How strange to call this planet 'Earth' when quite clearly it is ocean. Arthur C. Clarke

Wednesday, November 29, 2017

Dogwhelk rasping

My colleague Cory has been helping me try to record the rasping sounds of dogwhelks in the lab so we can tell when they are feeding and when they are just sitting still on a mussel. He's been working on figuring out all the hard- and software so far, and we are getting close! It turns out a small group of researchers at Western Washington University in Bellingham, WA is also developing a way to do this! And they shared one of their recordings online!

Ever wondered what dogwhelk drilling sounds like? Wonder no more.

Thursday, November 23, 2017

More November cage sampling

Here are more photos of my field work last week.

We have to take all the lids off every time we go out. 

On clear days we get a visit from these shorebirds! They blend in very well; how many can you see? 

Here is another borehole. 

Four painted snails in one shot! The orange one might be eating that large mussel.
These dogwhelks are from Lompoc, a site near Point Conception.

What is this arthropod-like creature squirming in the mussel matrix?

Monday, November 20, 2017

WSN conference poster

Last weekend I attended the Western Society of Naturalists annual meeting in Pasadena, California. I presented a poster about my ocean acidification study that tested the feeding behavior of drilling dogwhelks. It was a really fun weekend!

Saturday, November 18, 2017

Octopus on mussel bed

We found this little dude crawling around the mussels beds last week.

Check out this article on their cool eyes!:

Wednesday, November 15, 2017

Fun finds in the field

Today when we were checking the cages and counting the species in them, we saw some exciting intertidal things!

First, we found very obvious evidence that my predatory dogwhelks are indeed predators: there were many clear boreholes in mussels right next to them!

Here you can see a clean hole right through that mussel and my labeled dogwhelks—wearing pink and sparkly purple nail polish and circular orange number tags—in the background.

We also found an unexpected vertebrate in one of the cages!

Finally, a very active red octopus was crawling right next to us! I filmed it sliding by the cages and trying to hide under a flap.

It seems every time I go out I find something else I've never seen before, so check back soon for more updates!

Thursday, November 2, 2017

Quality-checking DNA Sequences

I have updates on my genetics work! I have tried amplifying all my snail tissue samples now (and in many cases, I've tried multiple times), and the ones that amplified I've sent off to be sequenced. I finally got the sequences back and now it's time to check them for quality! I had always wondered what files with DNA sequences looked like: perhaps a text file with As, Cs, Ts, and Gs? Perhaps visualized in some cool color scheme in a program I don't have?

It turns out the latter was closer to the truth—at least with the program I am using. In 4Peaks, you view the sequences as colored peaks, called a chromatogram, where each color is a different nitrogenous base. Yesterday I learned how to distinguish between a clearly defined sequence read and a messy read that can't be used in analyses because we won't be able to tell the bases apart. Here's what that looks like!

This is a very clear read and will be used to help me identify the snail species!

This is a poor read. You can see that in many cases, multiple colors are peaking. That means we don't know what base is at that site.

Friday, October 20, 2017

Dogwhelks outplanted

The predator dogwhelks have been outplanted! Let the experiment begin!

Me weaving the lids on the cages with cable ties.

Some lidded cages and a no-cage control quadrat.

Thursday, October 19, 2017

Cliff sign

Since my research site is so visible, I made a sign for people to check out when they see me working. So far, I've seen people reading it every day I've been out this week!

Wednesday, October 18, 2017

Baseline communities and predators ready

I am finally, finally, finally ready to record the official baseline communities in each plot and add the predatory snail treatments!

I thought I was ready to do this two weeks ago, but I didn't have a protocol for community assessment then, and by the time I developed it, the tides were not low enough so I had to wait two weeks. At least the low tides are in the daytime now!

I decided on a community sampling scheme that includes recording all the species of barnacles and algae in each cage, plus the total number of anemones and dead mussels, including those with boreholes. I'm also tracking the abundance of littorines (Littorina spp.), limpets (Lottia spp.), and turban snails (Tegula spp.). Right now those cover the vast majority of what I see in the plots; hopefully, that will change as the experiment proceeds, because it may mean my treatments are having an effect!

An open cage with a quadrat over it while we count 
the community of organisms living inside.

All the snails are labeled and colored according to what cage they will go in. All the cages have the same mean snail size so I don't confound predator treatment with size. In every cage, there will be five snails, and each is painted a different color so it will be easy to find all five each time I go out to check on them.

Two-thirds of the list of snail ID, color, and cage 
that tells me where each of the 120 snails goes.

I'll be out there every low this week, so if you see bright yellow construction vests down the cliff, you know what we're up to!

Friday, September 22, 2017

Cages installed and predators collected

All the mussel bed squares now have cages! Now I just have to hope no one will bother them. I'll put out signs and contact information at the next low tide. I can't wait until the low tides are in the daytime.

An experimental unit. Five snails will go in here.

I just finished collecting all the predator dogwhelks to be the treatments for my caged mussel beds. They came from three different sites around central and southern California. Now I just need to finish measuring and labeling them and put them in the cages!

Snails labeled with bee tags

Here are some photos during a post-collection hike at one of my central California sites, Soberanes Point in Garrapata State Park.

Soberanes point

Big Sur coastline

Friday, September 8, 2017

Field experiment installation

My mussel bed field experiment is coming together! This week I went out each day around 5 am to count what organisms are living in each of my plots and drill holes around them so I can install cages as soon as my cage material arrives. Here are some pictures of my work this week.

A sample cage on one plot.Plots with drill holes and bolt anchors, ready to be caged.A sample cage on a plot.Plots with drill holes and bolt anchors, ready to be caged.

Thursday, July 27, 2017

Field experiment prep + OA experiment update

This morning, in preparation for my nascent field experiment testing dogwhelk feeding behavior, I climbed down the cliffs by the Long Marine Lab and scouted spots to install 32 stainless steel mesh cages. My intern and I are excited to be making progress on this project, and once the permits are approved we'll be down there every < 2 ft. tide!

Me checking out spaces to put the experiment at Terrace Point.

The site where the experiment will take place.

Rows of 20 x 20 cm mussel plots where the 
snail predators will go.

Yesterday, my interns finished a large dataset on the shell thickness of all 519 mussels I used in my OA experiment last year. It feels really good to have that done. Huge shout out to Sandra, Xochitl, and Marcos!! Soon I'll be writing up that paper and then just one more chapter to go!

Friday, April 28, 2017

Winter and Spring quarters

It's time for some much-needed updates on my dissertation progress!

This winter I completed my third quarter as a TA for my favorite course: Invertebrate Zoology. Not only did I lead seven animal dissections, but I also baked seven animal-themed desserts for my lab students and held my own review session with lemon coconut doughnuts. I may be the only person in the state (or the country, or the world) who regularly uses snail-shaped muffin tins.

Animal-themed desserts I made last quarter; chocolate cupcake snails, ginger crabs, and assorted fruit tarts.

I worked hard to figure out how to extract and amplify DNA from all the snails from my field study so I can ID them by sequencing characteristic genes. Unfortunately, only two weeks ago did I get the PCRs working—I was hoping to do that much sooner. Thankfully, now the PCRs work, I have lots of amplified DNA, and I'm almost done with that project now. Next week I'll know which of two cryptic species were at my field sites.

Gel electrophoresis with long-awaited amplified 
snail DNA! You can see the DNA as the bright pinkish
dashes near the top of the gel. This gel is on a UV 
light so the amplified DNA, treated with ethidium 
bromide, fluoresces. Before winter quarter this
year, I had no idea how to extract snail DNA and 
use polymerase chain reaction to copy it a bunch
so I had enough to send to a sequencing facility. 
Now I've done it for weeks and weeks, and it's
really rewarding to see bright bands like that!
Notice how not all the blue dashes have bright 
pinkish dashes above them; that is because not all
the DNA samples amplified, and I have to figure
out (or guess) why.

This is a mini centrifuge for PCR tubes. The amplified DNA is 
in the green solution in those tubes. It took me only (ha) a 
month to figure out that only this special green reagent works 
with my snail DNA! Before that, I was trying other reagents 
with zero success.

I have an amazing team of efficient interns, and they collected lots of data on mussels from my OA experiment. After about 12 weeks, most of that collection is done, and now my two paid interns are preparing to present at a malacology conference with me in June! I'm excited to go with them and be marine scientists/ecologists/evolutionary biologists together. One of them just accepted graduate admission to UC Santa Barbara, so soon enough she'll be my colleague!

Planning field work has been a little stressful. I'm currently simultaneously planning two trips: one in Oregon in May and the other over the summer in California. On the Oregon trip, my collaborator (and great friend) and I will be collecting the last bits of info we need to finish a paper modeling the foraging behavior of dogwhelks. Once we have that info, we'll do a few lab experiments and then the model will be fully parameterized! I think it will not take long to write after that. This chapter of my thesis is particularly exciting to me because I came up with it apart from the direct suggestions of my main advisors, and it is my first attempt at using a computer model for something other than statistics. Usually, when I use models, the model gives credibility to the result; this time, the model is the result. 

My other field work will be executing a reciprocal transplant experiment in the intertidal zones at two sites. I am still not completely sure about what sites yet because I need to know what species I'm dealing with, so I'll need the DNA data first. As the clock ticks, the pressure builds, because I have to submit a scientific collection permit before I can do anything. Those can take months to get approved, but I basically only have June and July to do the experiment because the low tides are terrible in August and September. Luckily I have an intern working on writing up the methods for that because I am stressed and swamped preparing a paper for my committee members to read in a week!

A simple diagram of the reciprocal transplant design. Colors indicate site. There will be snails from each site at each site. The grids represent the cages containing the snails. Grey grids are control cages with no snails.

I have my first post-quals committee meeting in mid-May, and I really want feedback on the paper I'm writing about my field survey. I need to make it good because the more work I put into it, the more meaningful our discussion will be. I really want to submit the paper in June so it's out of the way. Since I'm not TAing this quarter, now is the time! 

More updates will come after my Oregon field work and the field experiment get started!