Adapting to a changing environment

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Like many of the animals we study, us Oregon Sea Grant Summer Scholars must adapt to our new environment.  I am fortunate to be a recipient of the 2018 Oregon Sea Grant Summer Scholar position with NOAA Fisheries.  Although working with NOAA Fisheries is a dream come true, this is not the work environment that I am used to. My experience working in fisheries includes wading through Eastern Oregon and Washington desert streams during the hot summer months while collecting population and habitat data. Common hazards during my prior field work included dehydration, rattlesnakes, thorny vegetation, slippery rocks, and getting shocked constantly while electrofishing. During my short time working in a federal office I have found the hazards to be extremely different.

To begin, my training started off learning about the hazard of data breaches and hacking. Recent hacking into large corporations and even during our last presidential election has led federal agencies to take a hard line approach to data security. Secondly, commuting may pose the hazard of getting your semi-formal clothes totally soaked by an unexpected thunderstorm. This will get you to think twice about grabbing your raincoat or umbrella on your way out the door. Lastly, given our current political environment there have been protests outside of our building in recent months seeing as we share floors with other federal agencies facing opposition from the public. This has led to tighter security and awareness of potential physical hazards to federal employees.

In summary working at a federal office has been quite the change for me coming from a field-based background. I have been learning a great deal about the organizational structure of NOAA Fisheries, diving into documents explaining the role of NOAA Fisheries under the National Environmental Policy Act, and meeting co-workers in different branches of the office. The people here at NOAA Fisheries are extremely passionate about the work they do and have been very welcoming to us interns. As there is much more to read about NEPA I will conclude my blog here.

Dungeness crab DNA sequencing and big data

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We have been collecting the megalopae life stage of Dungeness crab along the Oregon coast and extracting DNA from these individual megalopae. The next step is to sequence the Dungeness crab megalopae DNA so we can conduct statistical analyses that will help us understand how oceanographic conditions impact the Dungeness crab megalopae recruitment and the genomic composition of Dungeness crab along the West Coast of the United States.

Dungeness Crab Larval Recruits in Yaquina Bay,
Newport, Oregon (Megalopae)

Before jumping into the details to genomic sequencing, imagine you are given a stack of 100 cover-less books and told that there are several different book series mixed within this stack. You are asked to categorize the books by series.

What if you were given a pile of 100 books and asked to categorize them by book series?

You could read every book, but this might take a very long time… And, it may not be necessary to read every book cover-to-cover if your only goal is to categorize the books by series and not necessarily understand the storyline details of each book. Right?

So, what if instead of reading all 100 books, you systematically read the first paragraph of each chapter. Would you have enough information about each book to group the books into series? Chances are that each series has their own characters, settings, themes, or writing styles. By reading the first paragraph of each chapter in each book, you would be able to pick-up on the characters, settings, themes, or writing styles of each book that differentiate each series. You could then group the books together that had the same characters, settings, themes, or writing styles.

We do something similar with Dungeness crab DNA. Sequencing the Dungeness crab megalopae DNA involves reading the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up the DNA and then comparing the patterns of ‘A’s, ‘T’s, ‘G’s, and ‘C’s between individual crab megalopae to look for differences. Considering that the size of the Dungeness crab genome (all of its DNA) is quite large, it would be a costly, time-intensive, and computationally-intensive process to sequence the entire genome of every megalopae we want to analyze.

After collecting Dungeness crab megalopae and extracting DNA from individual megalopae, we use sequencing machines to read the DNA. But instead of reading the entire genome, we read many small sections from across the genome. This type of DNA sequencing is called reduced representation sequencing. Similar to the pile of books example, after this type of sequencing we couldn’t tell you everything about the genome of that particular Dungeness crab, but we would know enough about the individual crabs (or “books”) to tell if they are different from each other and if they were members of different groups (or from different “book series”).

Reduced Representation Sequencing (Truong 2012)

If the groups of crabs (“book series”) differentiate significantly, we can call them different populations. Alas, this is why we call ourselves population geneticists. We know that all Dungeness crab are of the species Dungeness crab (Cancer magister) and that all “books” are of the species “book.” But with population genetics, we are looking within species to to determine if there are sub-populations (or “book series”) within the species. Because of the social, economic, and ecological value of the Dungeness crab species along the West Coast, it is important that we understand the population genetics of the species so that we can continue to sustainability harvest this valuable fishery.

Dungeness Crab Commercial Fishery

A big year for small Dungeness crab megalopae

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Since I am studying the genomics of Dungeness crab megalopae, I first need to catch some megalopae and extract their DNA! Both last year and this year we have collected Dungeness crab megalopae in Yaquina Bay at the Hatfield Marine Science Center. The Dungeness crab megalopae are about the size of the eraser on a pencil.

 

We use a light trap to catch Dungeness crab megalopae. A light trap is a device used to collect the larval stages of marine fishes and invertebrates. A light is placed inside a clear container with several funnel entrances on the outside of the container and a mesh collection chamber on the bottom of the container. Below is a picture of the light trap that we use. The light trap is placed in the water and tied to a dock. The trap floats just under the surface of the water and shines bright like a beacon at night.

Light Trap Used to Collect Dungeness Crab Megalopae

Some larval stages, such as Dungeness crab megalopae, are attracted to light and move towards light sources. This behavior is called positive phototaxis. You have probably seen this phenomenon when you turn on an outdoor-light at night and then within the hour moths are surrounding the light. For this reason, marine light trapping is an effective way to collect live larval fishes, or live Dungeness crab megalopae.

Dungeness Crab Megalopae

At night, Dungeness crab megalopae are attracted to the light in the light trap. They swim towards the trap and through the funnel entrances where they are then entrapped within the container. In the morning, the trap is pulled out of the water and the collection chamber is emptied. We count how many Dungeness crab megalopae are collected each night and preserve a subsample of the megalopae for genomic analyses.

Light Trap Floating Below the Surface in Yaquina Bay

Our light trapping for Dungeness crab megalopae in Yaquina Bay follows methods from Dr. Alan Shanks’ Lab at the University of Oregon’s Oregon Institute of Marine Biology (OIMB) on Coos Bay in Charleston, Oregon. At OIMB, the Shanks Lab has been light trapping and documenting the daily abundances of Dungeness crab megalopae for over a decade. They are studying how oceanographic conditions impact Dungeness crab megalopae recruitment patterns. Dr. Leif Rasmuson, a 2011-2012 Malouf Scholar, worked on this long-term project.

You may remember from my first post, that I am specifically looking at how coastal upwelling, the timing of spring transition, and the Pacific Decadal Oscillation influence annual Dungeness crab genetic composition. The reason I am studying these three specific ocean conditions is because Shanks and colleagues have found relationships between these three ocean conditions and the annual abundance of recruiting megalopae collected by light trap in Coos Bay, Oregon.

Megalopae Light Trapping Locations in Oregon 
(Photo Adapted from Rasmuson 2013)

The Dungeness crab megalopae recruitment season is April through September each year. In 2017, we caught a total of 12,000 megalopae in Yaquina Bay throughout the season. Currently, we are only two and a half months into the 2018 Dungeness crab megalopae recruitment season, but it is already turning out to be a big year for megalopae recruitment catches. This year we have caught over a half-million Dungeness crab megalopae in our Yaquina trap! And the Shanks Lab at OIMB has also been seeing record numbers of megalopae recruits this year. It is a very exciting time to be studying Dungeness crab megalopae!

A Big Daily Catch of Dungeness Crab Megalopae in the Yaquina Bay Light Trap (May 2018)

So, I mentioned that we preserve some megalopae from the light trap for later genomic analysis. To study the genomic composition of Dungeness crab megalopae, we need to extract the DNA from the megalopae. In fisheries genetics, we immediately preserve fish or crab tissue while in the field by placing a fish fin, a crab leg, or a full megalopae into a plastic tube of ethanol. This ensures that the DNA does not degrade before we can extract the DNA from the fish or crab tissue.

Preserved Megalopae Collected from Yaquina Bay, Newport, Oregon
(Photo by Ketchum 2017)

DNA extraction sounds like it might be a complicated process, but it is relatively a simple protocol. You can actually extract your own DNA quite easily with ingredients from under your sink! Take a look at the below video if you want to try and extract your own DNA!

 

When we extract fish or crab DNA in the laboratory, we use slightly different chemicals than in the above video, small plastic tubes instead of plastic cups, a heating step to break the double stranded DNA into single strands, and a centrifuge machine and filters to separate the DNA from the rest of the solution. Think of the centrifuge machine like the spin cycle on your washing machine. The wet clothes spin at high speed and the water is removed from the clothes by being forced out of the small holes in the sides of washing machine like a filter. You are left with only dry clothes and no water, just like you are left with only DNA and not the liquids you used to extract the DNA.

Laboratory DNA Extraction
(Photo from http://2017.igem.org/)

We extract the DNA from many Dungeness crab megalopae collected throughout the 2017 and the 2018 recruitment season. The next step is to determine the sequence of ‘A’s, ‘T’s, ‘G’s, and ‘C’s in the extracted DNA so we can conduct genomic analyses and better understand how ocean conditions are impacting the genomics of Dungeness crab.

The Hustle and Bustle of Ocean Resource Management

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I’ve been extremely busy since my last check-in, which is exactly how I love to work.  Remember, diamonds are made under pressure! 

I’ve learned a lot since publishing my last post –

  1. Creating and supporting ocean policy can be a difficult hands on process of legality, long timelines, and networking.
  2. Engaging the public is necessary at all stages of a policy process, and even though you pride yourself on opening new doors to make it easier to engage, you may not always like what you hear.
  3. Sometimes you have to be comfortable throwing away a meeting agenda while facilitating a large group.
  4. Not every hotel offers complimentary hair conditioner...

The Rocky Shore Road Show

Presenting some background on the TSP Part 3 to some community members in Brookings, OR.

Since we last spoke I have been involved with creating, distributing, and managing a public scoping process to make sure all voices are heard in the Territorial Sea Plan – Part 3 update.  Oregon’s 1st Land Use Planning Goal focuses on public engagement, and as an over controlling, too connected to communication outlets, millennial, I was pretty excited to dive right into doing my best to make sure we explored every way of engaging rocky shore lovers.  This included creating online and printed outreach material, 2 online questionnaires, partnering with organizations who can promote on social media, and hosting 9 public scoping workshops all over the Oregon Coast and Willamette Valley (hence the hair conditioner revelation).

Naturally, lots of pit stops were made during the Rocky Shores Road Show. My mentor Andy Lanier thought it would be fun to document my nearly getting blown off Cape Blanco while trying to take a photo down the South Coast. Update – I did survive these Gail force winds, but my scarf sadly did not.

Some exciting news came recently!  The NOAA Project of Special Merit that I applied for in January has been accepted (based on federal funding of course).  This is by far the largest grant I have ever applied to, let alone gotten!  It will provide nearly $250,000 to support the continuation of the Rocky Shores Management Strategy update process and will also fund the creation of a communications plan to help engage and educate the many people that love and use Oregon’s rocky coast!  Stay tuned, more information is set to be coming in soon!

 

There are some perks to your mentor doubling as a photographer =]

Some Other Thoughts

In addition to the rocky shores process, I’ve been lucky to have the opportunity to aid in other capacities around DLCD and with it’s partners!  Being able to expand into other projects has really opened my eyes to the multitude of things that Oregon’s Coastal Program is really involved in.  It’s astounding that the amazing people here are able to do so much with such a limited staff and a 30% funding cut.  I can’t even imagine what it would be like with full funding.

Reminded myself that I’m still afraid of heights at Blacklock Point!

Here are some of the other aspects of coastal management that I have been thrilled to be involved with – just to name a few

  1. Helping to staff another exciting Ocean Policy Advisory Council Meeting – and creating briefing materials to update the council on the Rocky Shores Process.
  2. Lead the efforts in promoting tribal nations correspondence for the Rocky Shores process and the Coastal Program as a whole.
  3. Learning about the many aspects of federal consistency and enforceable policies and bringing those into the Rocky Shores Process.
  4. Too many presentations to count!
  5. GIS – turns out I’m not naturally gifted at using ArcGIS…go figure…but I’m still working along to gain those skills!  Thank goodness for a patient mentor =]
  6. Gaining experience reviewing participant and company applications for different RFP’s and positions

I figured I should mix it up for once and show one of the amazing terrestrial things I’ve gotten to enjoy as a part of all of my travels. During one of our first trips to the south coast we got the most spectacular glimpse of a heard of elk in the Umpqua River Valley. The whole heard was grazing on the juicy grasses supported by the estuary. As we stood there the heard moved closer and closer until they were only tens of feet from us! Being an east coaster I couldn’t help but stand in aw of these vegetarian beasts and jokingly think “that’s the biggest white tailed deer I’ve ever seen!”

Finally, and somewhat non-related:  My possible over-use of #ILoveMyJob on Instagram has now become the butt of all my friends jokes…but what can I say… #ILoveMyJob and I don’t care who knows it!

The importance of outreach and good science communication skills and why I love this aspect of my job!

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Doing research is an essential part of the scientific process. In the scientific community, the epitome of valid research is having it published in a peer-review journal. Unfortunately, this is as far as many scientists go.  But what about sharing your research with local communities, i.e., non-scientific audiences, that might be impacted by this research? What about connecting your research to a bigger picture?  For the public to be able to make intelligent decisions in many areas–how to allocate the communities’ budget, what fish to eat, personal choices on use of plastic and other trash—they must be able to understand what is at stake.

Me presenting a poster at Land Sea Symposium in Yachats OR, sharing my research with other scientist and coastal community members. Photo: Cyndy Leoro

However, many in the scientific community have spent decades seemingly separating themselves from the non-scientific community. Scientists use a whole different vocabulary than the average person in an attempt to explain natural phenomena. They use complex statistical analyses to prove their theories, and some may even pride themselves in knowing what is best for the disadvantaged communities that are in need of a scientist’s help. But this is where we have gone wrong. As scientists, we have at times alienated ourselves into a bubble, stopped listening to others without fancy degrees, or have acted arrogantly towards those outside of the scientific community. Furthermore, many scientists find themselves embattled in the publish or perish dilemma, and may not see it as part of their job or even understand the importance of sharing their research outside of the scientific community.

Before I started my PhD at Oregon State, I was unaware of the importance of outreach and good science communication. It was at a NOAA internship at the Office of National Marine Sanctuaries in the Education, Outreach and New Media Division, where I learned what outreach was and its importance. Outreach gave me an opportunity to share my love and passion for the ocean and tell audiences why sea critters are so cool and why ocean resources are worth protecting and why I was so much in love with the work I was doing. In this manner, I also learned to love outreach.

NOAA’s yearly community outreach event. I got to help out and tell the communities about Marine Protected Areas, like National Marine Sanctuaries, and why they are important for Ocean conservation.

Once at Oregon State, I took my first science communication class with COMPASS. After addressing the American Association for the Advancement of Science (AAAS) with a call for a “New Social Contract with Science”, Dr. Jane Lubchenco and other like-minded scientists founded COMPASS on the “premise that ocean scientists, in particular, had a wealth of knowledge that was not reflected in public understanding or policy and management practices.” (Lubchenco 1998; Smith et al. 2013). In this class, students are encouraged to use a tool they developed called a message box to hone in on their main message, get rid of the jargon and tell their story (develop story-telling skills). I learned that while I may find my research to be absolutely fascinating, other people might find it more interesting if I tell them my story. In telling my story, I can also tell them about my research. Developing these story-telling skills is crucial for humanizing scientists and making our research more relatable.  If you have ever been to a lecture in college or school, in which the professor drones on and on in a monotone voice on some obscure topic using vocabulary and examples that no one else but him seems to understand, then you have witnessed bad science communication. The difference with a teacher or professor with good science communication skills, is that you fell connected to the topic being discussed and want to learn more. The scientist or professor does not bog you down with jargon or all the nitty gritty details of the research. Rather the scientist or professor may tell you a story related to their research, or take you on a journey that gets the class intrigued on the subject. This skill is the hardest one to develop. Letting go of this jargon and the nitty gritty details of our research may at first seem impossible. As scientists, we are trained to be very cautious in the conclusion we read and specific in the language we use. However, when we communicate our science to general audiences we must learn to forgo that and get the main point across.

Having good science communication skills does not only mean being able to express yourself and explain your research eloquently, but having good listening skills as well. Too many times, scientists have alienated the communities which they wish to help or work with, by not listening to them. Going into a community with open ears and hearing what their concerns and research needs are and how you can help has been shown to result in much more successful collaboration, than going into a community with a mindset that I, the outsider scientist, know what is in the best research interest for you, the lay people.  Local knowledge and wisdom have too often been ignored by many scientists, when they should be complimentary/collaborative to our research.

Kids area always super exited when they get to see and touch marine critters

 

 

 

 

 

 

 

 

 

 

 

Combining outreach with good science communication skills can help scientists connect their research with communities that may be affected differently, get public support for their work, inform policy to make the best science-based decisions, increase collaboration opportunities, inspire a next generation of scientists, make a difference, and possibly even get more funding for this research.

I had the great opportunity to teach kids about Marine Protected Areas with a game I created for them

I got to explain to kids what Marine Protected Areas are and why they help fisheries

Personally, I particularly love going to schools and telling kids about the ocean, seeing their face light up with fascination as I show them pictures of odd and beautiful sea creatures and answering their questions about the sea. I love answering questions from my friends about how to make smart choices when it comes to sustainable fisheries and about the health of our oceans’ marine resources. I love it when a stranger on a plane asks me what I do, and I get to tell them about all about some of the cool things I get to do for my research, like going fishing. My goal in life is to make a difference in conservation of ocean resources and ensure sustainable fishing practices so that we can continue to fish for generations to come. I hope that through the outreach work I do and the improved science communication skills I have acquired, I can inspire others to take care of our oceans whether by taking small steps such as helping in local cleanups or using less plastic, or by one day becoming scientists in this fascinating field.

Best part of doing outreach is that I get to have fun, work with amazing people that also love the ocean, share my knowledge, and its a great opportunity to be silly once and a while

 

Lubchenco, J. 1998. Entering the Century of the Environment: A New Social Contract for Science. Science 279(5350):491–497. American Association for the Advancement of Science.

Smith, B., N. Baron, C. English, H. Galindo, E. Goldman, K. McLeod, M. Miner, and E. Neeley. 2013. COMPASS: Navigating the Rules of Scientific Engagement. PLoS Biology 11(4):e1001552. Public Library of Science.

What’s so big about Dungeness crab?

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Hi, I’m Elizabeth Lee, and I am an Oregon State University master’s student with Dr. Kathleen O’Malley in the State Fisheries Genetics Lab at Hatfield Marine Science Center in Newport, Oregon. My first quarter as Malouf Scholar has been quite busy, but before I dive into my Fall quarter, let me provide a little background on my research.

When you think of the Oregon Coast, what comes to mind? Maybe rocky coastlines? Tides pools? Seals? Beaches? Boats? Seafood? Dungeness crab?

Oregon Coast, Yaquina Head Lighthouse, Newport, Oregon

Oregon Coast Tide Pools
Newport, Oregon

If “Dungeness crab” didn’t come to mind, you need to spend more time along the Oregon Coast! Dungeness crab (Cancer magister) is Oregon’s most valuable single-species commercial fishery. Its cultural, historical, economical, and ecological importance along the Oregon coast is prominent.

Dungeness Crab
(Photo: Delecia Loper)

In 2017, 20.4 million pounds of Dungeness crab were landed by commercial fishing vessels in Oregon, totaling $62.7 million in ex-vessel value. These may seem like large numbers to you, but I will argue, that from the perspective of my discipline, there’s another aspect of Dungeness crab that’s even bigger. The genome of the Dungeness crab.

Dungeness Crab Pots, Newport, Oregon

Let’s take a trip back to Biology 101, remember all the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up your DNA? These ‘A’s, ‘T’s, ‘G’s, and ‘C’s (or bases) pair-up to form the double stranded structure that holds the blueprints that makes each of us unique (or DNA). The complete DNA blueprints (or genome) of the Dungeness crab is over 2 billion base pairs long! And, every cell in its shell-encrusted body has a copy of these 2 billion base pairs. So, although we catch tens-of-millions of pounds of Dungeness crab per year in Oregon, the genetic composition that makes a Dungeness crab a Dungeness crab, is even larger!

DNA Diagram
(Figure: Wikimedia Commons)

Considering the importance of Dungeness crab along the West Coast, one would assume we know a lot about the Dungeness crab’s genome and genetics. But in fact, we do not. The O’Malley Fisheries Genetics Lab undertook one of the first large-scale genetics projects on Dungeness crab. They sampled over 7,000 adult Dungeness crab off the coasts of Washington, Oregon, and California to understand the population genetic structure, genetic connectivity, and genetic diversity of Dungeness crab within the California Current System (Jackson et al. 2017)

Dungeness Crab West Coast Range
(Figure: Rasmuson, 2013)

By determining the pattern of ‘A’s, ‘T’s, ‘G’s, and ‘C’s within the crab genome, we can study the genetic structure, genetic connectivity, and the genetic diversity of the population. These findings are informative for managers and conservationists. Defining the population genetic structure of Dungeness crab is important for determining how groups of crab in the ocean are connected and allows managers to define stocks within the fishery. Assessing the genetic diversity within and among populations provides insight into the species ability to respond to environmental changes.

Dungeness Crab
(Photo: Wikimedia Commons)

In their coast-wide population genetics study, Jackson et al. (2017) found that Dungeness crab were highly connected genetically within the California Current System. Interestingly, they found inter-annual variability in the degree of genetic connectivity. This suggests that inter-annual variations in oceanographic conditions are affecting the genetic population structure of Dungeness crab. Specifically, the strength and timing of coastal upwelling, the timing of spring transition, and the phase of the Pacific Decadal Oscillation that effects of the strength of the off-shore current systems.

So, how is it that these large-scale oceanographic conditions might be affecting the bottom-dwelling Dungeness crab? Because of the complex life cycle of Dungeness crab.

Dungeness Crab Life Cycle
(Adapted from: Wild and Tasto, 1983)

Before Dungeness crab become 6 ¼-inch-bottom-dwelling (benthic) harvestable organisms in the ocean, they spend 3-4 months as very small, floating (pelagic) larvae within the water column. The pelagic larvae are moved offshore and are dispersed for 3-4 months along the west coast by the ocean currents. The time-period the larvae spend in the ocean current systems and the strength of the ocean currents influence where the larvae finally land on the bottom at the completion of their 3-4 month ocean journey. When the Dungeness crab larvae land along our coasts, we call this process recruitment. After recruitment, the juvenile crabs grow into bottom-dwelling adult crabs.

Dungeness Crab Larval Recruits (Megalopae)
Yaquina Bay, Newport, Oregon

As a graduate student, I am studying the genetic structure and diversity of Dungeness crab larvae that are recruiting to our Oregon Coast. By combining this genetic information with information about the oceanographic conditions and ocean currents along our coast, we can better understand the inter-annual variability that is observed within the adult Dungeness crab genetic population structure. The findings of my research can inform scientists and managers about the population of Dungeness crab off our coasts. Our genetic research is one of the many research projects that can help us tackle the complex questions of ‘how’ and ‘why’ the Dungeness crab fishery and population changes from year-to-year.

I am looking forward to keeping you all updated on my Dungeness crab genomics research this year. And in the meantime, I am enjoying the start of the 2018 Dungeness crab commercial season in Newport, Oregon!

 

References:

Jackson, T. M., Roegner, G. C., & O’Malley, K. G. (2017). Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System. Molecular ecology.

Rasmuson, L. K. (2013). The biology, ecology and fishery of the Dungeness crab, Cancer magister. In Advances in marine biology (Vol. 65, pp. 95-148). Academic Press.

Wild, P. W., & Tasto, R. N. (Eds.). (1983). Life history, environment, and mariculture studies of the Dungeness crab, Cancer magister, with emphasis on the central California fishery resource. State of California. The Resources Agency. Department of Fish and Game.

 

Starting out as Malouf Scholar, ODFW Marine Team, and deep-sea research on the Okeanos

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Every day I get to go out on the Ocean I feel like the luckiest person in the world!

I was in Portland OR, attending the Ecological Society of America (ESA) meeting, when I first heard the good news that I had gotten the Malouf Marine Studies Scholarship! I could not believe it, and was so exited. I ran all over the Oregon Convention Center, trying to find my adviser to tell him the good news! I finally had the funding to start doing field work and begin my PhD research.

During September I had my first chance to go out with Oregon Department of Fish and Wildlife (ODFW) Marine Reserves Team, and learn how their Hook and Line survey methods works. A method I plan to use as part of my research.  I learned so much those few days I was out there with ODFW’s David Wagman (also known as Wolfe, bottom left). He is a really good mentor and gave me great suggestions on how to improve my proposed research.

Photos: Alex Avila, Participating in ODFW’s Hook and Line Surveys

Photo: Alex Avila. Wolfe measuring fish

Unfortunately that was the last outing of the season. I need to finish writing all my permit application in the winter in order to be ready to hit the ground running next year.

NOAA scholarships have given me the opportunities I would have never even dream possible. Just like Oregon Sea Grant is part of NOAA Sea Grant College program , so is another scholarship that has greatly impacted my life, the Dr. Nancy Foster Scholarship, from NOAA’s Office of National Marine Sanctuaries. I’m currently serving aboard the NOAA ship Okeanos in the Gulf of Mexico, as part of a program collaboration opportunity that was given to me as a Dr. Nancy Foster scholar. I’m here to serve as in data logging and samples processing. At the end of the expedition I will be writing a report that will help prioritize data for researchers, ensuring that the data can be efficiently used.

Photo courtesy of NOAA Office of Exploration and Research (OER)

Photo courtesy of NOAA Office of Exploration and Research (OER)

The  NOAA Ship Okeanos Explorer expedition is running from November 29 through December 21 2017, and is investigating deep-sea habitats and the associated marine communities in the Gulf of Mexico basin. Through the Okeanos expedition,  other researchers and I, are exploring and discovering vulnerable marine habitats and investigating areas relevant to resource managers, submerged cultural heritage sites,  and marine protected areas. Okeanos is equipped with telepresence, meaning people on shore – whether scientists or the general public – and anyone can watch the remotely operated vehicle (ROVs) dives live in real time (click here to stream video).  In fact, next week, we will be conducting a Facebook Live event from the NOAA Ship Okeanos Explorer in the Gulf of Mexico this Tuesday, December 12th 2017 at 11:00 am PST  (2:00 pm EST). Science Co-lead Dr. Diva Amon, Expedition Coordinator Brian Kennedy, and I will be there to answer everyone questions! Check out Diva’s, NOAA’s OER and my twitter profiles for daily updates from the Okeanos!

Left to right: Diva Amon, Brian Kennedy, Alex Avila. Photo courtesy of NOAA Office of Exploration and Research (OER)

 

 

Being welcomed into a new workplace

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Over the first few months of my fellowship I have been overwhelmed with welcoming gestures.  It wasn’t until a tiny hamburger sticker came my way that I actually stopped to think about it…

The first day of a position normally starts with an introduction to your work space and people you will be working with, and I did get those introductions…along with introductions to every single person in the Salem DLCD office.  Patty Snow, the director of the Oregon Coastal Program personally introduced me to every person in the office and showed me all of the good spots!  I was blown away that a program director would take the time out of her busy day just to show a fellow around (seriously!  She does a tone.  If you don’t believe me take a look at her desk!).  Andy Lanier, my mentor and the Marine Affairs Coordinator for the Coastal Program , then sat down with me during my first week and straight out asked me “what do you want from this fellowship?” He explained it was his goal to make sure I get the experience that I was hoping for.

My desk is right near some of the Geo spacial Team desks.  All of the “GIS” people as I like to call them.  ell the GIS people all have wooden letters symbolizing the first letter of their names hanging on the front of their work space. I was truly touched when Cy, the Geo spacial team leader (from what I understand) also got me one of these letters!  I have never felt so welcomed into a work space.

It really shows that small gestures go a long way.

I’ve thought long and hard about how I want to use this blog space and I’ve decided photos are much more fun than words.  So instead of describing all of my experiences, here are some photos from them!

As part of my introduction into this project, Andy and I have been making some pit stops along the coast while on our way to other meetings.  This spot is Sea Rock!
 Far from rocky, but still beautiful – Florence Dunes
 Cape Perpetua
 Yaquina Head – What you can’t see in this photo are the 3 whales swimming around within this cove.  The wave climate was intense this day and wave sets were coming in that I couldn’t believe.  Yet the whales were not phased at all and moved around the jagged rocks like dancers.

DLCD Month #1

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What a whirlwind of month!  Things have been very busy with exciting new personal and professional experiences!  From crab fishing to preparing for the first Territorial Sea Plan Rocky Shores working group meeting.  Traveling with the Coastal Program has been eye opening.  Even though I have been in Oregon for 2 years, there is still so much to learn about marine policy.  It has really made me appreciate the work that the coastal program does.

In preparation for the first TSPRS Working Group Andy put me to work on the OregonOcean.info website as well as the Citizens Guide to the Amendment Process and a needs survey.  Since, the website has been published along with the document.  Check it out at the link above!

We have also been traveling a bunch for different conferences spanning from Portland to Florence with many more to come!

Week 1 – OWET Conference in Portland.  Pictured is a marine cable cross section.

 

Week 2 (I think) – Coastal Staff Meeting in Newport, OR.  We also walked the evacuation route and tried to figure out how many fellows/past fellows we could fit in a photo!

 

Week 2 – My dogter, Timber, Mananita State Park after my first morning crabbing!

 

Week 4 – Florence Oregon for the Symposium by the Sea Conference

The end of summer, the end of field work, and the end of my scholarship with Oregon Sea Grant

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I sat down to write this final blog post right after I finished my final day of field sampling for the year… and what a year it has been! When Sea Grant awarded me the Malouf Scholarship I was just starting to get a grasp of what I wanted to do for my PhD. I knew I wanted to work with juvenile rockfish (because collecting them is one of the most fun things on the face of the earth) and examine the role of oceanographic conditions during rockfish development in determining rockfish growth and survival. Over the course of this past year I developed my research plans, successfully defended my dissertation proposal, and just wrapped up a successful (though at times very frustrating) rockfish collection season. While my time at OSU is focused on accomplishing my research, Sea Grant has encouraged me to branch out beyond academics and I’ve discovered the world of scientific communication and educational outreach. This last blog will be a recap of the field work and outreach the Malouf Scholarship enabled and inspired me to accomplish.

 

My field collections of rockfish involve a three-pronged attack, or a triple threat, to capture rockfish during their early, offshore life stage (pelagic juvenile stage), their transition from offshore to nearshore (recruit stage), and once they have settled to nearshore habitat (benthic juvenile stage). While I was only able to collect 7 pelagic juvenile yellowtail rockfish during a research cruise on a NOAA ship, I was able to team up with ODFW, the Oregon Coast Aquarium, and commercial urchin divers in Port Orford to collect 622 black and yellowtail rockfish recruits (these species look very similar at this stage and I still need to ID them all). In addition, I did some freediving (with the help of two amazing undergraduate students) and SCUBA diving to collect 120 black and 25 yellowtail benthic juveniles.

I teamed up with Professor Aaron Galloway at the Oregon Institute of Marine Biology to do some diving in Port Orford to collect rockfish. Photo credit: Aaron Galloway

I was fortunate to work with two undergraduate students this summer Zach (left) is a Sea Grant Summer Scholar working with ODFW’s Marine Reserves team and Madeline (right) is an REU student working with me on rockfish recruitment patterns.

 

Though collecting rockfish is an absolute blast, the oceanographic conditions this year made my field work frustrating at times. An unprecedented number of pyrosomes clogged and threatened to tear our nets on the NOAA research ship, limiting our ability to trawl for pelagic juvenile rockfish. Unexpectedly late storms in late April broke two of our moorings used for collecting recruit stage rockfish, and three more moorings (of a total of 16) disappeared for unknown reasons. Finally, quillback and copper rockfish (some of my targeted species) never really showed up this year. While highly variable survival and recruitment of rockfish is to be expected, it was quite disappointing not to see any of these guys. I had really fond memories of night time snorkel collections of them the previous summer. After several night snorkels, I learned that these rockfish sleep on Egregia menziesii (feather boa kelp) and when you shine your dive light on the kelp blades, their eyes and swim bladders reflect light and look like Christmas lights on an underwater tree (I wish I had taken some pictures to share with you!). Now that the field season is over, and all the stress of repairing/rebuilding/replacing broken moorings, scheduling boat trips, and all the other logistics that go into a collecting rockfish has washed away, I find that I am already looking forward to next spring/summer.

 

Collecting and learning about rockfish is my passion, however, over the course of this past year I have found that I really enjoy teaching others about rockfish. When applying for this scholarship and identifying where I wanted to focus my outreach efforts, I thought that teaching children would the most fun and effective way of teaching others about rockfish because children are so curious, excitable, and, if they were anything like me when I was younger, children can’t wait to tell their parents about everything they’ve learned. Through OSU’s Winter Wonderings program, I was able to teach 3rd-5th graders about how old rockfish can get, how scientists use their ear bones (otoliths) to age them, and tried to teach them how important this information was for fisheries scientists. I found that I got a little ambitious with the last point, but the students loved looking at otolith cross sections through a microscope. I also started volunteering for the Oregon Coast Aquarium as an interpretive diver. This was an incredible opportunity to be in the water and talking with an audience of aquarium visitors about our coastal resources. Most recently, I participated in an outreach event at Hatfield called the Sustainable Fisheries Workshop for Teachers where I taught several middle and high school teachers how to distinguish juvenile rockfish to species and how closely related species can have very different life history characteristics (life spans, reproductive capacity, and development rates). All of these outreach events have been really fun and I am excited to revamp my lesson plans to improve them for next year.

Helping teachers pick up the fine details of identifying juvenile rockfish to species. Photo credit: Su Sponaugle

 

Working with Oregon Sea Grant has really opened my eyes to the importance of outreach and communicating my work with the people it may affect. I now feel comfortable talking to fisherman (commercial and recreational) about rockfish populations and how they naturally change through time. As my research progresses I am looking forward to communicating how oceanographic conditions affect the survival of young rockfish and how survival of young rockfish translates into changes in the adult population. Now all I have to do is begin analyzing my data to discover this relationship! I wanted to take this opportunity to thank everyone at Oregon Sea Grant for awarding me this scholarship, and for all the encouragement and support this year. It has been an incredible experience working with you all. Thank you very much!

The Oregon Coast Aquarium provides a unique opportunity to interact with aquarium visitors while you are diving. I was able to teach these visitors about plastic pollution and about rockfish. Photo credit: Nick Brown