SSACgnp GB 661 MCR 1 3 Salmon Use

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SSACgnp. GB 661. MCR 1. 3 Salmon Use of Geomorphically Restored Streams at Point

SSACgnp. GB 661. MCR 1. 3 Salmon Use of Geomorphically Restored Streams at Point Reyes National Seashore Does stream restoration increase coho salmon use of streams? Use National Park Service salmon-use data to find out. Core Quantitative Literacy Topics Comparisons: Percent differences Supporting Quantitative Literacy Topics Bar graphs Calculating means Experimental design: control group Core Geoscience Subject Fluvial geomorphology; Fish habitat National Park Service Mark C. Rains Department of Geology, University of South Florida © 2010 University of South Florida Libraries. All rights reserved. 1

Getting started After completing this module you should be able to: • Know how

Getting started After completing this module you should be able to: • Know how to calculate percent differences. • Know how to make bar graphs. • Understand the role of a control in evaluating a “treatment. ” • Define “anadromous fish. ” • Understand that the balance between flow strength (e. g. , discharge) and flow resistance (e. g. , sediment supply) creates and maintains the characteristic patterns and profiles of streams which provide critical habitat for anadromous fish. California You should also know where Point Reyes National Seashore is. 2

The setting – Point Reyes National Seashore is in motion, and has been for

The setting – Point Reyes National Seashore is in motion, and has been for many millions of years. Here, the North American Continent has slid over the Pacific Plate and now moves slowly north by northwest along the San Andreas Fault. Movement is episodic, with little movement in most years and up to 20 feet of movement during infrequent large earthquakes occurring approximately every 130 years. Though in motion, Point Reyes is still located a short drive north from the San Francisco Bay Area, where visitors can still see tall, rocky headlands and broad, sandy beaches, forested, shrubby, and grassy hills and valleys, and cascading streams feeding placid estuaries, all of which provide habitat for over 1, 000 species of plants and animals including sea lions, elk, and salmon. National Park Service 3

Our star—Coho Salmon Coho salmon (Oncorhynchus kisutch), also known as silver salmon, are anadromous

Our star—Coho Salmon Coho salmon (Oncorhynchus kisutch), also known as silver salmon, are anadromous fish (Endnote 1). Anadromous fish are hatched and reared in streams, migrate downstream to live first in estuaries and then in oceans, and migrate back upstream to reproduce in the same streams in which they were born. For coho, this life cycle takes three years. At Pt. Reyes, spawning occurs in December-January. After spawning, every coho salmon dies and decays. Salmon are a vital part of food chains in all habitats they occupy: eggs and small juveniles in streams; large juveniles in estuaries; and adults in oceans. Spawning adults carry ocean nutrients back to streams where they are released when the fish die and decay. These nutrients fertilize plants and provide food to macroinvertebrates (e. g. , insects) that will provide cover and food for salmon that hatch the following spring. US Fish & Wildlife Service US Forest Service National Park Service But what do coho have to do with geology? 4

Fluvial processes and habitat, 1 Coho spawn and rear in streams. Streams, therefore, provide

Fluvial processes and habitat, 1 Coho spawn and rear in streams. Streams, therefore, provide critical habitat, without which coho could neither reproduce nor grow to maturity. The patterns and profiles of streams are controlled by the interaction between flow strength and flow resistance. Flow strength is largely a function of discharge (i. e. , how much water passes per unit time) and flow velocity (i. e. , how fast this water passes)—these are the forces of erosion. Flow resistance is largely a function of sediment supply (i. e. , how much sediment is delivered to a stream) and sediment size (i. e. , how large this sediment is)—these are the forces of aggradation. The interaction of these forces can be seen in the figure below, modified from the notes of the great 20 th Century fluvial geomorphologist E. W. Lane (Endnote 2). Climate and geology vary, even along a single stream. Precipitation and water use by plants vary in time and space, so discharge varies through the course of time and over the course of the stream. Geology varies in space, so slope, which controls velocity, and sediment supply and size vary over the course of the stream. These variations create complex fluvial features, even in individual streams. Modified from E. W. Lane 5

Fluvial processes and habitat, 2 The fresh-water habitat requirements of coho include upland riparian

Fluvial processes and habitat, 2 The fresh-water habitat requirements of coho include upland riparian vegetation to provide shade and stabilize hillslope and streamside sediments; varied water depths, flows, and flow velocities; cool, clean water; clean gravels, which are essential for spawning and egg-rearing; and adequate food. These are all interconnected—for example, the loss of upland riparian vegetation can result in direct sun and the rapid delivery of sediment to the stream, thereby warming the water, filling the deep pools, covering the gravels, and reducing the macroinvertebrate richness and abundance. Fluvial processes play a controlling role, helping to create and maintain all components of these fresh-water habitats. Many human activities degrade or destroy coho habitats. Culverts under roads are particular problems, resulting in sediment deposition upstream where water is slowed and sediment scour downstream where water can emerge at high velocities, particularly during storms. (Imagine what you could do with a fire hose to a pile of loose gravel!) Improper culverts can block coho passage if the flow velocities are too high, the water in culvert is too shallow, the resting pool below culvert is too shallow to support a jump, or if the jump height is too high (Endnote 2). 6

Fluvial processes and habitat, 3 Streams tend to form riffle-pool sequences. In the foreground,

Fluvial processes and habitat, 3 Streams tend to form riffle-pool sequences. In the foreground, you can see a pool; in the background, you can see a riffle. Further downstream, you can see some woody debris, which is addressed in the photograph at the far right. Riffle-pool sequences often occur in conjunction with meandering, with pools typically forming on the outside of meander bends, where flows are deflected downward and scour on the outside of the meander and deposit on the inside of the meander. Riffle-pool sequences also often occur in conjunction with large woody debris (LWD), with pools forming where LWD deflects flows and create local bed scour (e. g. , far background) or where LWD dams flows and creates backwater pools (e. g. , foreground). The pool on the left is on John West Fork, a small stream in the upper Lagunitas Creek-Olema Creek Watershed, which is the primary subject of the module. This photograph, like all of the photographs on this page, was taken at low flow, so the riffles above and below the pool were too shallow to permit coho to move upstream or downstream from the pool. Nevertheless, the pool supported numerous small juvenile coho at the time this photograph was taken. Those that survive will be able to move upstream and downstream when the wet-season rainfall begins a few months after these photographs were taken. These pools, then, are refugia, which allow coho to survive the annual dry season and repopulate the neighboring reaches quickly during the annual wet season. That’s a juvenile coho! 7

The problem The Lagunitas Creek-Olema Creek Watershed drains 267 km 2 and is the

The problem The Lagunitas Creek-Olema Creek Watershed drains 267 km 2 and is the primary source of inflow to Tomales Bay on the east side of Pt. Reyes National Seashore. The Watershed supports the largest remaining wild populations of coho in central California. These coho are part of the Central California Coast Evolutionarily Significant Unit, and are listed as endangered at both the state and federal levels. More than 50% of the historical coho habitat is currently behind fish-passage barriers, including five water-supply dams and many failing culverts. Significant efforts to protect and restore coho habitats are ongoing throughout the Watershed, including the repair of failing culverts currently acting as fish-passage barriers. In Fall 1999, a culvert acting as a fish -passage barrier on the lower John West Fork was repaired in an effort to improve coho passage and restore coho spawning to the stream reaches upstream of the culvert. This was done at considerable expense of limited resources. Question: Did the restoration effort work? How could we find out? 8

Let’s get the data, 1 The National Park Service has conducted coho surveys in

Let’s get the data, 1 The National Park Service has conducted coho surveys in Marin County watersheds, including the Lagunitas Creek-Olema Creek Watershed, since 1994. Results show that annual coho runs range from fewer than 10 to more than 200 individuals. Results also suggest that the culvert on the lower John West Fork was a fishpassage barrier prior to the repair in Fall 1999, as we will soon see for ourselves. We will work with data available in a recently published report (Del Real et al. 2007). The full reference for this report is included at the bottom of this slide. There are many ways to conduct coho surveys, including a variety of ways to directly count individuals at different life stages. However, let’s focus on an easy measurement of coho spawning. A redd is a depression on the stream bed created by the female coho and into which eggs and sperm are deposited. The female coho digs numerous redds, depositing hundreds of eggs in each during the one or two days during which she spawns. Redds are very obvious in the stream, being small depressions lined with clean gravel, and can be counted by simple snorkel surveys. That’s a redd! Bonneville Power Administration US Fish & Wildlife Service Del Real, S. C. , Carlisle, S. J. , Reichmuth, M. , Ketcham, B. J. 2007. Adult Escapement Monitoring Program Summary 2006 -2007. Natural Resource Technical Report NPS/SFAN/NRTR— 2007/001. National Park Service, San Francisco Bay Area Network Inventory and Monitoring Program, Point Reyes Station, CA. 9

Let’s get the data, 2 Here are your data. Click on the icon and

Let’s get the data, 2 Here are your data. Click on the icon and immediately save the file. The first tab contains redd data for John West Fork collected during the December-January spawning runs of 1997 -1998 through 2000 -2001. Let’s call this the “John West Fork data set. ” These data are the numbers of redds counted in successive one-kilometer (km) long stream segments upstream from an arbitrary point; “KM 0 -1” means 0 -1 km upstream, “KM 1 -2” means 1 -2 km upstream, and so on. Because the segments are one km long, the counts are immediately in units of redds per km for each segment, the same as “redd density” (analogous to population density). The data are from just the lower 15 km of John West Fork. The second tab contains redd data for the main coho-bearing streams in the Lagunitas Creek. Olema Creek Watershed, collected during the December-January spawning runs of 1997 -1998 through 2006 -2007. Let’s call this the “Lagunitas Creek-Olema Creek Watershed data set. ” These data are the mean (i. e. , average) redd density for the entire sampled length of each stream; i. e. , each value is the number of redds in the sampled length of stream divided by that stream length (in km). The value for John West Fork includes more than the just its first 15 km. Screen shots of both data sets are on the following page. Note two key features of these data sets. First, the culvert on John West Fork was repaired in Fall 1999, just before the December. January spawning run of 1999 -2000. Second, the culvert on John West Fork was located between KM 1 -2 and KM 2 -3 in the John West Fork data set. 10

Let’s get the data, 3 Below is a screen shot of the John West

Let’s get the data, 3 Below is a screen shot of the John West Fork data set located on the first tab in your spreadsheet. Below is a screen shot of the Lagunitas Creek-Olema Creek Watershed data set located on the second tab in your spreadsheet. Now let’s move on to the next slide and (finally!) begin our data exploration. 11

Explore the data, 1 Let’s start by making a 2 -dimensional bar graph using

Explore the data, 1 Let’s start by making a 2 -dimensional bar graph using the John West Fork data set on the first tab in your spreadsheet. The way you do this depends upon whether you are using Excel 2003 or 2007. When you are finished, your graph should look something like the one below. Return to Slide 16 Bar graphs (called column graphs by Excel) display discrete data in separate columns. Discrete data are data that fit into separate categories. In this case, our bar graph shows the number of redds in 1 -km stream lengths, where the 1 -km stream lengths are the categories named KM 0 -1, KM 1 -2, and so on. What does our bar graph suggest about the effects of the culvert repair on coho spawning on John West Fork? It may seem like we’re finished, but we’re not. We have compared the state of a variable before and after a treatment. By “treated system” we mean “a system in which we did something that may cause a change in a variable of interest” However, other things also may have caused a change in that variable. For example, perhaps stream discharge increased, which allowed coho to swim further upstream in the two years following the culvert removal than in the two years prior to the culvert removal. What we need is some kind of control, where by “control” we mean “a system in which we did not do something that may cause a change in our variable. ” 12

Explore the data, 2 For our case, let’s use as controls other streams in

Explore the data, 2 For our case, let’s use as controls other streams in the same watershed – ones that had no culverts removed. Again, let’s start by making a 2 -dimensional bar graph, this time using the Lagunitas Creek. Olema Creek Watershed data set on the second tab in your spreadsheet. Again, the way you do this depends upon whether you are using Excel 2003 or 2007. When you are finished, your graph should look something like the one below. Return to Slide 16 In this case, our bar graph shows the redd density, i. e. , the mean number of redds/km for the entire sampled lengths of each of the streams in the data set. The categories are now years covered by the December. January coho runs. What does our bar graph suggest about the effects of the culvert repair on coho spawning on John West Fork? We could use this graph to answer the question. However, we would be making absolute comparisons (judging differences in redds/km represented by the lengths of the successive bars from the same stream) and moreover making those comparisons visually from a busy graph. We would be better off making relative comparisons (percentage differences) in the redds/km at the various streams before and after the date of the treatment at the John West Fork. We can calculate those percentages easily on the spreadsheet. 13

Percent difference We need the percent change from an old quantity to a new

Percent difference We need the percent change from an old quantity to a new quantity. This is a common comparison, one that we frequently encounter when reading news. For example, in early May 2009, I read an article that stated that gas prices had increased 10% over the course of previous two weeks. The article meant that the new quantity—gas prices on the day the article was written—was 10% larger than the old quantity—gas prices two weeks before the article was written. This type of percent difference—one in which we are comparing a new quantity to an old quantity—is calculated using the following formula. Let’s do this with our data, with the old quantities being mean redd density on each stream before the culvert repair on John West Fork and the new quantities being mean redd density on each stream after the culvert repair on John West Fork. Put the following function in Cell B 12: =AVERAGE(B 2: B 3). Then put the following function in Cell B 13: =AVERAGE(B 4: B 11). Now select Cells B 12: F 13 and “fill right” by holding down the Control key and hitting the R key. Now let’s calculate the percent differences between our new quantities—mean redd density on each stream after the culvert repair on John West Fork—and our old quantities—mean redd density on each stream before the culvert repair on John West Fork. 14

Carrying out the plan Put the following function in Cell B 14: =(B 13

Carrying out the plan Put the following function in Cell B 14: =(B 13 -B 12)/B 12*100. Make sure you put the parenthesis around the subtraction in the numerator (i. e. , the top of the fraction). What happens if you don’t put the parenthesis around the subtraction in the numerator? Now select B 14: F 14 and “fill right, ” using the instructions above. Your spreadsheet should now look like this. Now we’re ready to answer our question: Did the restoration effort work? Return to Slide 16 15

End-of-module assignment 1. Print and turn in your spreadsheet, including the graphs that you

End-of-module assignment 1. Print and turn in your spreadsheet, including the graphs that you made on Slides 12 and 13. 2. Answer the question on Slide 12, using only information that you had up to that point in time. 3. Answer the question on Slide 13, using only information that you had up to that point in time. 4. Answer the question in the second box near the top of Slide 15. Write the value calculated if you don’t put the parenthesis around the subtraction in the numerator. In what order must the calculation proceed to arrive at this value? In what order does the calculation proceed if you do put the parenthesis around the subtraction in the numerator? 5. Answer the question in the fourth box at the bottom of Slide 13, using all of the information that you have in this module. 6. As previously presented, in early May 2009, I read an article that stated that gas prices had increased 10% over the course of previous two weeks. Gas prices on the day that article was written were $2. 25/gallon. What were gas prices two weeks before that article was written? Hint: Look at the formula on Slide 14. Multiplying the right side of the formula by 100 simply changes the left side of the formula from a proportion (e. g. , 0. 1) to a percent difference (e. g. , 10%). Change this formula replacing “%Difference” with “ 0. 1” on the left side of the formula, replacing “new value” with “$2. 25” on the right side of the formula, and omitting the “× 100” from the right side of the formula. Now solve this formula for “old value” using basic algebra. 16

Endnote 1 1. There are many species of anadromous fish. Perhaps the best-known anadromous

Endnote 1 1. There are many species of anadromous fish. Perhaps the best-known anadromous fish are the five species of Pacific salmon: Chinook (King), Coho (Silver), Sockeye (Red), Chum (Dog) and Pink (Humpback). They historically occurred in large numbers throughout the North Pacific Ocean Watershed. In recent years, many populations have declined, and some populations have been driven to extinction. For example, coho have been extirpated in the upper Snake River-Columbia River Watershed and the Sacramento River-San Joaquin River Watershed. Return to Slide 4. Charles Steinback and Andrew Fuller, Creative Commons Attribution-Noncommercial-No Derivative Woks 3. 0 17

Endnote 2 2. The figure on Slide 5 is reproduced below. Think through some

Endnote 2 2. The figure on Slide 5 is reproduced below. Think through some thought experiments to see what will happen. If there is more discharge (i. e. , greater flow strength) or less sediment (i. e. , lesser flow resistance), then the balance tilts to the right and the arrow points toward “degradation” (i. e. , erosion will occur). If there is less discharge (i. e. , lesser flow strength) or more sediment (i. e. , greater flow resistance), then the balance tilts to the left and the arrow points toward “aggradation” (i. e. , deposition will occur). Think also through what might happen if you increase or decrease the slope (see the end of the right side of the balance arm) or increase or decrease the size of the sediment (see the end of the left side of the balance arm). Return to Slide 5. Modified from E. W. Lane 3. Salmon require a 1. 25: 1 pool: jump ratio in order to generate enough speed to complete the jump. This can be a particular problem in shallow streams, such as those at Point Reyes National Seashore and the surrounding areas. Return to Slide 6. 18