Physical Habitat Simulation System Research Articles

Habitat suitability curves for brown trout (Salmo trutta fario L.) in the River Adda, Northern Italy: comparing univariate and multivariate approaches

Habitat suitability of brown trout (Salmo trutta fario) was studied in the upper portion of the Adda River, Northern Italy. Measurements were made for 528 individuals distributed in two life-stage classes, adult and juvenile, based on body length. In order to provide basic biological information for the physical habitat simulation (PHABSIM) system of the instream flow incremental methodology (IFIM) in the Italian regulated rivers, habitat suitability curves (HSCs) have been developed with respect to several microhabitat riverine parameters. Initially, current velocity, water depth, substrate class size and cover were analysed with an univariate approach, then bivariate habitat suitability models were developed from depth and velocity data. The comparison of experimental univariate HSCs with those from the literature outlined some differences that can essentially be explained by characteristics of the investigated river, confirming the necessity of using site-specific curves in relation to each experimental study area. To compare the univariate and bivariate approaches, the weighted usable area (WUA)–discharge relationships were calculated using both types of HSCs. Response curves obtained from the two approaches turned out to be quite different. In PHABSIM habitat modelling, HSCs univariate functions need to be aggregated to produce the WUA–discharge relationship. A multiplicative criterion is generally used for the combined suitability factor; by means of this aggregation criterion all variables have equal weight. According to bivariate models, depth is much more important than velocity in defining habitat suitability requirements. Copyright © 2001 John Wiley & Sons, Ltd.

Salmonid habitat modelling studies and their contribution to the development of an ecologically acceptable release policy for Kielder Reservoir, North-east England

1. Kielder Reservoir regulates the Rivers North Tyne and Tyne. It provides a regular supply of water for downstream users, supports abstractions for a major water transfer scheme and provides hydroelectric power (HEP). Kielder's release regime typically alternates between a 1.3 m3 s−1 compensation flow and 10–15 m3 s−1 HEP releases of between 3 and 7 days in duration. Occasionally releases of up to 30 m3 s−1 are made for the purpose of encouraging fish runs, for recreational events or to help in water quality management. The impacts of this release regime on Atlantic salmon (Salmo salar) and brown trout (S. trutta) habitat at four sites on the North Tyne are assessed and alternative regimes, designed to minimize impacts, are presented. 2. There is no evidence that the compensation flow results in extreme loss of instream habitat. A discharge of 1.3 m3 s−1 ensures that water is maintained over most of the channel area at sites representative of upper, middle and lower sections of the North Tyne. This discharge lies above breaks in slope of respective site discharge versus wetted area curves; thus, disproportionate increases in discharge would be needed to increase wetted area. Simulations using the Physical Habitat Simulation System (PHABSIM) suggest that the compensation flow provides between 50% and 90% of the maximum possible weighted usable area (WUA) for juvenile (0+) salmonids. 3. During HEP releases, juvenile salmonid habitat (WUA) apparently falls to between 20 and 40% of site maxima. Newly emerged juvenile fish (March and April) are most affected by HEP releases because they are relatively small (25 mm in length) and water temperatures are relatively low at this time of year. During March and April, critical near-bed displacement velocities for newly emerged fish may be exceeded across large parts (80%) of sites up to 8 km downstream from Kielder Reservoir; fish would either be displaced downstream or forced to relocate to flow refuge areas. 4. The availability of Atlantic salmon spawning habitat (WUA) at a key site is limited by the compensation flow; 1.3 m3 s−1 provides approximately one third of the habitat available at the optimum discharge (4 m3 s−1). At this site, a discharge of approximately 2 m3 s−1 is needed to ensure most of the bed is inundated by water. Regulation has reduced the duration of flows exceeding 2 m3 s−1 from 90 to 60% of the spawning season. 5. Simulations suggest that when discharge drops from 30 m3 s−1 to the compensation flow, up to 60% of the optimum spawning habitat available at the former discharge may be left stranded (dry). This could potentially lead to egg or alevin mortality. 6. PHABSIM simulations suggest that increasing the compensation flow to 4 m3 s−1 during the spawning period (November and December) is likely to increase the availability of suitable spawning habitat. Also, increasing the compensation flow to 2 m3 s−1 during the incubation period (January through March) would minimize redd stranding. Reductions in the number of HEP releases in March and April would limit the extent to which newly emerged fish are exposed to velocities that potentially displace them. Such changes to the Kielder release regime may have implications for water resource management. While it is important that the biological instream flow requirements of the North Tyne are incorporated into the Kielder operating policy, these should be integrated along with the need for channel maintenance flows, downstream water supply abstractions and HEP generation, as well as for transfers of water to other catchments. Copyright © 2000 John Wiley & Sons, Ltd.

Microhabitats of brown trout when feeding on drift and when resting in a lowland salmonid brook: effects on Weighted Usable Area

Summer habitat preferences by brown trout (10-20 cm fork length) were determined by daylight and night dive sampling in the Saint Sauveur brook, a tributary of the River Scorff (Brittany, France). Habitat change was analyzed from night and day sampling. At the geomorphological unit scale, fish preferred riffles during daylight hours and pools at night. According to behavioural data, night and day locations in the channel depended on the two activities: resting (night samples) and feeding on drift (daylight samples). Suitability curves drawn at the microhabitat scale showed differences between day and night, in terms of water depth (25-45 cm by daylight, 40-55 cm at night), velocity (15-45 cm/s by daylight, 0-15 cm/s at night) and substrate particle size (gravel, cobble and stones by daylight, silt and sand at night). Based on these habitat suitability curves, Weighted Usable Area was computed by EVHA, the French version for the Physical Habitat Simulation system. Results show that WUA varied in magnitude from 1 to 9 between night and day, depending on stream discharge. In addition, the need to modify the Standard Habitat Suitability Indices (HSI) is emphazised, owing to the differences in the shape of the suitability curves between Standard HSI and Feeding HSI according to water velocity.

Relationship between chinook salmon (Oncorhynchus tshawytscha) redd densities and PHABSIM-predicted habitat in the Merced and Lower American rivers, California

An index of chinook salmon (Oncorhynchus tshawytscha) spawning habitat predicted using the physical habitat simulation system (PHABSIM) component of the instream flow incremental methodology was compared with redd densities and locations for sites in the Merced River, California, during 1996 and with redd numbers in sites in the Merced and Lower American rivers, California, from 1989 through 1996. Predicted weighted useable area (WUA) was significantly correlated with chinook salmon spawning density and location at five of seven sites in the Merced River. At the microhabitat level, in the Merced River during 1996, there was a significant relationship between chinook salmon redd location and predicted WUA. Cells with more WUA in the Merced River tended to have more redds. At the mesohabitat level, there was a significant relationship between redd density and predicted WUA in both rivers. Transect areas in the Merced River with higher predicted WUA had more redds. Sites with higher numbers of redds had more predicted WUA. Significant correlations between predicted WUA and spawning locations increase confidence in the use of PHABSIM modeling results for fisheries management in the Merced and Lower American rivers as well as in other rivers.

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.

Impacts of groundwater abstraction on the trout fishery of the River Piddle, Dorset; and an approach to their alleviation

The River Piddle, a small chalk stream in Dorset, supports a valuable fishery for brown trout. It is also heavily utilised for water abstraction, with a licensed maximum daily quantity of 197 Ml/d, of which 43·5% can be taken from the groundwater. The largest licensed groundwater uses (by licensed volume) are public water supplies (PWS), of which there are four within the Piddle catchment. Investigations into the impacts of the largest PWS abstraction, at Briantspuddle, on the brown trout population and fisheries of the River Piddle demonstrated a spatial correlation between a zone of reduced river flow and an area of low juvenile trout abundance, and a reduction in the period during which good quality trout fishing was available. Trout habitat was quantified by applying the Physical Habitat Simulation System (PHABSIM) in conjunction with a groundwater model. The resultant habitat duration curves and habitat time-series corresponding with historical and naturalised (zero abstraction) flow, indicated large habitat losses for juvenile trout. Using discharge habitat relationships a preferred flow regime for the river at Briantspuddle, designed to satisfy both ecological and recreational needs, was identified. This flow regime, which will be maintained by stream support, includes a ‘survival flow’ for juvenile trout during the critical summer low flow period. Copyright © 1999 John Wiley & Sons, Ltd.

A habitat assessment approach to the management of groundwater dominated rivers

The Instream Flow Incremental Methodology (IFIM) using the Physical Habitat Simulation (PHABSIM) system, has seen increasing application to the assessment of changes in aquatic habitats in the UK over the last 10 years. In particular, the model has been applied operationally to chalk streams (e.g. the Rivers Allen and Piddle) in southern England for the alleviation of low flow (ALF) problems. More recently, the model has also been used to examine the effect of changes in channel morphology upon aquatic habitats, such as those that occur during flood defence, or river channel restoration, schemes. The paper outlines some of the issues related to the application of the model to groundwater dominated rivers, such as chalk streams, and provides examples of the application of the model to a water resource issue and to assess a habitat restoration scheme. The paper also reports on three areas of recent research to improve the methodology: (1) choice of representative study sites and habitat variation at the reach and sector scale; (2) modelling of time series and interpretation of alternative water management regimes; and (3) the development of rapid assessment techniques based upon the transfer of standardised relationships between available habitat and discharge. Copyright © 1999 John Wiley & Sons, Ltd.

TWO-DIMENSIONAL HYDRAULIC SIMULATION OF PHYSICAL HABITAT CONDITIONS IN FLOWING STREAMS

Instream flow needs (IFN) assessment studies are performed to provide guidelines for stream water management and to assess the impacts of different water projects such as weirs, dams and stream diversions on the available fish habitat. Many of the IFN assessment techniques require hydraulic parameters such as water depth, flow velocity, wetted perimeter or top width as input variables. The Physical Habitat Simulation System (PHABSIM), one of the most widely IFN assessment models used in North America, requires precise values of depth and velocity at numerous points within the study reach to produce relationships between streamflow and usable habitat area for different life stages of varying fish species. Numerical flow simulation is applied to obtain results for unmeasured flows. At present, the flow simulation techniques applied in most IFN assessment methods are rather simplistic. In PHABSIM, a one-dimensional approach, such as the application of HEC-2, is used to determine water surface elevations along the study reach. Then a technique based on a combination of Manning's equation and regression analysis is used to obtain the velocity distribution across the channel. As a typical length scale of physical habitat study sites is of the order of a few stream widths, the accuracy of the above approach is questionable, and a two-dimensional model may be more appropriate. The results of flow modelling of fish habitat based on one-dimensional and two-dimensional assumptions are compared. Firstly, the models are tested and compared for a hypothetical flow situation of flow over a side-bar, which shows a clear difference between the results of the one- and two-dimensional approaches. Then the two models are used to simulate the flow of water in a real fish habitat reach and the computed velocity results are compared with field velocity measurements. The results of the two-dimensional approach appear to be significantly better than the one-dimensional approach.

Microhabitat use by freshwater mussels and recommendations for determining their instream flow needs

AbstractA conventional application of the instream flow incremental methodology (IFIM) assumes that target organisms have specific microhabitat preferences and the ability to move to areas of suitable hydraulic conditions in response to changes in stream discharge. We investigated the use of the IFIM for determining the instream flow needs of a diverse mussel assemblage in Horse Lick Creek, a fourth‐order stream in the upper Cumberland River drainage in Kentucky. We determined habitat availability by measuring water depth, velocity and substrate at 60 cm intervals along 23 transects during low, medium and high flows. The distribution of mussels within the study site was highly contagious. Although habitat suitability curves developed from data collected on 2004 mussels indicated a clear preference for particular hydraulic conditions, the limited mobility of mussels in the coarse substrate of Horse Lick Creek implies that these curves are flow‐conditional—that is, mussels appear to prefer different hydraulic conditions at different stream discharges. Consequently, these curves are of limited value for determining conservation flows for mussels. Nonetheless, water depth and velocity were important factors limiting the distribution of mussels during base flow periods. Similarly, substrate characteristics were of limited value in defining mussel distributions; unfractured bedrock excluded mussels from portions of the study site, but mussels did not utilize all areas with preferred substrate. Because the larvae (glochidia) of mussels in Horse Lick Creek are obligate parasites on fish, data were also collected on habitat preferences of the host fishes. These data were incorporated in the physical habitat simulation system (PHABSIM) to determine the relationship between the availability of host fish habitat and stream discharge during periods of glochidia release and juvenile settlement.Unlike simple hydraulic variables, complex hydraulic characteristics such as shear stress were significantly correlated with mussel abundance for flows ranging from 0.03 to 2.18 m3 s−1. This range encompasses most flows during the period of juvenile settlement. We suggest that the high shear stress in some portions of the study site is a major factor limiting mussel recruitment. The lack of a significant correlation between mussel abundance and shear stress at high flow (9.35 m3 s−1) resulted from a variable relationship between shear stress and discharge among transects due to channel morphology. The higher shear stresses at most transects over mussel beds during a discharge of 9.35 m3 s−1 suggests that spates occurring during or shortly after juvenile settlement may result in a loss of juveniles.The unique life history and limited mobility of mussels necessitates a more complicated procedure than generally used for fish and other macroinvertebrates for determining conservation flows. Specifically, we recommend an approach that incorporates concepts of hydraulic stream ecology with the more common practice of modelling only simple hydraulic variables in habitat simulations. Estimating the complex hydraulic key characteristics can be performed with minimal effort through the selection of appropriate subroutines with PHABSIM. This approach may also be suitable for simulating habitat of other sessile organisms.

White Sturgeon Spawning and Rearing Habitat in the Lower Columbia River

Abstract Estimates of spawning habitat for white sturgeons Acipenser transmontanus in the tailraces of the four dams on the lower 470 km of the Columbia River were obtained by using the Physical Habitat Simulation System of the U.S. Fish and Wildlife Service's Instream Flow Incremental Methodology to identify areas with suitable water depths, water velocities, and substrates. Rearing habitat throughout the lower Columbia River was assessed by using a geographic information system to identify areas with suitable water depths and substrates. The lowering of spring and summer river discharges from hydropower system operation reduces the availability of spawning habitat for white sturgeons. The four dam tailraces in the study area differ in the amount and quality of spawning habitat available at various discharges; the differences are due to channel morphology. The three impoundments and the free-flowing Columbia River downstream from Bonneville Dam provide extensive areas that are physically suitable for rea...

Stream channel and habitat changes due to flow augmentation

AbstractA previously ephemeral stream is being used to convey water and create fish habitat as part of mitigation for impacts of a transbasin water diversion project. This stream, the South Fork of Middle Crow Creek, is located in the Medicine Bow National Forest, Wyoming. After two years of increased flow to the 8.8 km study reach, the amount of stream channel had increased 32 per cent and the total area of beaver ponds had more than doubled. Brook trout (Salvelinus fontinalis) stocked into the beaver ponds are surviving and growing. Factors limiting fishery development in the augmented stream include interrupted flow, discontinuous channels, and summer water temperatures exceeding 25°C. Analysis using the Physical Habitat Simulation System indicated that a flow of 0.07m3s−1 would maximize the amount of weighted usable area for brook trout under the channel conditions present in 1987.

REVIEW AND ANALYSIS OF METHODS FOR QUANTIFYING INSTREAM FLOW REQUIREMENTS1

ABSTRACT: Present guidelines for selecting a method to determine instream flow requirements and evaluating the validity of the results from a particular method are insufficient. This paper contributes to the efforts of researchers to develop a guide and critique for instream flow methods.A review of instreani flow methods and recommendations for their application is supplemented by a summary of a comparison of four independent analyses. The four analyses: the Physical Habitat Simulation System approach of the Instream Flow Incremental Methodology by the U.S. Fish and Wildlife Service, the Montana Method by Tennant, and two methods by Orsborn (Maximum Spawning Area Flow and Maximum Spawning Area) represent resource intensive and simplistic data collection and analysis methods. Each analysis was used to independently determine flows to support spawning by chinook salmon (Oncorhynchus tshawytscha) in Willow Creek, Alaska.Results of these analyses indicate that each method can be used independently or collectively to generate instream flow recommendations, if calibrated to the site or area studied. Once adjusted to the species and basin of interest, methods similar to the Montana and two Orsborn methods should be used to determine flow recommendations for areas where competition for water is minimal. The Instream Flow Incremental Methodology or similar methods should be applied when competition for water is keen or when detailed evaluations of the responses of species/life phases to flow variations are required.