The perks of writing a review paper

I’m writing my first review paper, and though it’s a lot of work, there are some perks. There’s the obvious perk of not having to worry that there is a 19 foot swell on the ocean today (seriously) and there’s no chance that divers will be out collecting data. The data for this paper has already been collected (mostly) by other people! And the less obvious perks – namely, that I got to spend time with actual books in the actual library last week. Sometimes it’s the small things that get me through a week of dissertation writing :)

The review is on pelagic-based trophic subsidies to kelp forest ecosystems. Think juvenile rockfish fresh from the pelagic ocean and recruiting to their adult kelp forest habitat only to be promptly eaten by adults, pelagic red crabs being dive-bombed by nearshore birds from above, and gelatinous zooplankton stranded in the kelp forest and getting sucked up by surfperches at every opportunity. Stay tuned for the paper to come out!

And for those interested in fish and fisheries in California, be sure not to discount information found in California Fish and Game Department bulletins going back to the early 1900s (images below) just because it hasn’t yet been digitized and put online. I found some incredible natural history information in these tomes. 

IMG_1871

IMG_1872

2017 Rockfish Recruitment and Ecosystem Assessment Cruise

R:V Reuben Lasker
The R/V Reuben Lasker.

I’m back out at sea on the NOAA Southwest Fisheries Science Center’s annual rockfish recruitment cruise. I’m on a slightly longer leg this year (June 1st-13th), but I’ve got a great route along the entire California coast – Eureka to San Diego. We’re also on a much swankier boat this year than in years past (the newly-commissioned NOAA R/V Reuben Lasker). The Lasker is a ship outfitted for science on the West Coast of the US, and provides a great platform for the trawl surveys that are the basis of the rockfish cruise each year. 

 

Diaphus_theta
California Headlightfish (Diaphus theta) – one of many fish we sample and measure on the rockfish cruise. 

Though the main goal of the cruise is to estimate the number of larval rockfish in the open ocean for management of California’s rockfish fisheries, we do all sorts of other sampling. Marine mammals and seabirds are counted during all hours of daylight, CTD (conductivity to measure salinity, temperature and depth/pressure) measurements are taken at every sampling site and at other sites up and down the coast to help us better understand the relationship between the physical ocean environment and the fish that we catch, zooplankton samples are collected and identified, and all species brought up in the night midwater trawl nets are identified, sometimes measured and recorded. This is everything from larval hake and market squid (two other very important fish species for California’s economy) to pelagic cnidarians (jellyfish!) and myctophid fishes like the California headlightfish. 

 

I’m on this cruise for several reasons. First, folks at NOAA’s Southwest Fisheries Science Center have been extremely helpful to me during my Ph.D. work. They’ve been generous with their time and happy to think about dissertation questions with me. So in turn, I’m happy to fill in on a leg of the cruise where they’re short-handed on scientists. Second, this is a great opportunity to collect some of my own samples. 

LostCoastfromthesea
The Lost Coast (Humboldt County) of California at sunset from the sea.
jelly
A Chrysaora colorata jellyfish.

 

 

 

 

 

 

 

 

I’m interested in the connection between ecosystems. In the kelp forests of central Californian, fish rely on energy derived from two distinct food chains – (1) energy from macroalgae (primarily giant kelp) in the forest itself, and (2) energy from phytoplankton in the open ocean (the system we’re sampling on this cruise!). A connection. Phytoplankton dynamics and prey resources in the open ocean impact the kelp forest food web. For example, the recruitment of juvenile crabs to the kelp forest (crabs that have been feeding on phytoplankton in the open ocean) could provide an energy-rich food source for benthic fishes. Or an influx of ctenophores (a jellyfish-like organism) from the California Current could provide easily accessible and abundant food for midwater-feeding blue rockfish. This seems plausible, even likely, but quantitatively showing the food web connection and the importance of the connection is not always straight-forward. 

I’m on the cruise taking samples of organisms that I know (or suspect) are occasionally carried to the kelp forest on currents. Size measurements will give me an idea of the size distribution of these organisms in the open ocean environment, and for now, I’ll have to assume that their size distribution in the kelp forest would look similar. Counts of the animals give me estimates of density. I’m still not sure how I can use open ocean density to estimate density in the kelp forest…that’s a work in progress. Finally, frozen samples I keep will be burned in a bomb calorimeter to tell me how much energy a fish would gain from eating one individual salp, jellyfish, pelagic red crab (or any of the other organisms that I’ve sampled). Basically, I’ll get a calorie count for each open ocean prey item that a kelp forest rockfish might eat. Based on my estimates of the density and average size of an open ocean animal in the kelp forest, and how much energy each provides, I can start a more in-depth analysis of the importance of this connection. If the energy provided is significant relative to the energy a fish gets from prey items that live in the kelp forest, I’ll continue to pursue these questions. If not, maybe prey from the open ocean provides a convenient and tasty treat for fish, but doesn’t influence wider population and ecosystem dynamics. Only time, samples, and more science will tell. 

 

We also had a NOAA Teacher-at-Sea aboard the Lasker during this leg! He’s an 8th-grade and high school science teacher creating lessons about West coast fisheries. Check out his blog here

at-sea_lab
Lab-at-sea on the R/V Reuben Lasker.
IMG_0924
An haul or mostly pink shrimp (Family: Pandalidae), an important species for California fisheries. The non-shrimp-looking things in this photo are pyrosomes, a colonial pelagic tunicate.
IMG_0961
One of our trawl catches on a station off San Clemente Island (San Diego area). Most of the fish are juvenile anchovy, but there are a lot of rockfish mixed in!
IMG_0968
Counting juvenile anchovy.
IMG_0981
We measure the total volume of the catch in each trawl, then identify each organism in the mix. This is 5 L of trawl catch, pre-sort.
IMG_0985
After sorting, many of the species get measured. One of the research questions currently being answered by NOAA scientists is whether hake (Merluccius productus, and an important fishery in CA) breed entirely in Southern California or throughout the entire state.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Fieldwork on the Mokelumne – an excuse to think about individual trait variation

mokulumneThere are many benefits of being part of a large, diverse lab. One of the most fun (and I think most valuable) of these is the opportunity to help other grad students with their fieldwork. A few weeks ago, I spent the day on the Mokelumne River with Megan Sabal, a Ph.D student in the Palkovacs and RC Labs

Aside from getting to watch juvenile salmon swim through a staged “migration route” with and without predator cues (the scent and sights of predators), I got a window into the thought process of another scientist. Because I study social-ecological systems and ecosystem food webs, I think that I sometimes overlook dynamics that occur at the level of the individual organism. Megan, on the other hand, is always thinking about how individual differences in behavior or physiology of any given fish might impact the wider environment or the population that it is a part of. In the experiment that Megan just completed, she’s hypothesizing that differences in individual salmon’s behavioral response to predators impact their migration rates, potentially their feeding ecology, and ultimately their survival and whether or not they recruit into the fishery as adults. 

In the context of the group of rockfish that call the kelp forest ecosystem home (my study system), individual differences in rockfish feeding ecology almost certainly exist. And though my approach will remain one that brushes over this individual variability to characterize the community or population, a day on the Mokelumne was a good reminder to take time now and again to focus in on the individual fish. 

Society for Applied Anthropology 2017

SfAA_logo

 

sfaaI attended the 2017 Society for Applied Anthropology meeting in Sante Fe from 28 March – 1 April with my mentor, Carrie Pomeroy. The highlight was presenting a paper in the session titled “Interdisciplinary Perspectives for Managing Marinescapes” along with talented folks from University of Alaska Fairbanks, U Saskatchewan and the U of Maryland. 

 

For my talk, “Social-ecological coupling in the central California nearshore, commercial fishery”, I focused on fisheries landings data from 1995-2015 and interpreted trends in this data using qualitative data collected from interviews with nearshore fishermen. Despite the fact that I got many suggestions to significantly expanding this project (something I’m not currently looking to do at the end of the 5th year of my PhD work), I gained so much just being able to interact for a week with professionals doing fisheries anthropology, oral history work, resilience theory work, and generally social science that is directly relevant to fisheries policy. 

 

Oh, and Sante Fe was beautiful. EVERYTHING was blooming and the art was incredible. 

thumb_IMG_0093_1024thumb_IMG_0039_1024thumb_IMG_0195_1024

New publication in BioScience – Long term studies are important!

Check out a new publication from the UCSC Raimondi-Carr Lab and the Lubchenco-Menge Lab at OSU!

https://academic.oup.com/bioscience/article-abstract/67/3/271/3057250/Long-Term-Studies-Contribute-Disproportionately-to?redirectedFrom=fulltext

and the press release to go along with it:

http://news.ucsc.edu/2017/03/long-term-studies.html?utm_source=03-14-2017&utm_medium=email&utm_campaign=tuesday-newsday

Raimondi-Carr Lab visits Mar Vista Elementary School

img_5545The RC Lab’s famous kelp forest made another appearance! This time at Mar Vista Elementary School. The kelp forest (which we pair with underwater video of actual monitoring transects) gives the students an idea of what marine surveys actually entail. In the lesson we’ve developed over the last several years, students learn the ID of several common species, think about habitat associations, make hypotheses, survey the “kelp forest”, and graph their data. We also let students try on and model our SCUBA gear which ends up being pretty entertaining (and hopefully sparking interest in marine research).

If anyone knows elementary (or middle school) teachers in the area that might be interested in our traveling kelp forest show, shoot me an email!

Climate growth relationships in the Pacific Ocean Perch – new publication!

wa_dfw

Ecology is one of the natural sciences, and for many people, that means that ecologists are left-brain dominated folks. We use the scientific method, apply ecological theory, and work to understand patterns in the natural world. What people don’t always see is that ecology requires an enormous amount of creativity. In fact, this is one of the things that draws many of us to the field.

pop_fisheryAs fishery ecologists begin to think more about our changing climate, creativity is essential. One of the major goals in the field is to understand how our fish stocks will respond to future ocean conditions. Often the best place to start is looking at how fish stocks responded to climate shifts in the past. Easy, right?

Fish stock responses in the Past  +  Climate predictions for the Future   =   Predicted fish stocks in the Future

But wait. Where do we look to understand how fish responded to climate shifts in the past? NOAA wasn’t around 100 years ago monitoring fish stocks and measuring oceanographic information. And though we have anecdotal evidence from fisheries, this isn’t always sufficient to truly know what a fish stock was doing.

 

[Enter creative problem solving.]

Tree ring scientists have been hind-casting climate (predicting what climate was doing in the past) using tree rings for a very long time. The basic method is simple.

  1. Core tree to expose tree rings
  2. Count the tree rings (assigning the latest ring to the current year) and assign a year of formation to each ring
  3. Measure the width of each ring assuming that a wider ring means that the tree grew more in that year
  4. Based on an understanding of the factors that make trees grow faster (i.e. rain, certain temperature ranges), use tree ring widths to predict rainfall and temperatures in the past.

But, what does this have to do with fisheries and fish responses to climate change? Take a look at the photos below. The first is the rings of a hardwood tree, the second, analogous rings in the ear bone of a fish! Fish produce rings – very similar to tree rings – in their otoliths (ear bones) as they grow. Borrowing methods from tree ring science, we can use the width of these rings to make predictions about ocean conditions in the year that each ring was formed.

tree_rings

94201001301_244_20x_a_rz

 

 

 

 

 

 

My collaborators and I used this method in a new paper out in Climate Research about Pacific Ocean Perch (Sebastes alutus) and past climate conditions in the Bering Sea. Since Pacific Ocean Perch can live to ~100 years old we were able to make climate predictions (using otolith ring width data) back to 1919! The chronology shows that shifts in the Pacific Decadal Oscillation (a shift from relatively warm to relatively cool Pacific Ocean temperatures) have critical and long-lasting impacts on the growth of this rockfish. Read the paper here for more detailed results:

http://www.int-res.com/abstracts/cr/v71/n1/

One of my favorite things about working with this group of collaborators has been the strong focus on making this work available and applicable to management of Pacific Ocean Perch, a high volume and economically important fishery in Alaska. Two authors on the paper are staff at the Alaska Fisheries Science Center, tasked with managing the fishery. This collaboration ensured that our work was relevant and that it is now in the hands of those making decisions for the sustainability of this culturally and economically important fish stock.

Photo credits: Live fish in ROV image: Washington Department of Fish and Wildlife; Pacific Ocean Perch haul: Alaska Fisheries Science Center. 

Western Society of Naturalists 2016

A few thoughts following the 100th meeting of the Western Society of Naturalists
Monterey, CA; 11-13 November 2016
Photo: A few of the past and present Raimondi-Carr Lab members at WSN 2016. 

rclab_wsn2016

NATURAL HISTORY
Two of the invited talks from WSN stand out to me. First, Jackie Sones won this year’s Naturalist of the Year and gave an inspiring speech on the study of natural history. A lifelong naturalist, Jackie discussed ways that she inspires others through her love of nature. Second, Jim Estes gave the closing keynote at the 100th anniversary of the Western Society of Naturalists. He used stories to discuss his serendipitous career in marine ecology. After the meeting, I’m still thinking about two things he said. Jim – a highly respected figure in ecology – told nascent ecologists that our science does not need to be hypothesis driven. I’ll repeat that. We don’t need to have hypotheses going into every study that we do! As someone who often learns best through simple observation, this was so reassuring. This doesn’t mean to me that hypotheses aren’t important for structuring science, simply that there is more than one path to discovery. He also made the point that the study of natural history is an amorphous thing. Natural history doesn’t have to simply mean being an expert in the taxonomy of organisms. Being in nature, observing and internalizing patterns and processes is also natural history. As always, I walk away from WSN with a renewed motivation to spend time in nature, watching and learning from ecology in action.

SHARING IDEAS
Imposter Syndrome has a perhaps too-close-to-home meaning for many graduate students. Like many, I go through periods of doubting my own ideas, interests and conclusions. However, the meeting of ecologists in Monterey this weekend helped to assuage these doubts. I met a recent faculty hire who is thinking about some of the same pelagic-nearshore marine connectivity questions that I’ve been thinking about for years. This seems minor, but was surprisingly affirming. So affirming, that I’m now considering writing a synthesis about what we know and don’t know on the topic!

100 YEARS
100 years is a long time! This society has promoted the study of natural history on the West coast, and members have been incredibly influential in shaping the larger field of ecology. I now find myself grappling with what I think the future of the Western Society of Naturalists should be. I think that maintaining a focus on natural history (in an era when mathematical models and global syntheses often fill top journals) is essential. To lose this focus and the inspiration that it gives to me would be a shame. But, what else could the future of WSN look like? Could the society use its large, influential membership to encourage diversity in ecology (more on this below),  encourage open and reproducible science, or shape relevant marine policy? Faced with collapsing fisheries, large-scale coastal habitat degradation and difficult decisions regarding marine use, should WSN continue to shy away from advocacy? I’m not sure how this would look (and certainly acknowledge that advocacy from respected scientists is risky), but I’m now pondering if there are issues today that warrant this risk.

WOMEN IN ECOLOGY
As part of the 100th anniversary celebration, President Jay Stachowicz solicited recommendations and votes for the 100 most influential papers in the field of ecology to-date. On Saturday night, he presented the results, and the top papers are all certainly deserving of accolade. However, I came away from the presentation deflated. Not a single paper discussed was first-authored by a woman. While I understand that we can’t change the history of the sciences (few women, dominated by rich white men), we can make a conscious effort not to overlook contributions made by women now (how were Jane Lubchenco’s papers not mentioned?!). I am disappointed that Dr. Stachowicz didn’t think to acknowledge that men may have been the history of the field, but that moving forward and tackling the wicked ecological problems of today will take a much more diverse set of minds, including the minds of the many women in ecology.

** WSN 2017 – Pasadena, CA **

 

Who knows what black surfperch in Carmel Bay are really eating?

Sometimes the data come in, and you learn only that you understand less about your study system that you had ever realized. I’ve been poring through stable isotope data lately, and not everything is as expected.

Background
Before I talk about that, a bit of background. One of my dissertation chapters focuses on the kelp forest food web, and how trophic connections (e.g. species A eating species B) shift on a seasonal and annual basis. One of my major questions in this chapter addresses whether adult rockfish – the fish that we all love to watch while diving and that many of us love eat in tacos – tend to eat more juvenile fish in the spring and summer when juvenile rockfish recruit to the kelp forest. I’m focusing on four species of rockfish (Sebastes spp.), but also sample black surfperch (Embiotoca jacksoni) as a control species (a fish that NEVER eats fish regardless of the time of year). Species photo illustrations below are by Larry Allen (CSU Northridge).

fish_w_perch

Before moving on, here’s a typical food web as I understand it in the kelp forest of central California (I know that my lack of artistic ability leaves something to be desired, but use your imagination).

zuercher_foodweb

What we know about what these fish eat
Black surfperch: amphipods! and other small crustaceans. What do amphipods and other tiny crustaceans eat? Algae, decaying algae, maybe even smaller crustaceans, phytoplankton.

Rockfish: any animal that they can fit in their mouth! OK, there are some nuances, but they are generalists meaning they eat a diverse group of prey items. Things like smaller fish, octopus, crabs, amphipods, jellies, brittle stars, shrimps, barnacles, urchins, the list goes on and on.

This information led me to the assumption that my four rockfish species would be eating approximately one trophic level higher than the black surfperch.

Nitrogen stable isotopes
The data in question here are stable isotope data. Stable isotopes (ring a bell from high school chemistry?) are a powerful method for understanding food web connections in nature. Though I won’t go into a full explanation, the important thing is that I can sample nitrogen stable isotopes to tell me the trophic level of a particular fish (i.e. how high on the food chain that fish eats). In my study, this translates to whether a fish is eating something that eats something that eats primary producers (making them a secondary consumer), eating secondary consumers (making them a tertiary consumer), or somewhere in between.

The plot that I’m confused about
So, here’s the relevant data. On the 1st plot, each color represents one of the species pictured above, each point represents an individual fish that I sampled, and the vertical axis shows N stable isotope values. The second plot translates those N stable isotope values to trophic levels. As you can see, the black surfperch (that well-understood species that I used as a control) came out at a completely different trophic level than I expected – higher than all of the predatory rockfish!

sidata_surfperch

trophic_level

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Running Hypothesis

1. I screwed up my sampling, processing, analysis. 

2. Because of the anomalous blog and El Nino ocean conditions happening during the years that I sampled, surfperch were eating their own offspring.

3. Surfperch prey on the eggs of other fish in the kelp forest. 

4. Some of the amphipods that surfperch eat are actually scavengers that eat dead fish (meaning that they actually are eating higher on the food web than the fish).

Right now I’m exploring why surfperch are eating at a higher trophic level than rockfish.  I’ve got help from several dedicated undergraduate techs who are combing through surfperch diet contents, and from Peter Slattery (MLML) who is identifying amphipods in the stomach contents to genus and teaching me about the feeding ecology of those amphipods.

If anyone has additional hypotheses for the unexpected high trophic level of black surfperch, send them my way!

Teaching in the field: ecology immersion courses

IMG_0998I had the amazing opportunity to TA the Ecology and Conservation field quarter (commonly referred to by students as the Supercourse) from March – June 2016.  Not only did I learn an incredible amount of natural history alongside students, but I got to observe two very talented field instructors (Don Croll, UCSC Professor of EEB and Gage Dayton, Director of UCSC’s Natural Reserves) to learn the field teaching ropes that they have perfected over the last 20 years.  Now that the the quarter has wrapped up, I have time to jot down a few thoughts on field learning, ecology immersion teaching, and the benefits of teaching natural history alongside ecology theory.

What is the Supercourse?
This course is a field-based, 19-credit course (!) for Ecology and Evolutionary Biology (EEB) and Environmental Studies (ENVS) majors. It is typically taken by juniors and seniors, though open to any students with the appropriate pre-requisites.  Students apply and interview for this course, and entry is competitive. Once accepted, the students spend an entire quarter (days, nights, weekends) immersed in ecology, conservation and research in outdoor settings. Last quarter, we spent time at Ano Nuevo Reserve, UCSC Campus Reserve, Landels-Hill Big Creek Reserve and in Baja California Sur on islands in the Gulf of California (the incredible resource that is the UC Natural Reserve System will have to be the discussion of another post). Students design and conduct several field research projects during the course, learning everything from natural history to experimental design to writing and presenting a scientific paper.

Why Supercourse?
Getting students outside to learn science by doing science is a good idea. We know this. Many benefits accrue when students are presented with hands-on learning opportunities in low student-instructor ratio courses.  I’m sold on field courses, have a goal of developing and teaching a field course after leaving UCSC, and could write a long blogpost about the many merits of immersion-style teaching.  However, instead I want to quickly point out several new things that Supercourse showed me.

Fostering excitement through field learning
Students came into the course clearly burnt out from college lectures, tests, and the competitive nature of the search for internships and research experiences. Students came out of the course excited to attend their next quarter of lectures having seen first-hand how ecology theory and statistics are used in research, eager to put their natural history knowledge to action, and invigorated to seek more research experience. No other time that I have spent with students has yielded such a drastic change in motivation (not to mention understanding of the academic material) in such a short time. Graduating seniors cited the course as the first university experience that has truly showed them what a career in research means, and said that the course provided clarity for their next steps in the field of ecology. Field courses foster excitement for ecology in a major way.

Bringing natural history back to ecology curricula
Throughout the course, students become intimately familiar with the places where they are working – familiarity with a system that one can’t learn from a text book, PowerPoint or video. Students learn the names or plants, the calls of birds, the habits of reptiles. They discover species-area relationships, patterns in the distribution of species, and biophysical feedbacks for themselves. The ecology theory, biological concepts and major paradigms that we teach in the EEB department were largely developed by scientists with a broad and detailed knowledge of natural history. Expecting students to understand these concepts and move into productive ecology careers without a basis in natural history seems crazy. However, you and I both know how dull a lecture on the identification of insects can be. Supercourse provides for a seamless integration of natural history back into the EEB and ENVS curricula (sans lectures), and I think that this alone makes the course incredibly valuable.

Learning stats using data YOU collected
I don’t remember a single thing from my undergraduate statistics course, and have yet to come across a student that is fluent in even simple statistics after AMS 60 (the UCSC undergraduate science-majors stats course). While the goal of Supercourse is not to teach statistics, data management and analysis are woven into the curriculum. Students use statistics on data that they collect, organize, and truly understand and care about. Though not expecting to, every student was conducting t-tests, ANOVAs, and doing linear regressions in JMP by the end of the quarter. This is a major accomplishment! I truly believe that undergraduate programs would be well-served to rethink current statistics requirements for ecology majors and move toward integration of statistics into research-based courses.

Building student confidence
Students begin Supercourse not knowing their classmates, TAs or instructors, having only a vague idea about the experience they’ve signed up for, and for some, having no outdoor or camping experience at all. This course challenges students academically, physically, socially and mentally. And when students come out alive (and successful) at the end of the quarter, the change in confidence is apparent. One of my favorite parts about TAing this course was watching students transition. Many students came to Supercourse uncomfortable with big ideas in ecology, afraid to voice opinions about experimental design, and shy to ask questions for fear of looking silly. By their final Baja projects, the same individuals were engaged in detailed discussions of sample size and how to test major ecological ideas in the desert ecosystem, and were asking me non-stop, interesting questions about natural history, ecology, and data analysis. These students walk out of Supercourse better academically prepared for graduate study, and better physically and mentally prepared for what a career involving field ecology entails.

Equity and diversity in field courses
UC Santa Cruz is a national leader in field immersion courses, and students here benefit immensely from the faculty and staff that have worked to make field courses a priority and reality. However, I feel strongly that we need to continue working to ensure that these courses are widely available. An incredible amount of faculty and staff time, logistics, and supplies go into teaching a field course, and as such, field courses are expensive. Though private donors and universities pick up a large portion of the bill, some of this cost is necessarily passed on to students. In my limited experience, it seems that typically only students with families that are able to cover the bill are able to enroll. Universities and organizations widely acknowledge that STEM fields have a diversity problem (a cultural, racial, gender and economic diversity problem), and finding ways that minority students can take advantage of these field courses should be a priority. These courses give students a competitive research and academic background to move into a job or continue to graduate school, and can be a much-needed tool for retaining minority students in STEM fields.

I left Supercourse with a many-page document of notes on field teaching and the motivation to seek out the experience I need to develop and teach a field course after leaving UCSC. I also left with a renewed excitement for my own research, and renewed dedication to my own development as a natural historian and field ecologist. As it turns out, TAs might just get more out of the course than even students do.

thumb_IMG_3923_1024

 

thumb_IMG_4526_1024

IMGP1473thumb_IMG_3820_1024

thumb_IMG_4246_1024

DCIM106GOPRO