Physical+habitat+1

=**50% DRAFT and PEER REVIEW**=

Physical Habitat
//By A. Martinez and M. Sims//

** Defining Physical Habitat (MAGGIE) ** The overall health of a river is based on a number of physical, ecological, and biological components. River restoration efforts, therefore, must take into consideration each component and its relationship with other elements of the system. Assessing the condition of physical stream habitat is critical in evaluating the overall health of a river (Thomson et al., 2001). In order to assess the health of a system’s habitat, there must be some understanding of how the system would function in the absence human influence (Davies et al., 2000).

Before river health can be assessed, physical habitat must be defined. Physical habitat is comprised of structural features including channel size, channel shape, gradient, and bank structure; furthermore, physical habitat also carries with it biological significance (Maddock 1999). For the purposes of this paper, physical habitat will be defined instream. Aquatic habitat varies __varies__ greatly from system to system because it is characterized by velocity, depth, cover, temperature, and substrate (Jacobson et al. 2001), all of which are related to a river’s flow regime. Physical habitat is clearly dynamic, both spatially and temporally, and depends upon the interaction between hydrological regime of a channel and various structural features (Maddock 1999).

In the realm of river restoration, understanding the characteristics of a given physical habitat is critical because of the role it plays in gauging the health of a river. According to Stalnaker (1979), water quality ( *link to water quality wiki page ), energy budget (i.e. temperature regime, nutrients), physical channel structure, and flow regime all contribute to the productivity of a stream system.

// Flow regime (MAGGIE) //

Flow regime is a primary determinant of physical habitat in rivers and, thus, greatly influences biotic composition (Bunn and Arthington 2002). Aquatic species - specifically fish for the purpose of this paper - rely on specific habitat characteristics to propagate and thrive. Petts (2009) points out that flow regime is a complex concept and provides two fundamental general principles related to flow regime:

(1) The natural flow regime shapes the evolution of aquatic biota and ecological processes and (2) Every river has a characteristic flow regime and an associated biotic community.

Many rivers and streams throughout the world have undergone significant changes in channel shape and structure because of both direct and indirect anthropogenic activities (Maddock 1999) related to flood control, agriculture, and urbanization. Channel modifications have tremendous impacts on instream physical habitat, which is one of the reasons why river restoration efforts should be concerned with environmental flows (*link to Ryan M’s wiki) that mimic a river’s natural flow patters. (Naiman et al. 2002).

// Assessment of river health (MAGGIE) //

The importance of using physical habitat to gauge river health is becoming increasingly important in restoration efforts (Maddock 1999 and Davies 2000). Evaluation of instream habitat can be used to judge the integrity of a river system (Muhar and Jungwirth 1998). A healthy ecosystem is characterized by flourishing native species populations; thus, a river containing healthy biotic composition will likely be indicative of a relatively healthy aquatic habitat.

Having a sense of a river’s health is beneficial for a number of reasons. It allows for more effective river management and also promotes greater understanding of what biological, ecological, and physical components have the greatest effect on overall health of a system. This information is critical to instream habitat evaluation because it can aid in the determination of what levels of detail are worthwhile yet cost-effective (Maddock 1999).

( More to come in this section )

// River degradation (MAGGIE) //

River degradation results from a number of direct and indirect anthropogenic alterations to the natural landscape (Maddock, 1999). Channelization, river engineering, hydro-modifications, watershed development, livestock grazing, construction of dams, agriculture, and deforestation are all activities that contribute to the degradation of a river. These activities, while economically beneficial, are detrimental to physical habitat (Jacobson et al., 2001).

There are a number of key considerations when assessing river degradation. For instance, knowing whether biological impairment is a result of habitat degradation or water quality degradation may allow for more tailored and effective restoration efforts (Davies 2000). Another consideration is understanding how exactly activities surrounding the stream affect the aquatic habitat.

( More to come in this section )

** Spatial scales (ADRIENNE) **

Many different habitat defining methods exist today and each method requires different data requirements from the next. These methods are applied over varying spatial spaces (redundant wording? or did you mean spacial scales?) and are important to define when deciding what restoration measures and fish habitats will be improved. Spatial habitat sizes are broken down into three distinct levels: macro, meso and micro. (Perhaps switch these 2 paragraphs, leads more into the subsequent 3)

(switch with previous paragraph? )Habitat mapping is a technique of surveying different spatial scaled areas and identifies the physical features of the ecological setting(?). This type of mapping requires a mixture of qualitative assessment and physical measurements that make up the form and structure of the river. These surveys require manual data collection, and because time is generally limited in the field the data is not always as complete as would be preferred. The smaller the surveyed area usually means the more detailed and accurate the collected data will be.

Macrohabitats consist of three levels of stratification and are used in modeling analysis; drainage basins, networks, and segments. Drainage basins are the largest of the three habitat components and can range from the size of tens to thousands of square kilometers (miles?). Networks are generally made up of two or more sub-basins and segments are considered to be the reaches in the river.

Since large areas and sizes are of concern, macrohabitats are broken down into smaller areas of mesohabitats. Mesohabitats are characterized by a common slope, channel shape, and structure and the length is about the same order of magnitude as the width of the channel. Mesohabitats are commonly known as pools and riffles but can also consist of cascades, glides and runs. Riffles are an important feature of freshwater channels and have a broken water surface providing excellent hiding areas from predators and since the current is fast it offers a great source of food. Riffles also oxygenate the water providing ideal congregating locations for fish and other aquatic life. Pools provide depth and still water areas not commonly associated with rivers and offer protection from predators.

Microhabitats are considered to be a combination of the hydraulic and structural features area the aquatic species lives within on the smallest of scales. These include the depth, velocity, substrate and cover available. The range of size for a microhabitat is usually less than one to several square meters. Microhabitats are the most studied areas for specific aquatic species due to the relatively small size areas and accessibility. Rio Grande spatial scales….

** IFIM (ADRIENNE) **

Federal involvement in dam construction began in the 1820’s in the effort to improve navigation along the Ohio River. After the Civil War, storage dams were built on the Mississippi River, dams were being built in rapid succession and by 1935 the Hoover Dam was completed. With the implementation of dams, reservoirs and water development methods came concern for the quality of aquatic habitats for wildlife.

The late 1970’s and early 1980’s signified the beginning of small hydropower development in the United States. Federal and state fishery agencies began looking more closely at the hydropower site practices. One of the main concerns with the hydropower companies were their enormous water releases and the effect on the environment. Rapid fluctuations in river flow can cause devastating results in many freshwater biota and the large amounts of water associated with hydropeaking greatly raises the height and flow rate of water in the river. Previous water management believed in setting minimum instream flows to define the amount of water in a river at which below this level fish and other aquatic life could not survive. Aquatic habitats in very small amounts of water were more susceptible to fatality during a hydropeaking event from one of these hydropower sites.

Instream Flow Incremental Methodology was developed under the guidance of he U.S. Fish and Wildlife Service and was the answer to handling the problems associated with these types of dam releases. Since the late 1960’s, biologists and hydrologists have developed instream flow methods that dealt with the problems faced by water development managers. As mentioned previously, the popular water management methods for maintaining water levels was to keep only the minimum amount needed for aquatic life in the river. This methodology has not been beneficial to the survival of fish and the western United States has since realized that it is not feasible to set minimum flows and rather have opted to mimic seasonal flows in these rivers using incremental methods. ( [], IFIM Historical Backdrop)

"IFIM is based on the analysis of habitat for stream-dwelling organisms under alternative management treatments. One could logically question why habitat was chosen as the decision variable in IFIM when there are so many other factors (such as stream productivity or fishing mortality) that can potentially influence fish populations. The simplest reason for basing the analysis on habitat is that IFIM was designed to quantify environmental impacts, and impacts to habitat are the most direct and quantifiable." (Stalnaker et al., 1995, p. 16).

In 1970 the National Environmental Policy Act(NEPA) was enacted. This new act helped in the decision to change water management practices from setting fixed minimum flows to using incremental methods. Early research focused on life-stage-specific relations for selected species; fish passage, spawning, and rearing habitat versus flow. From these studies came the development of habitat versus discharge functions. Researchers correlated the health of fish populations to the physical and chemical attributes of the flow regime and found that the following set of variables greatly affected the changes in fish survival:

These variables became the basis of incremental methods and are used to determine how water is managed in the withdrawal and storage-release activities of rivers and federal water projects. Water quality and quantity for ‘potential habitat’ became the foundation for the IFIM and once again took into account the relationship of habitat versus flow. IFIM is a simple general problem solvingapproach that uses five successive phases for planning: problem identification, study planning, study implementation, alternative analysis, and problem resolution.
 * water velocity
 * minimal water depths
 * instream objects such as cover
 * bottom substrate materials
 * water temperature
 * dissolved oxygen
 * total alkalinity
 * turbidity
 * light penetration through the water column

The Rio Grande Watershed is approximately 1.9 million acres in New Mexico. Along its length it collects a number of streams that drain into it: the Rio Chama, the Jemez River and the San Jose/Rio Puerco. Although there are smaller watersheds that connect into the Rio Grande in southern New Mexico, they are most often ephemeral. The Rio Grande flows almost entirely due to snowmelt in the spring and rain from summer monsoons. The river runs low in the winter with a peak between early April and mid-May (snowmelt) and another low flow in June with small peaks throughout the summer (monsoonal rains). The Rio Grande has been drastically affected by dams, diversions and reservoirs and does not see the same flow patterns of the past. The river has been channelized and flooding is nearly impossible due to the structure of the banks. Using IFIM and other modeling approaches, the goal is to mimic and release flows typically seen in the normal flow regime of the river.

** PHABSIM (ADRIENNE) **

The Physical Habitat Simulation System (PHABSIM) is a computer modeling system that is part of the IFIM and like IFIM, is based on flow versus life stage specific habitat requirements. PHABSIM uses field measurements of channel shape, velocity, depth and substrate of a microhabitat along with combined hydraulic modeling and habitat knowledge of specific aquatic species. The result is a simulation of the quality and quantity of the existing habitat versus flow relationships based on current conditions and a ‘potential habitat’ using smarter proposed water development. PHABSIM is able to calculate the amount of microhabitat available for different life stages at different flow levels of a target species. ( THERE IS STILL MORE TO COME ON THIS SUBJECT )

** HEC-EFM (ADRIENNE) **

The Ecosystem Functions Model models the ecosystem responses to changes in the flow regime of a river. HEC-EFM uses statistical analyses of relationships between hydrology and ecology, hydraulic modeling and the use of Geographic Information Sysems (GIS). HEC-EFM results show existing ecologic conditions and can map out areas of desirable restoration sites and can assess and rank alternatives for predicted changes within an ecosystem. The modeling system is not dependent on just one specific relationship to test ecological changes but rather multiple relationships and flow regimes.  ( FREE MODELING SYSTEM )

**ECOPATH (ADRIENNE)**—not flow, more food webs. ( more on this subject after some research ) Another computer modeling simulation software system being used around the world is Ecopath with Ecosim (EwE). EwE combines the Ecopath software for ecosystem trophic mass balances (biomass and flow) analysis and the dynamic modeling Ecosim software to investigate the past and future impacts of habitats. The Ecosim models can be combined with Ecospace to view policies over a spatially dynamic map grid of protected areas.  ( NOTE: free modeling system )

Meghan's comments- looks really good. Nice and cohesive, just watch your tenses. Other than a few grammatical errors (which we all obviously will fix before the final draft), didn't see anything major that is in need of improvement. I would like to see an example of a study or restoration that uses any of these models, might help put a face to the concept?

 Ryan's Comments: Your paper is a good start. I like the font, I didn't have to strain my eyes. Are there going to be any figures? Incuding some figures will give the reader insight on physical habitat within a stream (riffle, pool, glide, habitats for fish, etc). I would recommend spelling out the whole acronym in the heading of a discussion area (ex. Instream Flow Incremental Methodol ( IFIM), Phab Sim, etc) it will give the reader an understanding as they read than guessing or trying to remeber by just seeing the acronym. I would also recommend putting your names at the beginning of the topic, so people know who developed it. Because there are two of you, I would of recommended one doing instream and one covering riparian forest as physical habitat because they serve a great role in rivers/streams and are part of a river/stream system. There was one word used twice in the beginning that I highlighted in red. Harris Nassam's comments: As Ryan mentioned, the paper has a great and strong start. The introduction is compelling and well put. However, adding few conceptual pictures of the stream might be a helpful thing not only for visual aid purposes but also to engage the readers. Like Ryan said, defining the acronyms once the first time sounds like a great idea to help readers not trying to keep up with their meanings. All in all, you guys did a great job considering this is the first draft. Way to go folks !

I agree with all of the above. You have put together a well structured paper so far. I would also add that a discussion on the positives and negatives of the various approaches to modeling physical habitat would be helpful to the reader. Overall, good work!- Jeffrey =**REFERENCES**=

Davies N.M., Norris R.H. and Thoms M.C. (2000). Prediction and assessment of local stream habitat features using large-scale catchment characteristics. Freshwater Biology45: 343–369.

Jacobson, R. B., S. D. Femmer, and R. A. McKenney. (2001) Land use changes and the physical habitat of streams - a review with emphasis on studies within the U.S. Geological Survey Federal-State Cooperative Program. U.S. Geological Survey, Circular 1175, Reston, Virginia.

Maddock, I. (1999), The importance of physical habitat assessment for evaluating river health. Freshwater Biology, 41: 373–391. doi: 10.1046/j.1365-2427.1999.00437.x

Muhar S. and Jungwirth M. (1998) Habitat integrity of running waters — assessment criteria and their bio- logical relevance. Hydrobiologia, 386: 195–202.

Naiman, R.J., S.E. Bunn, C. Nilsson, G.E. Petts, G. Pinay, and L.C. Thompson. (2002) Legitimizing Fluvial Ecosystems as Users of Water: An Overview. Environmental Management 30: 455- 467.

Petts, G. E. (2009), Instream Flow Science For Sustainable River Management. JAWRA Journal of the American Water Resources Association, 45: 1071–1086. doi: 10.1111/j.1752-1688.2009.00360.x Stalnaker C. (1979) The use of habitat structure preferenda for establishing flow regimes necessary for maintenance of fish habitat. The Ecology of Regulated Streams (Eds J.V. Ward & J.A. Stanford). Plenum Press, London.