Echinoderm anatomy made easy

The things that randomly cross my mind when I'm should be busy with work...

This one made me happy in invertebrate zoology class back in my 3 seas days.

 

The water vascular system song

The madreporite's connected to the... stone canal

The stone canal's connected to the... ring canal

The ring canal's connected to the...radial canal

The radial canal's connected to the... ampullae

The ampullae are connected to the... tube feet

And that's the way a starfish works!
Yay!

Mr. Pentaceraster and Mr. Nidorellia would like to inform everyone that the label 'starfish' is a gross misnomer and wrongly represents their true affiliations. They would like you to know that they have nothing to do with those smelly, stuck-up, vertebrae-possessing fish, and are in fact part of the phylogenetically oppressed 97% of animal life. Mr. Eucidaris, who is lurking about in the background, would like to inform Mr. Pentaceraster and Mr. Nidorellia that they are "a pair of spine-less weenies, and should go stick their complaints up their cardiac stomachs."

Smurfing up the stats

Things have been ridiculously busy, and my final year of undergrad is flying by like its pants are on fire. I've been tied up with class, starting applications to graduate school and contacting potential advisors, and research. The field and lab part of my research is gone till January break, but there is always plenty of the other half: organising data and analysing data and writing, writing, writing.

Scuba Smurf is a little sad about being out of the water this long (as am I) but he is keeping me company as I try to run statistical routines that I am unfamiliar with, on software that I am fairly new to. And because I am working through it slowly and over long periods of time, I came up with another work song...


The Variances Song
(To the tune of 当我们都在一起 aka 'The More We Get Together')

What's wrong with my variances, my variances, my variances
What's wrong with my variances, they are unequal
Transformations are futile
Rank-sum tests lack power
And so to fix the variances
I tried GLMs*


* and by GLM, I mean a generalised linear model, not a general linear model

RI intertidalling

This weekend was the first weekend of the semester that I wasn't in Nahant, which was a bit of a relief. I really love being in Nahant and doing research there, but constantly traveling and doing homework on the train/in the lab is a little tiring. Nevertheless, I still got to go out into the field over part of the weekend to help set up an algal transplant experiment in Little Compton, RI.

Field site in Little Compton. I love how you can see the diversity of reds, greens and browns from a distance here.

Intertidal cormorants!

 Kylla's been setting up reciprocal transplants of Fucus vesiculosus (which Wikipedia says is the 'bladder wrack' - I don't know the common names for any algae!) from the low and high limits of its intertidal range, at sites spanning ~500 m of New England coastline to figure out if low and high zone Fucus show different survival rates and nutrient uptake, and if the patterns vary geographically. This weekend we set up the transplant for one 'south of the Cape' site in RI.

This means abducting the algae and re-attaching them either to the same tide height or the other end of their range over the course of 2 days' fieldwork. We have (bright! coloured!) cable ties around the algae to act as anchors into the z-spar on the rock. There are also temperature loggers deployed at the low and high tide height to monitor temperatures experienced by the transplanted Fucus.

 

Scuba Smurf helped out too. Here he is with the numbered setup and Fucus transplanted to the high zone!

Scuba Smurf with the little PVC hut that holds the temperature logger. 

Yay for interspecific variation!!

Return of the petri dishes

So far this semester has been: 2.5 days Brown - 4 days Nahant - 3 days Brown - 4 days Nahant. Last Friday-Monday I was back up there running a full isopod herbivory experiment. Basically, the trial we ran the week before showed that isopods might actually graze enough to be important, so we should look at their grazing patterns in greater detail.

 Multiple-choice petri dish setup: we have 6 species in there. You can just see an isopod in front of the rubber band on the far chamber.

 

70 petri dishes, 210 isopods, 63 grams of freshly collected algae.

Here we go again...

Unfolding the Earth

I'm currently taking an introductory class on working with spatial data using ArcGIS. We've been discussing the use of different coordinate systems and their components this week, including the various projections used in projection coordinate systems.

This is a video of some of the many ways you can unfold the Earth into a flat map...

Old field romping

We're into the second week of Fall classes so things should be settling down somewhat. Yay for classes that have a field trip the second week. And yay for classes that make small sotongs and their marine friends do terrestrial fieldwork.

Yesterday we drove about 45 minutes from Providence and sampled old field communities in Glocester, RI for an experimental design class. I'm always slightly surprised by how big the quadrats for terrestrial work are...I'm not sure if this is a general pattern. We quantified white pine abundances at different distances from the forest edge, and milkweed abundances on 10 x 10 m grids.

Old field with goldenrod and milkweed, and the forest edge in the background.

Counting milkweed in a square metre quadrat on a 10 x 10 grid.

Also, everything was remarkably clean, i.e. there was nothing wet or slimy or particularly smelly. I guess everything is weather-dependent (we got a tiny bit of rain) but still, nothing comparable to algae-covered butt.

Scuba Smurf came along too. Somewhat out of his element, but he quickly made friends with the milkweed.

More fun with herbivory

School started on Wednesday, which means that I had to leave Nahant and go back to Providence and actually sit in classes. My classes this Fall are fairly interesting - Conservation Biology, Methods of Applied Math, an Introduction to GIS - plus I'm auditing an experimental design class. Still, interesting classes are less exciting than actual research, especially actual research that still needs to be done. I have a very nice 3-day class schedule (Tues-Thurs) so Friday found me right back at the Marine Science Center working, again.

This summer I ran a big herbivory experiment looking at Lacuna snail preferences among different species of subtidal algae. This weekend I'm trying to figure out if other herbivores like isopods may also be important in grazing the algae.

The baltic isopod, Idotea balthica. This is a fairly large individual; the ones we find in our algae are generally around 1 cm in length.

To do this we're running a much smaller-scale pilot experiment with just a couple of algal species and only 6 replicates each. The isopods go in little modified petri dishes with a similar structural theme to the containers I used for the Lacuna experiment - identical amounts of algae in both chambers of the dish, herbivores in one chamber.

One of my petri dishes. The right chamber has herbivores; you can just see an isopod at the top-right of the tag number 08. The left chamber is herbivore-free to account for loss/gain of mass that is not due to herbivory.

The overall setup. Petri dishes are zip-tied down to the aqua mesh to keep them submerged. You can see that they are arranged nonrandomly because my arms are short and I can't reach the area in the middle right of the water table. They are interspersed, though...

Scuba Smurf did a dive to check that everything was well attached and working.

Scuba Smurf approves of this experimental setup.

Introducing...Scuba Smurf!

Today I got a new dive buddy: Scuba Smurf.

Scuba Smurf was a gift from my five-year-old friend Caden. He is all decked out in his flashy dive gear, complete with octopus, power inflator and dive gauge/computer. Scuba Smurf is going to have great adventures, but first he needs a check-out dive in the lab touch tank...

Scuba Smurf meets our resident blue lobster (newly moulted!!)

You can follow the adventures of Scuba Smurf here, on his photo album.

The things you find in algae, part 2

Sometimes when it is 11pm and I am still in the lab and I have been sorting algae for 8 hours, I need something to remind me why I love marine science. Sometimes that thing is an itty bitty brittle star.

:)

It is 5 millimetres long. To this brittle star, the one little piece of algae I am holding in my hand is a forest.

The things you find in algae

My big herbivory experiment is done, and the summer is coming to a close - classes start in less than two weeks! There's still plenty that needs to get done - yesterday we did a trip down to Connecticut and Rhode Island to collect some algae. Similar to what I was doing at the start of the summer, we are trying to quantify the species composition of algal communities in different locations, where the invader is present.

So I am back to sorting algae out of bags, which is long and somewhat mind-numbing, but there are many happy distractions in the form of little critters hiding out in the algae.

Today is arthropod day...

A little spider crab sitting on the tip of my finger.

Itty bitty little crab - it looks like an Asian Shore Crab, which is also invasive to this region. For scale: it is sitting on a microscope slide.

A very pretty pycnogonid (sea spider) on the same microscope slide.

Egg masses

Q: What do you do when you find yourself in a large, locked room with 29 other guys/girls and an abundant but finite amount of food?

A: Make plenty of babies, of course!

(This makes perfect sense if you are a 4 mm long snail)


I took down my herbivory experiment today and re-weighed all the algae after 4 days of snail grazing. It took about 10 hours in total. But other than grazing on the algae, the Lacuna have been busy making little Lacunas. There were egg masses in all of the snail mesocosms, and most of the algae had at least one egg mass attached. (This made my job a little more difficult because I had to remove the masses before weighing the algae.)

Lacuna eggs on the edge of a sugar kelp (Saccharina latissima) blade

Eggs on the branch of an articulated coralline alga, Corallina officinalis

Also, if you're not a big fan of the algae, you can lay your eggs on your neighbour's back instead. That's what friends with hard shells are for.

:)

Sea lion vs. camera

Digging into the backlog of things I've meant to post, here is an excerpt of one of the videos from the fish diversity recordings featuring a curious sea lion trying to eat the camera...




As it swims off it goes right for the transect tape, which is why you see the tape move up into the camera frame. We've seen this kind of demonic intrusion before...

Summer in Nahant: a first alphabet

This came out of a random conversation with Kylla - the kind of conversation you have when you are both still! in the lab on a Sunday evening - about intertidal Latin name ABCs. I have modified the idea somewhat.

Things that make my life easier

One of the projects I'm working on in this last month of summer is a repeat of an intertidal experiment we ran last year, with an additional control treatment. In our lab's various studies of rocky intertidal communities, a general method is to conduct regular surveys of the number and abundances of algae and invertebrates like snails.

Two of the most abundant intertidal herbivorous snails. The little snail is Littorina obtusata, the smooth periwinkle (and my favourite intertidal snail!) and the larger snail is Littorina littorea, the common periwinkle.

Survey method: 1. Place PVC quadrat on spot; 2. Record all algae and invertebrates found in quadrat

For field experiments, we set up permanent plot using bolts and washers so we can survey the same plot and track changes over time. However, the markers can be frustratingly hard to find again under all the algae, even if you know where the plot is.

One of my plot markers from last summer. When the tide comes in and out it vanishes under a canopy of algae.

So, the thing that has made my life better: pretty, eye-catching fluorescent zip-ties on the plot market bolts! They significantly reduce search time and make it possible to find and survey 40 plots in a low tide.

Bright yellow zip-tie tag on one corner of a permanent quadrat, labelled washer on the other.

They are so visible among the algae!! You can see more in the background...

Intrusion intrusion

There is a fishy intruder in my seawater table. I don't know how it got there, but it certainly wasn't there when I set up the experiment yesterday. It most likely got sucked up the pipes for the seawater system, but it looks kind of big for that...

o hai.

Fun with herbivory

This blog has been awfully quiet as of late, mostly because I've been insanely busy. I've been back in Nahant for about two weeks now and am working hard to get all the planned research for my algae project done before class starts on the 7th of September and I need to be back in Providence. I've also been helping out with other projects in the lab. But I just got a big experiment up and running, so things will be a little less hectic for a couple of days - mostly simple maintenance and checking up on it.

When I last wrote about the algae project I talked about the big question of "what is it doing here?" We're trying to figure out how the invader is impacting the ecological community. In any introductory ecology class you learn that two of the main interactions between species are consumption (e.g. herbivory, predation) and competition (for space, light, food). My experiment is looking at the first interaction and asking, do the native herbivores in the community eat the invader? How much of it do they eat in comparison to other native algal species? Could this impact growth and survival of the invader relative to other species?

In this case, the herbivore is a tiny little snail, Lacuna vincta, that can occur in relatively high densities on the algae. It is found mostly at shallow subtidal depths, though I have seen it on algae in the low intertidal zone.

Here it is on a ruler. awww.

To see if it has significant preferences for the invader or for the native algae, I put a bunch of Lacuna in a little snail mesocosm (=a food container with holes drilled and mesh glue gunned on) and offer it a choice of the invader, plus five other common algal species. At the same time, I have other snails in other mesocosms that have only one species of alga, so I can compare how much of each species they eat when they have 6 choices vs. no choice over about 3 days.

Multiple-choice mesocosm. There are 6 species in each chamber, and the one on the left has 30 Lacuna snails. The one on the right is a control for any loss/gain of algal mass not due to herbivory.

I have 10 replicates of everything, so 10 x 6 species for single-choice + 10 multiple choice = 70 mesocosms. This means 240 pieces of algae which had to be collected and individually portioned/weighed and 2100 snails which had to be collected and counted. You can see why I've been busy.

Hours and hours of collecting and sorting snails...

Final experimental setup on two seawater tables at the MSC:

5 AM field days...

...bring great intertidal sunrises :)

5:25 AM at 40 Steps Beach

On Leslie matrices and ceviche

In the introductory ecology class I TA'd for last spring, the Leslie matrix is the bane of many students' lives. Many students come in expecting more saving the earth and/or charismatic megafauna and less mathematical models. About a month into the class, they are introduced to this:
which can be understood a little better by this, where each circle is one size class (1 is the smallest, 4 the biggest). P1, P2 and P3 are the probabilities of advancing (growing up) into the next class over a set time period and F1, F2, F3 and F4 are the probabilities of reproducing (making more little class 1's) for each respective size class. The number of individuals in each class after the time period is dependent on the number of individuals before the time period and all these probabilities - that relationship is described by the matrix equation.


So what does this look like in real life?

Let's say you have a snail about the size of your palm that is known to be a key predator of barnacles - this is important because barnacles act an 'entry point' of energy from the open-ocean (pelagic) to the ecological community that lives on/around the rocks and ledges (benthic). Barnacles eat plankton from the water column and use that energy to grow, making that energy available to predators like Hexaplex snails, which in turn get eaten by fish, etc. So there is a transfer of energy from the pelagic plankton to animals like fish which wouldn't happen without barnacles and their predators.

Hexaplex feeding on Megabalanus barnacles at about 8m depth.

At some sites in the Galapagos archipelago, Hexaplex is also fished to make the local dish ceviche. Presumably, the bigger snails are fished (this can be confirmed using fishing records and/or data from shell piles). How does that affect the way the population changes (grows/shrinks) at different sites? And from a bigger-picture view, how could fishing impact the flow of energy into subtidal Galapagos communities? If you can estimate the parameters of the model accurately enough, you can use the model to answer these questions. You could also model changes in the intensity of fishing to predict how the population would respond - information that can be useful if you'd like to set fishing limits or decide which population(s) are more worth protecting.

Leslie (who is very appropriately named for this research project) has been setting up to estimate class-specific Hexaplex growth rates (the P's) by measuring, tagging and releasing them at our study site. When we get back in January, we'll be looking out for these tagged snails and re-measuring them to track their growth.

Photographic record of size and shell morphology.

Newly freed Hexaplex at Isla Baltra. The bright green rock is the release point.

January is also supposed to be the reproductive season for Hexaplex, so we'll also be looking out for egg masses and laying Hexaplex in order to estimate reproductive outputs (the F's).

Hexaplex egg mass from last January, photo by JW.

Somewhat encouragingly, we recovered one of the Hexaplex that we did some preliminary tagging on in mid-June with 8-year old Z-spar epoxy. I think we only tagged 8 or 9 individuals then, so a return of one is pretty good news. We'll see what happens when we return to Baltra in 6 months.

Happy Leslie with the recaptured Hexaplex.

Sharing space

Working on a sheer subtidal wall can be interesting, especially when the wall has exactly two (2) ledges that you can put cameras and research equipment on, and exactly one (1) of them is occupied by a sleepy sea turtle that doesn't want to move.

I have seen and swum with many turtles before, but this is the first time I have ever looked one straight in the (sleepy blue) eye. It is a little bit surreal to be stared at by a turtle.

I see you too.

We wrapped up our last Galapagos dive yesterday, making a total of 48 for this trip. The next week and a half will be some data analysis and a side trip to the western island of Isabela for Leslie and me, then it's back to Nahant and more algae work. The summer goes by quickly.

Something missing

My brain works in funny ways. Yesterday, out of the blue, it occurred to me that I haven't seen or heard a kingfisher in a really long time, and I started missing them. When I lived next to the Sungei Serangoon in Singapore, I used to be able to sit at my window with a pair of binoculars and watch several different species of kingfisher in action (along with herons, egrets, white-bellied sea eagle and Brahminy kite).

The very common white-throated kingfisher. Picture by Manjith Kainikara, used under a CC license.

Kingfishers are found almost globally but are very species-poor in the New World. I definitely haven't come across the single (?) species from North America. Even South America with its insanely diverse birdlife only has 5 or 6 species, and unlike the finches, none of them ever made it out to the land of the tortoises.

The Galapagos islands are full of amazing birdlife, and the seabirds are particularly spectacular. But when little things like this nag at me, I remember that my home is where there are kingfishers and bird's nest ferns*.


*I spent a good part of my first year in New England missing heavily epiphytised trees, particularly the ones with big bird's nest ferns between the branches (e.g. this one)

Cages and friends

Over the past few days, we have been working hard to get everything ready for our big trip up to Isla Baltra, where we'll be working on multiple big experiments. I am going to be setting up my Pentaceraster cages this week, so I've been pulling together all the necessary materials and tools, and compacting them for transport.

Rolled-up cage sides and a stack of cage tops in the corner.

Someone has been busy in the week since I last worked on the caging material.

Rebar as cage anchors. I bought 6m of it at the construction store for $3.50 and asked them to cut it into 30cm pieces. They must have been very confused - I don't think they have ever cut rebar this small.

At the same time, we'll be setting up concrete bases for a large-scale sea urchin predation experiment that the lab will be running for the next couple of years. The bases will be put in the water this trip to accumulate a mat of turf algae for the urchins to graze on when the experiment actually gets going next summer. We moved them from the hardware/construction store to the loading dock yesterday. I'm excited to start putting them down using lift bags.

Jon on the station dock with his concrete bases.

The marine iguanas really liked them too.

We leave for Baltra tomorrow morning, so we loaded all our equipment into the boat today - there is a lot of it. We piled up all our stuff into a water taxi and it took two trips to get all of it on board our boat, the Pirata (probably the most adorable boat I have ever seen, complete with little pirate flag).

A very full water taxi at the loading dock. You can see: about half my cages, concrete bases, green oxygen box, GoPro camera stands, plenty of rope, quadrat, containers for Hexaplex snails. All our dive gear is in there as well, under the cages and rope.

Loading the concrete bases onto the boat. We were getting stared at by everyone in the passing boats and water taxis.

Will be hard at work for the next few days. There will eventually be photos.