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

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!

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

Participation in the interview process for a Sea Grant Fellow position was one of the most valuable parts of my Fellowship. While initially it may seem like an extra task added onto an already busy schedule is actually exactly the kind of preparation Sea Grant seeks to provide its fellows in order to help them enter the work force. Just the initial read of applicant’s materials helped me see how to improve my own, and not just because they had better word choice. I started to see where I had not fully explained something and left an area open to interpretation that I actually had very specific answers too. I realized that if I cannot fully explain a subject in my cover letter that I should not bring it up at all, because the blank will be filled in by the reader and that distracts from other more important subjects. I also finally understood the value of letters of recommendation, especially from those who had clearly developed a personal working relationship with a student. Letters of recommendation that highlighted the same projects or attributes of a students cover letter demonstrated that the student was under no delusions about their strengths or even weaknesses they sought to improve. While grades where a factor and where important to complete the full picture of a student they carried far less weight than I thought. Really all they are need for is to demonstrate is that a person is capable of hard work and following through, or that they have acquired skills needed for a particular job.

Through discussion of the materials with other members of the selection committee I began to understand what parts of a cover letter we all responded to. Direct statements such as “This is my dream job, I would take it above all others.” where incredibly well received. While statements such as “I would like this job so that I can stay in Oregon” were less well received unless they were followed up with further explanation of a person’s commitment to the area or a particular issue. Sea Grant really responds to passion and commitment, they want students who are going to use this opportunity to develop further, not just as something to do while they figure out a better option. It was especially interesting to see how we all balanced the multiple parts of an application against each other, grades verse dedication to a certain area or letters of recommendation verse personal statement. Each person on the panel valued things differently and through our conversation we started to put together a whole picture of what this person would look like as a fellow. I really understand now how to make myself stand out to different kinds of interviewers.

The actual interviews helped me understand how my personality and interview style is viewed by different people. There was an incredible amount of understanding from the panel about nerves and how those are presented in different people. I learned that it was ok to be nervous as long as I addressed it if my composure slipped or I answered a question weirdly. Observing this part of the process and discussing it afterwards will definitely save me some sleep at 4 am in the future. I used to think that panel interviews were worse than one on one interviews but through this process I learned that they are actually better. Every person carries with them unavoidable biases based on their personal experiences, but its is also our experiences that help us balance them out, especially when combined with other peoples. As we discussed the differences in each candidates in person interview there were some things we all noticed and agreed on and others that surprised us and needed explaining from another person. I deeply value this experience and took away a lot more than I thought I would initially.

So I think I’ll start off by saying that I am writing my final yet very late blog post from Kawasaki, Japan. It’s currently 6:41 in the morning and my jet lag has still not adjusted itself. I got here three days ago and it’s been quite the culture shock. After leaving Oregon, I drove and stayed in Santa Cruz for two days, then I drove back home to Redlands where I stayed for a week, until going to San Diego for a night before leaving for Japan. This rapid change in scenery and cultures that’s occurred in the last week and half has me a bit discombobulated, making my time in Oregon feel like it was a year ago rather than a week. Being here in Japan especially, where the only things I can say to anyone is “Konichiwa” and “Arigato,” really make me appreciate the fact that I was living in a place where I could actually communicate with its members of society. So this final blog post is dedicated to those members of Oregon’s South Coast that I befriended during my 10 weeks and the knowledge I gained from them about something my knowledge is a bit rusty on: relationships.

I think it’s fairly obvious that older people are full of experience and knowledge about many subjects, sometimes with wisdom, sometimes without. It’s been a while since I was in a real relationship myself so whenever I get the chance to connect with the older generation I make it a point to observe them and ask about their love life if they’re comfortable discussing it. I spent my free time with more “old” people than people my age this summer so I will tell you some of the advice they imparted upon me and what I learned through observing them with their significant other. I would prefer to give a more detailed account about the event where each person gave me advice because I think it gives the advice context and depth but in order to preserve anonymity I will just list the things that I learned from all these good ole geezers.

• Find someone with similar interests with you. Whether it’s something like bird photography or yoga or any other niche little thing, I think having someone you can share these unique experiences and interests with is important.
• A person who you can laugh with is truly sweet or as one person put it, “someone you can talk sh*t to.” The two people who told me about this one would just clown on each other constantly and both would just laugh about it afterwards. The world seemed lighter being around them and their banter.
• Now this one was a bit more explicit but someone who you can link up with in bed in a cooperative and positive manner is apparently very important.
• Be real. Don’t try to be the cool guy. Know what you’re feeling and say how you feel.
• Find someone where you genuinely love the person that they are. 
• “Realize that all the sh*t you think is big in your twenties is little minor sh*t when you look back on it in your thirties.” Ex: “He wants to hang out with his friends tonight. Back then I would freak out and be all upset but now I’m like pushing him out the door to do it.”
• Get your heart broken as much as possible. As tough as it is in the moment, looking back on it you’ll realize it’s the times you grew most as a person and learned the most about yourself.
• Don’t forget your friends in a relationship. You should never have to ask for someone’s permission to hang out with your friends, especially not your significant other.
• “The second marriage is usually the right one.” (ain’t that encouraging?)
• Cherish the times you have away from that person. That’s the time you have to do something for yourself, like watching TV where you’re the one in control of the remote.
• Find someone who you want to take care of. People don’t stay healthy forever and being with someone whom you genuinely want to care for is special
• “Acknowledge and accept that every relationship is f***ed up.” Relationships are hard and they require work from both parties in order to succeed. 

In standard fashion, a week after finishing this internship, it is really starting to hit me how lucky I was to have been surrounded by such incredible people this summer. From prepping for the final presentations to the last minute literature review on community engagement evaluation, the last two weeks of the internship were a whirlwind with no down time. Since that time there just hasn’t seemed a time to collect my thoughts and finish off this final blog (sorry Sea Grant!) Two flights and a U-Haul trip later (more on this in a hot minute), I was right back in the swing of things. Four hours after my getting picked up from the airport I was sitting in a lecture hall in New Britain Connecticut getting briefed on the syllabus for the upcoming semester. I know I’ve got plenty more to experience, but I’d like to think I’ve done a fair share of traveling for my age. Yet of all my experiences, coming home always feels the weirdest. Feeling like your experiences have given you new perspectives on life and helped shape you more into who you really are. Then coming home to find that, while you were out there exploring and growing, life at home had just kept on going without you. Home hadn’t changed a bit. Which to be honest can be pretty nice, but at the same time makes you just want to scream. I’ve got so many stories to share, but no audience to listen to them.

This summer has been different to all the traveling that I’ve done in the past. I wasn’t backpacking my way through Europe while I should have been in class, hitch hiking through Nepal or diving in the South Pacific in the name of science. Newport Oregon was the closest to home that I’ve spent an entire summer in 3-4 years. That feels pretty odd when I write it out. But what’s even weirder, is that it I felt more out of my comfort zone this summer in my own country than I did in any of my trips in recent memory. For the longest time I couldn’t figure out why that was. The people I was surrounded by were incredibly friendly and I was in a state that I had dreamed about visiting for years, why would I be out of my comfort zone?

Until this point I had only met individual peers whose commitment and motivation just caused you to respect them. This summer I found myself living with 18 of those people all at once. Every single one of them joked around like a normal person, but get them on the topic of their field or their passion and they would blow you away. It was humbling and inspiring. Being surrounded by so many incredibly intelligent and motivated people properly intimidated me at first. What was I doing there? I was older than they were and still procrastinated so hard that my final blog post was a week late (my bad). Did I have what it would take to make it in this field? Oddly enough, at the same time that I was nervous, I was hopeful that there were so many amazing young people who hadn’t decided to chase the money. Instead they chose a career to make a difference in the world. I had found a group of people who cared more about helping the planet more than the nice things money could buy. Intimidation gave way to motivation and I wanted to do as much as I could for the environment that I loved so much. Maybe I couldn’t make it in the hard sciences, but I feel like I knew that all along. I’m a people person who loves the environment and I reckon the best way of doing my part is to work with the people.

Alright introspective monologue over. Onto more important things:

The Objective Top 3 list of the Summer at Hatfield Marine Science Center

Forward: Top 3 was a joke that originated in Angelina making fun of me for saying it constantly. It turned into a way to exclaim something that is properly epic. Saying something in the top 3 does not rank first, second or third, but rather a collective top 3. These are some of the things that stood out this summer and get the nostalgia running pretty hard.

Top 3 Modes of transportation:

1. Hatfield marine science center foldable bikes
2. Begging the Californian interns to drive us around
3. U-Haul Truck: Zach and I had our flights home out of Seattle. We had originally figured we’d be able to hitch a ride with someone, but the Wednesday before the internship ended we realized that was not the case. As a semi joke a friend of ours suggested renting a U-Haul since we had to be 25 to rent a car. After having a good laugh we took a look into it. Not only was it cheaper than renting a car or taking a bus/shuttle combo, we only had to be 16 and could drop it off in any of the U-Haul drop off points in Seattle! So without further hesitation we rented a full size (the only size available) and drove this bad boy 6 hours north. Was it the most extra mode of transportation? Possibly. Was it genius? Well.. we would like to think so. Did we have a blast doing it? You betcha.

Top 3 Cinnamon Rolls (No brainer on this one):

1. Fishtail Café
2. Fishtail Café
3. Fishtail Café

Top 3 Waitresses at Fishtail Café

1. The sweet middle-aged lady that calls Zach and I baby
2. The sweeter older lady that refers to Zach and I as her boys
3. The 20 something lady that assumed we were there to flirt with her (We just wanted cinnamon buns)

Top 3 “Songs” of the Summer

1. Norf Norf by Vince Staples
2. The entire Moana Soundtrack
3. The entirety of Funk Wave Bounce Vol. 1 by Calvin Harris

The last two albums were basically extended songs as that is all we listened to this summer.

Top 3 Movies of the summer

1. Moana – watched it 3 times and listened to the soundtrack ~a million times
2. Shrek – ability to quote this movie is amazing
3. The Dark Knight – So many people hadn’t seen this movie??

Top 3 worst Lil Yachty lyrics – Lil Yachty is a terrible rapper, but his terrible lyrics are one of the things that really brings people together.

1. “You need to stay up out them streets if you can’t take the heat. Cause it get cold like Minnesota, cold like Minnesota.” – Because he’s been to Minnesota and its “really cold there”
2. “Almost had a lifetime sentence, but I beat it, shout out to Pat! Pat, that’s my lawyer, he got me off them charges. 8 stacks for that boy, he took care of the boy” – Hits a soft spot because we, regardless of gender, are part of the “boyssssss”
3. “Remember that time I put those pepperoni on your face. Made you a creature. Now I think about you, every single time I eat pizza.” – Top 3 most heartfelt love lyrics of all time, FOR SURE.

Top 3 Activities to Participate in on the Hatfield Dorm Porches

1. Cold Ones and Ice Cream Porch Nights – A time for people to come together and talk about science, our feelings, Lil Yachty, race relations in the U.S., travel stories, and anything that comes to mind. A proper judgment free zone.
2. Beer Can Hockey w/ broom sticks– self explanatory
3. Impromptu dancing while waiting for any of the Californian’s to drive us places.

Top 3 Exclamations

1. YA BOYYYY – A true classic way to welcome someone into your home or welcome yourself into someone else’s home
2. TOP 3 “insert object being pointed at”, TOP 3 “insert another object” – just a great way to display affection of whatever you’re looking at.
3. I AM SHOOK, I TELL YOU, SHOOK. – Usually exclaimed after Game of Thrones.

Top 3 Things to get stressed about

1. Lack of proper signage at the Marine Reserves
2. Lateness of blog posts
3. Game of Thrones

Top 3 things spotted while snorkeling in Newport Harbor

1. Some kelp
2. Rocks
3. TWO crabs

This could go on forever, but this is already super late. So I will finish it here. Thank you everyone for a wicked summer. Especially Sea Grant staff for organizing everything and constantly being supportive of us.