Getting it Right – after Publication: A Multifunctional Journey?

Sometimes, you have to publish a paper to have the hit-yourself-in-the-head revelation of the real right answer.

Earlier this year, along with a great cohort of colleagues, I birthed a really neat piece summarizing how you can look at simultaneous change in multiple ecosystem functions. We were interested in how changes in diversity can affect the simultaneous performance of multiple functions, but, really, anything can be put on the X axis – warming, fertilization, lemony-fresh-scentedness – it doesn’t matter.

This was a problem that had been vexing the field of biodiversity-ecosystem-function, or, really, anyone who wanted to look at multiple functions. Our group spent multiple sessions bashing our heads against a wall trying to derive a solid analytic strategy to look at changes in so-called multifunctionality and in the end came up with something that I’m pretty proud of. The basic idea of our approach was to look at the slope of the relationship between a predictor and the number of functions ≥ some threshold of their maximum – but then do it for lots of thresholds. Why is it important to looks at lots of thresholds? Well, if you look at the lines for each choice of threshold, you get something like this:


Note, that’s from the multifunc R package vignette, and its the analysis from our paper.

Anyway, you can see how the slope and intercept change with different threshold choices. We eventually looked at how slope changes with threshold, and used that to divine a fingerprint of multifunctionality. But, a plot of threshold v. slope – it’s kind of abstract, and can be hard to parse. It was the best we could do, though, as we thought and thought about it.

While working on a recent analysis, I began to wonder – one of the key numbers we want is something like, how does multifunctionality change with the addition or removal of one species? We can look at how one function changes with diversity – but we still don’t have a good something with our predictor on the X-axis. And yet, the question I want to answer is key if we want to think about the consequences of, say, losing species for a multifunctional world.

Discussing this with Jon Lefcheck, I was suddenly struck by something he had done in a figure on a manuscript. He drew a plot like the one I showed above, only, he also put a line across the top at the maximum number of functions observed in an experiment. I noticed that as my eye moved across the plot – from low to high diversity – I could see the color change along the line, indicating that the maximum number of functions were able to hit progressively higher levels of function. At low levels, nothing was able to hit any threshold. At high levels, a few were. So…one could in theory plot diversity against the highest threshold that all of the observed functions could hit all at once.

Lines drawn on top of the same figure for 5 functions and for 2 functions. Let your eye wander along them and note the change in color. Also, note the weird optical illusion at F=2. Yes, that line is actually straight.

Lines drawn on top of the same figure for 5 functions and for 2 functions. Let your eye wander along them and note the change in color. Also, note the weird optical illusion at F=2. Yes, that line is actually straight.

Moreover, if I were to, say, draw a line at a lower number of functions, I would see the same pattern – but the relationship would change. Now, higher thresholds could be reached by a lower number of functions – but, eyeballing it, it looked like the linearity changed. In some ways, it made me think of, in the BEF literature, if we have only one function, we get a saturating curved relationship between diversity and function. But for multifunction, a few of us have long wondered if we might get a more linear relationship.

So, for the German example, I decided to whip up some simple code to explore the relationship between diversity, number of functions, and maximum threshold those functions can achieve. I used the fitted model, and then just calculated which thresholds could achieve some number of functions at a given level of diversity, and grabbed the maximum. The results are interesting.


You can see that fewer functions can simultaneously achieve a higher threshold – this is predictable. But there’s a suggestion that the curvilinearity of the relationship switches from linear to concave-up as more functions are considered. That’s it’s linear to begin with is notable, as with few functions I would expect more concave-down-ness. And you kinda get that if you run it down to one function, but, this site in general in earlier papers didn’t have an incredibly strong saturating relationship compared to some other classic examples.

Overall, while it takes a bit of a moment to realize what’s going on, I think this is a far more interpretable graph than what we presented in the paper. I haven’t subjected it to the same in-depth can-this-be-fooled simulations that we did for the MEE paper, but, I have to admit…I kind of like this, and think it might be the answer we tried to get at oh so long ago.

A Kelpy Time Machine

This is x-posted from my guest post at Deep Sea News about the new Floating Forests citizen science project I’m part of. If you’re excited about it, go check out!

avatar_kelpThere’s something I’ve always wanted. Something that would take kelp forest science to a new level. Something that would let me do the kind of work that I dream about, quietly, secretly, peering into the mysteries of kelpiness.

It is something impossible.

It is a time machine.

And now I have one. But with a catch. For you, my dear friends, are its pilot.

OK, OK, first, why use a time machine as a tool of science, and not, I don’t know, to right wrongs and make the world a better place? Well, first off, temporal paradoxes, y’all. Come on. Be realistic. Has Doctor Who taught us nothing? Or decades of Star Trek? Or Primer? (seriously, see that last one, as it will hurt your brain in a good way).

But then, why, kelp? What? Hear me out.

There are so many things that we as marine biologists want to know about the state of ecosystems in the past. For many things, we hardly ever have records that are older than ten usually for just one small area. This is really problematic – especially for something like Giant Kelp.

You see, Giant Kelp (that’s Macrocystis to you!) is kind of the bad-ass of the algae world. It’s pretty damn huge – up to 60m long in some places – and grows up to a foot or two a day. It’s so damn big, we can see it from orbit1.

Photo courtesy of the Seaweed Industry Association

It’s also everywhere – from Alaska to Baja to South Africa to much of South America to New Zealand to the sub-Antarctic islands. And, according to the Lane et al. phylogeny, it’s all one species2. It gets *around*. And wherever it is, it feeds, houses, and nourishes much of the life in the sea around it.

So, where does the time machine come in, and why are you piloting it?

Simply put – Keeeelllppp Innnnnn Spaaaace!

The Landsat family of satellites have been orbiting earth, taking photos of the whole globe twice a month since the early 1980s. Photos where we can see kelp. They are a time machine we as scientists can use to go back and see how kelp has changed over thirty years.

Can we see the near-extinction of giant kelp from Tasmania? Can we see it moving around the coast of South Africa? Has it been walking away from the warming equator? Is there more or less now than there was in the past?

OK, this sounds pretty cool. But where do you, our time-traveling pilots come in?

Basically computers suck.

OK, no, really, we love them. *pets shiny Apple laptop* BUT – they cannot tell kelp from waves or clouds in the Landsat images. My collaborators (the real remote sensing part of this team) have tried. It’s a no-go. We actually need people – kelp hunters, if you will, to peer at the millions of images of potential kelp habitat and help us discover these Floating Forests.

We need you.

Working with the Big Momma of online citizen science, Zooniverse, my collaborators from the Kelp Ecosystem Ecology Network (KEEN) and I have created an online citizen science project called Floating Forests. In it, we ask you to take a look at images. Help us cull out bad ones (they’re satellites – they take pictures cloudy cloudy rain or (often still cloudy) shine, or take pictures of more than we think.

And if you see kelp, circle it!

We'll give you images of coastline - like this July 2001 picture of Santa Cruz on the left. You circle the kelp beds, and that yields data about kelp abundances, as you can see on the right.

We’ll give you images of coastline – like this July 2001 picture of Santa Cruz on the left. You circle the kelp beds, and that yields data about kelp abundances, as you can see on the right.

It’s really quite meditative to see images of the land and see whisk by, pausing periodically to lasso a green bed of kelp.

Maybe you’ll see a wave-swept vista of Point Lobos. Maybe you’ll see the Googleplex (I did – by accident). Maybe you’ll see somewhere you’ve never dreamed of traveling, but with that big kelp bed sitting there, you know the destination of your next dive trip.

So, please, go hop into the pilot’s stick of this magical kelpy time machine. Poke around. And ask questions! We scientists are there to talk to you! What are you waiting for?

Yes, this is the entrance to a time machine.

Yes, this is the entrance to a time machine.

1.Cavanaugh, K., D. Siegel, D. Reed, and P. Dennison. 2011. Environmental controls of giant-kelp biomass in the Santa Barbara Channel, California. Marine Ecology Progress Series 429:1–17.10.3354/meps09141
2. Macaya, E. C., and G. C. Zuccarello. 2010. DNA barcoding and genetic divergence in the Giant Kelp Macrocystis (Laminariales). Journal of Phycology 46:736–742. 10.1111/j.1529-8817.2010.00845.x

The Beatles and Kelp

For a blog post somewhere else, I’m trying to re-work the Beatle’s classic Kelp!, er, I mean, Help!. But my first draft got all urchin-y. I love it, though, so I thought I’d post it here.

KELP! (from the perspective of a growing urchin)

Kelp! I need some algae.
Kelp! not just any algae
Kelp! You know I need some kelp!

When I was younger (So much younger than) so much younger than today
(I never needed) I never needed any growing kelp in any way
(Now) But now these days are gone (These days are gone), I don’t eat just diatoms
(I know I’ve found) Now I find I’ve changed my mind and opened up my jaws

Kelp me if you can, I’m hungry now
And I do appreciate kelp being ’round
Kelp is great food for me oh right now
Won’t you please, please kelp me

(Now) And now my spines have changed in oh so many ways
(My Aristotle’s lantern) My Aristotle’s lantern is big and ready to graze
(And) And every now (Every now and then) and then I feel so insecure
(I know that I) I know that I just need kelp like I’ve never needed it before


When I was younger (So much younger than) so much younger than today
(I never needed) I never needed any growing kelp in any way
(Now) But now these days are gone (These days are gone), I don’t eat just diatoms
(I know I’ve found) Now I find I’ve changed my mind and opened up my jaws

Kelp me if you can, I’m hungry now
And I do appreciate kelp being ’round
Kelp is great food for me oh right now
Won’t you please, please kelp me, kelp me, kelp me, ooh

Damn, That’s Some Big Kelp!

I’m not sure what it is this year, but the kelp we’re seeing in the Southern Gulf of Maine is just fracking huge. Last year, yeah, there were kelpy areas, and there were kelps that were ~1-1.5 meters long, which, you know, impressive. But this year…

It started when Team Dive (this summer, we have Team Marsh – #marshlife – and Team Dive going on) hit up the outer Boston Harbor Islands. We hadn’t been out much since winter. They found vasty fields of Laminaria digitata and Saccharina latissima (well, with their super-long stipes, they looked like S. longicruris, but it looks like they are now the same species – e.g., Cho et al. 2000 and others). How big? Twice the size of a grad student!


But this was at the mouth of Boston Harbor. Maybe a fluke, or eutrophication?

As we kept working up in Salem Sound, though, the kelp seemed…well…big! But, eh, still urban-ish, still maybe an urban thing… (although it was *not* so big last summer).

If anywhere should be free of the urban influence, it should be Appledore Island in the Isles of Shoals. It’s a few miles offshore, and has lots of microenvironments. And yet, everywhere we look – big-arse kelp! Super dense kelp area where last year an intern almost lost her mind counting kelp stipes? Still mind-exploding. Except now you have to count stipes by feel while your face gets wrapped up in the giant lasagna-blades of Saccharina. And it’s just as big.

OK, I’m 6’2″. And a half. (~1.88m). Here’s me, with my fins just barely touching the seafloor.

It’s everywhere! Even in the wave-protected low-kelp density Heterosiphonia sites, while we do find lots of smaller kelps, the monsters still abound. See how it compares to the size of Team Dive.


This isn’t to say it’s *all* that huge. A size distribution from the site that piece came from for reference:


But, still, what is up with this? Big kelps coupled with very cold water temperatures of course has my California trained brain thinking more time with high nutrients, but I don’t know whether that relationship is as strong here in the southern Gulf of Maine. It’s making me very excited to see the oceanographic work that comes out in the next year or so to see just what forces are driving all of this!

And even more curious to know what’s going to happen next year, as we’re seeing massive numbers of tiny urchin recruits (and a lot of sea star recruits) often folded up in the eroding tips of many of these big honkers. Or on Desmerestia, like ornaments on a Christmas tree (240 in a square meter plot yesterday!).

Cho, G. Y., H. S. Yoon, S. M. Boo, and C. Yarish. 2000. Atlantic kelp species Laminara longicruris and L. saccharina (Laminariales) are conspecific. Journal of Phycology 36:12–13.

The Launch of the R/V Botryllid

Woohoo! It’s another amazing research season out here at the Shoals Marine Lab. We’re in the midst of our push to sample SML, Salem Sound, and the Boston Harbor Islands. The weather is glorious, and the water is…ok, not warm. 47F this year. Last summer at this time it was a good 5 degrees F warmer. But, either way, here we go on our summer Shoals sampling adventure!


Searching for Opportunities in Ecology & Environmental Science for Recent Grads

So, you’re graduating with a biology or environmental science or marine bio degree! Hurray! You’ve finished your stint at college, and you’ve gained a lot of new skills. Maybe you’ve done some time in research, maybe not (!!!), but now that you’ve wrapped up, you want to find a job in the environmental sciences. Something that will give you research experience, and help you on your way to either a career or deciding whether you want to go into research.

OK, where do you go now?

I’ll be honest. For me, this was easy. I was lucky enough to have had experiences (and more to be honest) that channeled me into a top-notch research lab as an undergrad, which opened up further opportunities for an REU program at SML. The one-two punch of a great mentor and a great REU experience gave me a publication under my belt, and let me know, yes, this is what I want to do with my life. So I docked around for a year as a tech in different places, but I knew I was grad-school bound.

This is not always the case. I’m teaching a Marine Biology & Ecology course this year and my students, all seniors, vary greatly in background. For some, this is their first time taking marine bio or anything related, as we haven’t traditionally had a lot of regular offerings in the past. Others have done a lot of environmental science work, but don’t have much field experience on research projects.

But now they’re fired up. And they’re great students. And they want to know what to do next. Because they’re graduating.

Or I was recently approached by a friend who finished her undergrad years ago, and has been working in advertising (kinda sorta). But she’s been taking marine bio and other courses on the sly. And now wants to find a position that will give her a leg up and a last piece of experience to determine where to go next in her career path involving science.

She’s tremendously talented. Motivated. And doesn’t quite know where to turn next.

I have a few ideas on the topic, but, I tweeted out a query on the topic, and got far more.

So, without further ado, here’s the list of places to look when interested in a job just out of undergrad for more experience in ecology & environmental sciences. This list is by no means comprehensive, and if you have any suggestions, let me know. I plan to incorporate this onto my lab website as a resource in the near future.

  • Sign up for the Ecological Society of America’s mailing list. Lots of opportunities flow through there
  • The ESA Phys Ecology job board has a ton of jobs, and for far more than just physiological ecology work. Check out their staff and seasonal positions.
  • The same group also provides a great list of job boards worth checking out. Start there, and go down the rabbit hole of the wide array of positions available, although some are for more senior folk.
  • Birder? Check out the extensive listing at the Ornithological societies of North America job page.
  • To start to get into government research, see the USGS jobs page. Many of the listings are for research internships as well as government positions.
  • Texas A&M Department of Wildlife and Fisheries Sciences provides a wonderful job and internship listing for positions around the world
  • One way to get into field work is to, well, work at a field station! The Organization of Biological Field Stations provides a listing of current positions.
  • One way many recent grads get involved in more management and conservation is with jobs and internships at the Student Conservation Association.
  • The American Society of Limnology and Oceanography maintains a job board that is a mix of tech-level positions and upper level positions. So, some filtering required
  • Environmental Career Opportunities posts a wide variety of job types.
  • For the more geography inclined, see The Society for Conservation GIS.
  • If you’re interested in education, museums, and wildlife, the Association of Zoos and Aquariums has a wide variety of opportunities.
  • And last, for a ton of additional information for postgrad and beyond, Marissa Baskett maintains a superb website. It’s a bit beyond the scope of what we’re talking about here, and just academia focused, but it provides a great jumping off point.

Updated with more links from Sadie Ryan on 12/19/13