Canopy Vegetation Monitoring Project

Megan Gaitan and Brian McIsaac

The Copeland Creek Monitoring Plan has grown from an ecological model formed at the start of the semester into a full blown project that now includes a baseline level of data and clearly outlined methods for monitoring in years to come. This investigation stems from eight attributes our class identified as the most important qualities we value in the creek: hydrology/channel morphology, native understory plant community, native canopy, aquatic community, avian community, the western pond turtle, steelhead, and wide-ranging/apex species.

With our love of plants and passions for biodiversity, our pair was tasked with creating objectives aimed at restoring the native canopy of the creek. The first one we formed was aimed at removing those willows (Salix spp.) that posed the largest threat to flooding the surrounding neighborhoods and replacing those trees with Alders and Cottonwoods. With data already having been collected form previous years on the willows, our group chose to focus on our second objective. This goal was targeted at improving the structure and composition of the canopy layer in order to provide more suitable wildlife habitat and more shade to cool water temperatures in the creek. With so many trees residing on the banks of the creek we were excited to get our hands dirty and learn about what’s going on in treetops.


Photo by C. Christian

As we’ve learned this semester, baseline data is key in measuring the success of restoration. You have to know where you want to go but you also need to remember where you started. And so, we identified three indicators that would help us and future classes assess progress. We determined canopy cover, density, and composition were the ways to gauge success. We evaluated the first indicator with a tool called a densiometer. This tool is as simple as it gets. It’s a hinged wooden box that opens up to reveal a convex reflective lens that is used to estimate overhead cover. Density and composition used species present in the creek and their diameters at breast height (DBH) to obtain information on the canopy’s structure that will determine where plantings of native tree species can be made that will improve weaker areas of the creek.

We couldn’t wait to get out on the creek and investigate current conditions of the canopy. Looking at riparian research methods in published journals allowed us to get an idea of how to design our sampling protocol in order to obtain substantial data. Along the four zones of the creek were six predetermined locations on the south bank where we would be collecting data. We marked these points and set up our transect facing north. Densiometer readings were taken at 3 m intervals beginning at 0 and ending at the edge of the bank. Each reading consisted of counts made in four directions: N, S, E, and W. Beginning again at the 0 m mark, we walked along the reel with a meter stick and recorded species names of trees whose bases fell within range of 1 m to the left and 1 m to the right of the line. Diameter at breast height was recorded for these species. If the diameter was less than 1, it was recorded as a sapling. Overhanging branches of trees whose bases were outside the range of the transect were ignored. This process was repeated at each of the six locations.

Data obtained from our bit of fieldwork was entered into Excel for calculations and graphing. Three figures were produced: percent shade at each transect, average diameter at breast height at each transect, and a scatter plot of average diameter at breast height against percent shade. Our results were not as informative as we hoped and they did not capture a full representation of the canopy or its structure and composition along the entire length of the creek. Much of the shade accounted for in the densiometer calculations of percent shade comes from the surrounding trees whose bases fell outside the range of the transect lines and shade levels of deciduous trees were not taken into account. Also, very few trees were encountered along the six transects. These factors make it difficult to understand what’s fully going on in the canopy. In the future, having a larger sample size will allow for a better understanding as well as collecting data from the opposing bank.

Despite challenges of not securing enough data to have more informative results, there were plenty of positive outcomes for our group. Together, we gained experience in experimental design, we learned how to practice various sampling techniques and data collection methods in the field, we learned how to quantify responses of canopy cover, species richness and composition, we have suggestions that can improve upon this protocol, and most importantly we learned firsthand how the restoration process is done. This set of skills we’ve developed through working with the campus on Copeland Creek is incredible. The challenges we faced in accomplishing this project will allow future classes to make great strides in successful restoration of the creek.


Copeland Creek Understory Restoration

By Jana Johnston and Jessi Laughlin

We were tasked with collecting base line data for the under story vegetation of Copeland Creek. To do this, we measured whole plot species richness as well as absolute and relative cover of herbaceous species by using a point intercept method and percent cover of shrub species using a line intercept method . 

Our two objectives were 1) to increase ground cover of native species to 25% or greater by 2020 and 2) to ensure a 1 meter radius around native plants with 0% Himalayan blackberry (Rubus armeniacus) cover.

First, we located and mark all seven transect lines. The transect lines were established by previous classes so we were provided with GPS coordinates to locate these points. Once we found the point we marked each one by hammering a piece of PVC pipe into the ground and spray painting a bright pink arrow pointing to the location. Once we found all seven transects we moved on to data collection.


Megan Gaitan marking our first transect of the day. Photo © Jessi Laughlin

We used a point intercept method to measure herbaceous species. To do this we extended a measuring tape from the PVC pipe to the top of the creek bank facing north. Next we walked along the transect line with a flag dropping it at every half meter. At each point we recorded every species (or bare ground) the flag touched, as well as within a 5 cm radius of the flag. For any unknown species we encountered, we documented them on our “unknown species master list” and took a small sample to take back to the lab for identification.

We also collected whole plot species richness of herbaceous species. To do this we flipped a coin, student ID, car key or any other flippable item we had, to determine whether we would measure the east or west side of the transect. Once we decided this, we walked along the transect with a meter stick recording all species present within this area.


Transect line crossing an unknown species. Photo © Jessi Laughlin

To measure percentage of shrub cover we used a line intercept method. Using the same seven transects, we took the measurement (meter) of any shrub foliage overlapping our transect. From these measurements we were able to calculate percent cover of each species for each transect. We also measured the shrub height at every 2m along the transect.

 During this process we encountered several stabbing, stinging and poisonous plant species and acquired a few injuries along the way. We discovered, as we were expecting, that many sections of the creek have been over taken by invasive species particularly Himalayan blackberry. Himalayan blackberry is a huge problem because it can grow extremely fast and large, choking and shading out other plant species. For more information check out the problem species blog post. However we also found that many native plant species are thriving including snowberry, California grape and California rose.

Based off of our data it’s clear that in order to promote a healthier creek habitat the Sonoma State community and future Restoration Ecology classes need to focus on removing Himalayan blackberry especially around the native plants we are hoping to keep alive. Removing the Himalayan blackberry will allow for planting of more native species that will have a better chance of succeeding along the riparian corridor.

One of the most interesting parts of this process was seeing the dramatic shift in vegetation from the overgrown black patches to the bare redwood grove up stream.

Throughout this process we created a step by step lab guide for future students to use to collect the same data we did. As the creek restoration project continues, students will be able to document the progress of the understory vegetation and will hopefully see a shift from an invasive dominated habitat to a more healthy, fully-functioning native understory system. 

Monitoring Plan for the Channel Morphology of Copeland Creek

By: Jordan DeSilva and Jasmin Perdue

The Plan

Channel Morphology of Copeland Creek–that was our task.  What did that mean?  What do we measure?  Where do we start?  Those were the thoughts racing through our minds upon our assignment.  The semester long project clearly began with research research research, which is always the most tedious task, but provided us with all the basis to develop our plan for monitoring the channel morphology, which if you don’t know is the  physical shape and geological composition of the creek channel. Our research led us to two monitoring protocols that we found relevant and decided to implement on the creek–cobble size distribution, which would lend us information about water velocities that may effect erosion rates; and creek cross sections, that would give us information to compare to future years in order to observe the ever changing channel.


The thought of counting hundreds of cobbles was nothing short of exciting. With calipers in hand, we walked the creek, surveying for an interesting spot. We laid down a transect line, and got comfortable, to record for what would be the next hour and half of rock measuring. Picking up rock after slimy, cold rock we measured the three axes of each rock. With aching backs, we finished measuring the final rock until we called it a day after finishing only one transect.


Data sheet for our cobble size monitoring © Jasmin Perdue


Jasmin measuring one of one many along a transect line. © Jordan DeSilva

The next day we marched back out to the creek, determined to finish the next two transects. Just when we thought cobble measuring couldn’t get any more exciting, it did! We had just laid out our second transect line when a swarm of Sonoma County Sheriffs came through, surveying the area for evidence concerning the murdered body recently found on campus.

Meeting with Michelle

Michelle Goman (who totally rocks!) came to our rescue when we realized we didn’t have a clue about what we were doing.  We walked into her office and this ray of sunshine whipped out all sorts of equipment in her tiny cubicle of an office, like she does this everyday of her life.


Practice with the auto-level equipment. ©Jordan DeSilva

She had us test out the equipment a couple of times and we all acted like we had the procedures down pact, but really we didn’t even begin to understand the foreign language she was speaking. When we finally got out in the field and realized we still didn’t know what we were doing, she came out to guide us through the process once again. Without Michelle, who knows if we would’ve gotten anything done!

Cross Sections

Oh man, did we have some problems with the cross sections. Thanks to Michelle it only took three days to figure out how to collect the surveying data, but there were more hurdles to come. Laying the transect lines meant that we had to have a straight path across the jungle of a channel that is completely dominated by Himalayan blackberry. This meant that we had to use loppers to cut back all the brush and blackberries in the way–that was fun!  Covered in cuts and scrapes and dirty as heck we managed to laugh our way through the struggle.

The paths were clear ,we knew what to do, and still no cigar. When we went to attempt a fourth time we realized that there was no way to secure the transect line on the opposite bank and that we needed help.  We went back to class, and with Caroline’s encouragement, we were able to recruit the lovely Amy and Danielle to help us hold the transect line secure and to help us record data. Ta-da! We had all the components for success finally. The four of us went out to the sites and busted out all three collections in roughly three hours.


A transect site that needed a lot of brush clearing. ©Jasmin Perdue


Jasmin reading the stadia rod through the auto level. ©Jordan DeSilva

The collections and struggles within them have secured in our minds that restoration ecology is no joke, but that with hard work and determination it can be done and the learning process is always interesting.

Salmonid Field Trip

Devil's Gulch

Devil’s Gulch

Restoration Ecology’s final field trip of the Fall, 2016 semester was a wonderful adventure in the redwoods, looking at restoration projects aimed at restoring habitat for salmonid fishes, including chinook and coho salmon. Our hosts for the day were Sarah Phillips of the Marin Resource Conservation Department (RCD), Erik Young, a lawyer affiliated with Trout Unlimited, and Eric Ettlinger of the Marin Water District. Each of them shared with us a different perspective on the creek, and how restoration projects happen.

You can read the rest of this story on my personal blog, Teacup Rex:

Salmon Crossing!


Written by: Gianpaolo Solari & Beverly Wong

Slide 1

Photo Credits:

It is widely accepted that California’s native fish (largely our salmon, steelhead, and trout) are experiencing a consistent, momentous decline. Many of these populations are diminishing at a dangerously rapid rate. Of course, there are many factors that drive our gilled friends towards extinction. Climate change and out mismanagement of water are large ones, but human population growth and destruction of habitat are large contributors as well. So what exactly is natural salmon habitat? To understand that, we must first understand the Salmon life cycle. The cycle starts in freshwater, when a female fertilizes her nest of eggs (also called a redd). These eggs will hatch as alevins (tiny fish with the yolk sac still attached to their body). These alevins will slowly grow, and emerge from their redd, and become fry. Fry generally live in their natal stream for about a year, and it is for this reason that they depend on appropriate habitat. These fry need logs, shade, and large rocks to rest and hide in. The fry will eventually migrate towards the ocean, where they will live for one to seven years. Salmon will then head back to their natal stream, where females build their redds, males fertilize these redds, and both the males and females die. With this in our minds, on November 18th we made the trip on a foggy Friday morning to Lagunitas Creek.


Sarah speaking about her role in salmon restoration at Lagunitas!

We were met by three friendly professional faces — Sarah, Erik, and Eric with a ‘C’. Because much of the salmon habitat have been degraded or completely destroyed, restoration projects that Sarah and her team have started focus on improving current habitat by mimicking conditions in the past when salmon were abundant. For example, a significant project that has been worked on includes implementing woody debris in the creek. Naturally, trees along the bank would occasionally fall over or branches would drop from the canopy and into the streams. These woody structures would catch onto the sides randomly, which creates deep pools, areas to hide from predators, as well as a slowed down velocity so fish do not get washed away down the creek.


Looks real, huh? Nope, just woody debris structures that have been plopped here in the creek!

It was a real treat to actually see the woody debris structures in place at Lagunitas Creek. Despite the fact that it is artificial, it did seem to fit in with the habitat aesthetically. However, the most important part was that it was improving the life of the salmon population, as well as other organisms that occupy the watershed. In fact, we happened to see a female salmon digging little egg depositories in the Creek as Erik was speaking about the very subject. It was a good feeling knowing that these structures actually were allowing salmon to survive and do other salmon-y things like hiding behind and within substrate when a huge storm hits.

While many individuals think that  restoration mainly focuses on the environmental and scientific aspects, the financial, political, legal, and social aspects of it all are overlooked. This trip in particular gave insight on all of the different but equally as important factors that play a large role in restoration and conservation. For example, Sarah told us her journey through learning about the difficult process of permitting and how she had to speak to the local community about and of the restoration projects that were being planned. Without getting a permit and without speaking with the community about their thoughts and needs, there wouldn’t even be a restoration project!


Making our way down to check out Lagunitas Creek!

Switching to Eric Young’s role on salmon restoration, he is someone you wouldn’t think would even be involved in a project: a lawyer – more specifically, an environmental lawyer that focuses and handles all of the legal aspects of a restoration project. There are always laws and regulations to follow, especially with heavy alterations to the environment like the woody debris that had been put in place along areas of Lagunitas Creek and Devil’s Gulch. And finally, the most commonly thought of to be a part of restoration is Erik’s role as a biologist that focuses on the statistics and science behind salmon populations in different areas.

With all of Sarah’s, Erik’s, and Eric’s knowledge and abilities in different fields, they come together as a well-rounded team to implement important restoration and other projects of environmental and social importance. Despite their differences in each of their fields, it is actually beneficial to have such different minds and personalities work together and it really showed during our trip.

Coming Together for the Coho Salmon

By Niall Ogburn, Danielle Wegner, and Michael Lutz. (All photos: Lutz)


The welcoming committee, comprised of Sarah Phillips (right), Eric Ettinger (middle), and Erik Young (left).


Eric Ettlinger standing in front of Lagunitas Creek

Cruising through the meandering roads of west Marin County, the students of Restoration Ecology at Sonoma State were about to experience salmon restoration efforts performed in the real world. Pulling into the parking lot of the Leo T. Cronin Fish Viewing Area, we were greeted by an eclectic salmon welcoming committee. The group comprised of SSU alumna Sarah Phillips of the Marin Resource Conservation Department (RCD), Erik Young of Trout Unlimited, and Eric Ettlinger of Marin Water District. Each of these individuals provides a distinct viewpoint fromtheir different areas of expertise towards one common purpose: restoring the Coho salmon (Oncorhynchus kisutch) population of west Marin.  This provides a perfect example of a critical concept learned in the classroom: understanding how to build bridges across various agencies and stakeholder viewpoints to get everyone on board with a restoration project.


Large woody debris visible from the Leo T. Cronin fish viewing area

In the shaded parking lot of Leo T. Cronin Fish Viewing Area, our first of three stops, we received background information on the history of salmon restoration in Marin county along with a perspective of different agency roles within the restoration process. Sarah kicked things off by providing background information on the anadromous lifestyle and the ocean-to-freshwater stream journey these fish traverse in order to spawn. We also went over the importance habitat health of streams and riparian habits have in order to protect the salmon eggs, and salmon babies, officially known as fry, as they grow into adults and make their way back to the ocean.

Sarah also explained the unique role she plays as Urban Stream Coordinator,  finding ways to connect the local community to the restoration project, opening up resources along with developing ways to promote sustainable living to protect salmon streams from degradation.

After explaining her role at the RCD, Eric Ettlinger of Marin Water District stepped in and explained the importance of woody debris and his task in monitoring abundance of Coho salmon along with creating woody debris restoration sites. We learned that past efforts to clear streams of woody debris are exactly the opposite of what is needed for the stream! Eric explained how he has to develop projects that will reinstate loss woody debris piles that are needed in the upper stream and creating slow moving wider rivers downstream.


Erik Young and Sarah Philips giving a game plan after for next stop

Next, we heard from Erik Young, a retired lawyer and professor who now works with Trout Unlimited. Erik shared with us some stories about the entanglement of litigation that comes with creating and implementing a restoration project that involves an endangered species under the Endangered Species Act.


Splashing of water from a female chinook salmon digging out a redd

With all of this information on the complexities of salmon conservation efforts, it was time to move on to the second stop. Hopes were running high for the opportunity to see this infamous fish.

At Lagunitas Creek, Eric Ettlinger explained the process female salmon use to create their nests. He was mid sentence when we heard a large splash in the water behind him. What could it be?! It was a female salmon creating the very thing that Eric was just talking about! A Chinook salmon was in the process of creating what is known as a redd: the female digs out a small pocket in the stream bed by flopping around and using her tail to create a safe spot where she can lay her eggs.

After the excitement of seeing this endangered salmon, we headed back up to the vans and drove to our third and final spot, Devil’s Gulch. 


Students gathered around the area in Devils Gulch where we ate lunch

Upon reaching our final stop, we decided it would be a good time to stop and have lunch, so the whole class sat down on the ground and enjoyed the warm of the sunshine on a brisk day while listening to Sarah talk about her days at Sonoma State where she once took some of the classes that we are in now!

After we all finished lunch, we headed out of the sun and into the shade of the creek canopy, as we went down to Devil’s Gulch to view several woody debris restoration projects that had been completed by Sarah and the rest of the team. Along the way, we tried to avoid the poison oak that was abundant along the path. We learned how the woody debris was brought down to the creek using machinery that would cause minimal damage to the surrounding areas of the creek. At our last spot on the creek, set beside patches of stinging nettle that give Devil’s Gulch its name, Sarah shared with us some of the struggles involved with getting permits and working with local government and community members in order to make these types of projects happen. She explained to us that it was a difficult area of her job that took a lot of effort, and stressed a need for the will to never stop trying to achieve your goal, even if your project proposals are rejected the first couple of times.


One example of the large woody debris installed at the Devil’s Gulch Restoration site with a large subsequent pool visible

It was extremely interesting to learn about the projects that were done in the Lagunitas Creek and how many benefits the woody debris has for the restoration of the salmon. It was also an absolute pleasure to have three very different backgrounds in the form of Eric, Sarah, and Erik to bring together the vast amount of knowledge they had on the subject and inform us of the importance of their work that they have been doing. They really showed us that even though you may come from different fields of work and focus on different aspects of a project, it is extremely valuable to have different minds come together to unite and complete a common goal for the betterment of the environment and the species that live in it.

Our Rainy Adventure at the Laguna de Santa Rosa

By: Jessi Laughlin and Jasmin Perdue

Our class got the opportunity to take a tour of the Laguna de Santa Rosa located off Highway 12 just outside of Sebastopol. Wendy provided us with some articles from Brent Reed (our tour guide and Ecological Program manager for the Laguna) to read and give us an introduction to the area and the changes that have taken place. It was neat to see some of the historical photos of the Laguna.

The morning started out with a downpour that caused us to leave a little later than usual. The weatherman said the rain would stop mid-morning but all we could do was keep our fingers crossed. Wendy called Brent to confirm we were still good to go and we were! Our very soggy group pilled into the vans and away we went.

We were greeting by Brent and Aaron and only a few sprinkles. Brent started our tour at Meadowlark Field where 3,000+ trees and shrubs have been planted as part of the overall restoration work in the Laguna. What was once a recreation area that later developed into a dumping ground is now being restored and preserved as the unique wetland it is.


Signage showing the history of Meadowlark Field. Photo © Jasmin Perdue

This area was the most recently restored part of the Laguna. Brent took us on a “journey through time” and we saw restoration work through the last decade. He shared photos of the area before restoration work had begun and little landmarks helped orient the photos for us to see the progress in plant growth.

The riparian corridor of valley oaks, Oregon ash, and box elders thickened as we progressed on the path. Brent pointed out that the wildlife seemed more abundant along the corridor as well. We came across a unique land bridge that is utilized by the Laguna Foundation that has to be removed in the winter due to flooding. This flooding is very important for the vernal pools nearby. There is an endangered plant that calls these vernal pools home. Aaron talked about some of the restoration efforts that have involved the process of disturbance and even some herbicide use when the endangered species is dormant.

The rain returned just in time for lunch. We struggled to open a little shelter tent and finally got it opened once the rains started to die down. The next part of our trip was planting basket sedge. Using the tools Brent and Aaron provided we cleared the top soil (and hopefully an exotic seed bank) for planting. Two large trays of basket sedge plugs were waiting to be planted. We planted in three different plots and then mulched with straw to help reduce exotics from germinating and to keep the moisture in the soil.


Cutting back the top layer of soil. Photo © Jasmin Perdue


Amy planting a basket sedge plant. Photo © Jasmin Perdue

With the rain gone and the plants in the ground we cleaned up to head home. We were so grateful for the time and information that Brent and Aaron shared with us. The Laguna de Santa Rosa is a diverse watershed that is moving towards healthier functions. It’s a beautiful place that we are lucky enough to have right in our own backyard. There are trails for the public to enjoy and we highly recommend it.