially constant. Development of indicator mathematical models can be facilitated when a species’ ecology is carefully considered and where mathematics and biology are equally incorporated when conceiving and developing indicators.

MesoHABSIM: A concept for application of instream flow models in river restoration planning

Abstract This paper describes the methodological concept for application of physical habitat models to restoration planning at a whole river scale. The design proposed here builds upon the Instream Flow Incremental Methodology but is focused at the need for managing large-scale habitats and river systems. It modifies the data acquisition technique and analytical resolution of standard approaches, changing the scale of physical parameters and biological response assessment from micro- to meso-scale. In terms of technological process, a highly detailed microhabitat survey of a few, short sampling sites would be replaced by mesohabitat mapping of whole-river sections. As with more traditional stream habitat models, the variation in the spatial distribution and amount of mesohabitats can provide key information on habitat quality changes corresponding to alterations in flow, channel changes, and stream improvement measures. However, the scale of simulations more closely matches restoration and system analyses...

Physical habitat modelling for fish - a developing approach

Quantitative physical habitat modelling is a river management methodology that has been developed to aid the assessment of the impacts of altered river discharge on freshwater aquatic communities. In this paper we outline the potential value of habitat modelling in advancing the study of fish (particularly 0+ fish) habitat use, and also issues surrounding the inclusion of young fish in environmental impact assessments. Young fish have often been used as target species during such assessments, due to their perceived sensitivity to environmental changes, particularly associated with altered river discharge. However in the past, the paucity of information on young life stages, combined with the general difficulty in quantifying their habitat requirements has limited the use of habitat models for this purpose. Firstly we describe the context within which habitat modelling has been applied traditionally: the development of water resources, and the predictive assessment of associated environmental problems. Alternative approaches to habitat modelling are briefly mentioned. Overall, these techniques, which combine physical and biological data offer a broad perspective for the ecological management of degraded rivers, and can assist in developing our understanding of the processes that influence aquatic organisms in running waters. In the 20 or so years since its inception, habitat modelling has undergone considerable improvement. However there has not been a recent review of such advances. Therefore in the main text, we describe the current state of habitat modelling, emphasising recent developments. Many of these offer possibilities for the advancement of our knowledge of 0+ fish.

FROM FLOW TO FISH TO DOLLARS: AN INTEGRATED APPROACH TO WATER ALLOCATION1

ABSTRACTThis paper details a case study of economic and natural system responses to alternative water management policies in the Cache La Poudre River basin, Colorado, 1980–1994. The case study is presented to highlight the value and application of a conceptual integration of economic, salmonid population, physical habitat, and water allocation models. Five alternative regimes, all intended to increase low winter flows, were investigated. Habitat enhancements created by alternative regimes were translated to population responses and economic benefits. Analysis concluded that instream flows cannot compete on the northern Colorado water rental market; cooperative agreements offer an economically feasible way to enhance instream flows; and establishing an instream flow program on the Cache La Poudre River mainstem is a potentially profitable opportunity. The alliance of models is a dynamic multidisciplinary tool for use in professional settings and offers valuable insight for decision‐making processes involved in water management.

The importance of physical habitat assessment for evaluating river health

Summary1. Physical habitat is the living space of instream biota; it is a spatially and temporally dynamic entity determined by the interaction of the structural features of the channel and the hydrological regime.2. This paper reviews the need for physical habitat assessment and the range of physical habitat assessment methods that have been developed in recent years. These methods are needed for assessing improvements made by fishery enhancement and river restoration procedures, and as an intrinsic element of setting environmental flows using instream flow methods. Consequently, the assessment methods must be able to evaluate physical habitat over a range of scales varying from the broad river segment scale (up to hundreds of kilometres) down to the microhabitat level (a few centimetres).3. Rapid assessment methods involve reconnaissance level surveys (such as the habitat mapping approach) identifying, mapping and measuring key habitat features over long stretches of river in a relatively short space of time. More complex appraisals, such as the Physical Habitat Simulation System (PHABSIM), require more detailed information on microhabitat variations with flow.4. Key research issues relating to physical habitat evaluation lie in deciding which levels of detail are appropriate for worthwhile yet cost‐effective assessment, and in determining those features that are biologically important and hence can be considered habitat features rather than simple geomorphic features.5. The development of new technologies particularly relating to survey methods should help improve the speed and level of detail attainable by physical habitat assessments. These methods will provide the necessary information required for the development of the two‐and three‐dimensional physical and hydraulic habitat models.6. A better understanding of the ways in which the spatial and temporal dynamics of physical habitat determine stream health, and how these elements can be incorporated into assessment methods, remains a key research goal.