Tuesday, April 24, 2018

Extreme makeover: oyster edition

When I was in high school, there was a show on every Sunday night called Extreme Makeover: Home Edition. I remember watching it with my family as we snacked on popcorn. The premise of the show was simple: a needy family, usually one with a sick child and insufficient resources to afford the necessary accommodations, was sent on vacation while their home was ripped to its studs and remade for free. The family would return home to find a house they didn't recognize, but which finally had the wheelchair access or hospital-quality air filtration their child needed, plus a sunny living room and a landscaped front yard.

This week, I couldn't help but remember those evenings of watching another family get a brand-new house, because I just performed my very own extreme makeover. Do you remember the oyster paper? I've been working for over a year to analyze a dataset about swimming behavior in oyster larvae. I have written code, made graphs, and counted the number of times a larva swam in a helix. When I started the analysis, I calculated all the parameters possible, then spent months whittling the data down into a meaningful story. The paper has gone through countless drafts and iterations as it has been passed among the co-authors. I have started over more than once.

We finally got to the point of submitting the manuscript for publication, and it was reviewed by two independent scientists. (For more about the peer-review process, see this post and this post.) When the reviews came back, the comments indicated that we needed to overhaul the paper yet again.

It took a lot of thought, a lot of iterations, and a lot of revision, but the manuscript is now much better. It tells a clear, cohesive story. I worked with my co-authors, including my advisor and some of her former students, to re-vamp the paper. We have now finally resubmitted it to the journal, so here's hoping the reviewers appreciate our overhaul. We'll see if it is accepted this time!

Friday, April 13, 2018

Name that copepod!

"Got a question for you," I told my friend, Kristina. "What copepod lives at 79 N, 4 E, 2500 m depth?"

Kristina thought for a second. Copepods are small crustaceans, related to crabs and shrimps. They are abundant all over the world, and they form an important link in the food chain. Copepods are most abundant in the surface ocean, but some live close to the seafloor. Kristina's research focuses on the distribution of copepods in the Arctic, so I thought she might be able to answer my question. Instead, she gestured across the room.

"This gentleman might now," she informed me.

AY looked up from his microscope and came over. I introduced myself, then repeated my question. He put a hand up to his chin. He thought for a second. Then he asked, "Do you have a sample?"

The amphipod specimen AY helped me identify. Two
individuals are attached to and being eaten by a carnivorous
sponge. They're the clear lumps with red eyes in the center-
top of the photo. The sponge is the pale pink stalk.
"I do!" I exclaimed. It's actually rare for me to have a physical specimen of an animal that I need help identifying. Usually, the things I need help with are rare species, ones I only see in pictures. I'll send my best photo to a taxonomist asking for help, and the most common response I get is "Do you have a sample?" Well, in this case, I did!

AY has an incredible eye for detail. I gave him two jars with copepods, and he promised to identify them over the next few days. I thought I would have to wait until next week to get an answer from him, but just a few hours later, there was an e-mail in my inbox from AY. One of the specimens I had given him was not a copepod after all but a different kind of crustacean called an amphipod. The other specimen was a juvenile copepod in the genus Xanthocalanus.

I was amazed. The specimens I had given AY were not in good shape. They were preserved in ethanol, which is not the best preservative for morphology. Both were in the process of being eaten by a carnivorous sponge. In fact, the Xanthocalanus specimen was stuck to a sponge like velcro, and the amphipod was even partially digested. I was extremely grateful for AY's taxonomist eye.

Now that I know what the small crustaceans are, I can look up information on their population dynamics. Variations in prey abundance can influence the growth and reproduction of their predators, so I want to know if there's any connection between the abundance of copepods and the recruitment of the carnivorous sponge. It's just one more avenue to pursue for my analysis of the long-term recruitment experiment from last summer. We'll see if there's any connection!

Sea ice analysis

I clicked the blue text to open the link for the folder. August 2003. Before me appeared a list of files, each with blue text as well. One for each day in the month. I clicked on the first one, and the file for August 1 downloaded to my laptop. August 2. August 3. One by one, the daily files streamed onto my hard drive.

I clicked through files for hours. Each one contained data on ice cover in the Arctic, with a separate file for each day from August 1, 2003 to August 31, 2017. That's the period when larvae may have settled on my recruitment panels in the Arctic deep sea. I've been trying to figure out what environmental factors might influence recruitment, based on results from the long-term experiment I recovered with my German collaborators last summer. So far, I've looked at changes in water temperature, bottom current, and food input to the seafloor. Nothing seemed to quite line up. So I started looking at the ice cover.

Sea ice in the Fram Strait
Sea ice has a profound effect on the Arctic ecosystem. The thick floes of ice form a blanket on the sea surface that dampens waves and creates a very stable water column. Phytoplankton are less likely to get mixed down in the ocean, out of the reach of light, and as a result, the ice edge is usually an area of very high productivity. Some of the plankton that grow at the surface end up falling to the seafloor, so they serve as a food source to benthic organisms.

There appears to be some connection between sea ice cover and recruitment to my panels, with the highest recruitment occurring in years with low ice cover that are preceded by years with high ice cover. I still need to look into it more before drawing any conclusions, but I'm very excited to relate my recruitment data to what's going on in the surrounding environment.

Thursday, April 5, 2018

Porcupine

As some of you know, I'm currently working to analyze data I collected last summer, about recruitment in the Arctic deep sea. I worked with German collaborators to finish a long-term experiment, and we collected a set of brick and plastic panels that had been on the seafloor for 18 years. Since the cruise last August, I have counted, identified, and measured all the recruits that were on the panels and begun writing two papers about my findings.

I wanted to compare the recruitment patterns of my animals over time to environmental data, to see if there was any connection between what was going on in the environment and what animals settled on the panels in different years. My German collaborators have incredible long-term data sets from the Hausgarten observatory, where the recruitment experiment took place, so I'm able to mine the data and look for patterns. The most important environmental factor for my recruiting species is the current. All of the most common species on the panels eat particles or small animals in the water, so they rely on the bottom current to deliver their food. I wanted to see if there was any connection between current velocity and recruitment of these suspension feeders.

So I downloaded the German data. Friends, I'm not talking about a handful of numbers here. My German collaborators have measured the speed and direction of the bottom current at the central Hausgarten station every hour for the last 14 years.

That's 135,092 data points, in case you were wondering. No way I could do the analysis by hand.

Thankfully, there are some really great tools out there for working with gigantic datasets. I ended up using the code-based program Matlab for my analysis. Matlab is nice because it's so flexible - you can literally do anything with it - but the drawback is that you really have to know what you're doing. There are no buttons to push; you have to tell the program everything you want it to do in lines of code. More and more, I find myself doing code-based data analysis, and it's an incredibly important skill to have as a scientist.

Matlab is also a good tool because there's a community of people who use the program and help one another out. I spent a few hours today searching through help forums online, trying to figure out how to do what I wanted to do. In the end, I figured it out - in fact, I was even able to piece together other people's scripts to accomplish what I needed to. I was able to plot my data.

Check out the figure at right here. Each stick shows the speed and direction of the bottom current at the central Hausgarten station on one day between 2003 and 2017. They're arranged chronologically left to right. Personally, I think the pile of sticks looks a bit like a blue porcupine, but it tells me some important things: (1) most of the time, the current is to the northwest, and (2) sometimes, the current is to the south or southeast. It's those anomalous days that I'm going to focus on, because they seem to be more common in certain years. I wonder if years with anomalous current have any differences in recruitment compared to other years.

It was a long day of coding, but my analysis is moving forward. I can't wait to see how my data match up!

Sunday, April 1, 2018

Garbage Beach

It is April! The weather in Massachusetts is warming, and I find myself thinking more and more about the upcoming summer. I have a number of projects that require field work in the summer months, so I'm spending my spring preparing for them. I got a small study funded to examine the fauna on shipwrecks in New England, and collecting my samples will require me to SCUBA dive at some pretty challenging locations. I need to be at the top of my diving game this summer, so that translates into a lot of dive training this spring.

Our group of divers at Garbage Beach
Carl and I loaded the car and headed out on Saturday morning to Garbage Beach in Woods Hole. We had invited some friends along and ended up gathering a group of five. Garbage Beach is just a little strip of beach down the street from my office at WHOI, and it is an easily-accessible site with interesting animals living on the bottom. The catch? The only place to park and prepare your dive gear is the parallel parking spots on Water Street, a narrow road lined with cafes, boutiques, and research buildings. It's usually clogged with tourists in the summer, but we were early enough in the year to claim some space. Still, we got plenty of weird looks as we assembled our tanks and donned our dry suits.

We swam out from the beach toward the southwest, gliding over the sandy seafloor. We passed patches of boulders covered in the boring sponge, Cliona sp., and strands of algae. As we swam deeper, the light waned, and the water grew colder. The coldest temperature my dive computer registered was 40⁰ F - and I became ever more grateful for my dry suit. Eventually, we turned around and headed back to the shallows. We passed eelgrass swaying in the sand, and there was a giant jellyfish caught among the blades. Eventually, I could see the surface of the water above me. We stood up and walked back up the beach. It was a great dive!