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!

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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.
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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.

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

14508450178_38a07a7ff0_k

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!).

References
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!

maiden_voyage_of_the_rv_botryllid

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

Here a Tau, there a Tau… Plotting Quantile Regressions

I’ve ended up digging into quantile regression a bit lately (see this excellent gentle introduction to quantile regression
for ecologists
[pdf] for what it is and some great reasons why to use it -see also here and here). In R this is done via the quantreg package, which is pretty nice, and has some great plotting diagnostics, etc. But what it doesn’t have out of the box is a way to simply plot your data, and then overlay quantile regression lines at different levels of tau.

The documentation has a nice example of how to do it, but it’s long tedious code. And I had to quickly whip up a few plots for different models.

So, meh, I took the tedious code and wrapped it into a quickie function. Which I dorp here for your delectation. Unless you have some better fancier way to do it (which I’d love to see – especially for ggplot….)

Here’s the function:

quantRegLines <- function(rq_obj, lincol="red", ...){  
  #get the taus
  taus <- rq_obj$tau
  
  #get x
  x <- rq_obj$x[,2] #assumes no intercept
  xx <- seq(min(x, na.rm=T),max(x, na.rm=T),1)
  
  #calculate y over all taus
  f <- coef(rq_obj)  
  yy <- cbind(1,xx)%*%f
  
  if(length(lincol)==1) lincol=rep(lincol, length(taus))
  #plot all lines
  for(i in 1:length(taus)){
    lines(xx,yy[,i], col=lincol[i], ...)
  }
  
}

And an example use.

data(engel)
attach(engel)
 
taus <- c(.05,.1,.25,.75,.9,.95)
plot(income,foodexp,xlab="Household Income",
     ylab="Food Expenditure",
     pch=19, col=alpha("black", 0.5))
 
rq_fit <- rq((foodexp)~(income),tau=taus)
 
quantRegLines(rq_fit)

Oh, and I set it up to make pretty colors in plots, too.

plot(income, foodexp, xlab = "Household Income", 
    ylab = "Food Expenditure", 
    pch = 19, col = alpha("black", 0.5))

quantRegLines(rq_fit, rainbow(6))
legend(4000, 1000, taus, rainbow(6), title = "Tau")

All of this is in a repo over at github (natch), so, fork and play.

Statistics Made Marvellous Through Dance

You all know I’m one for silly science videos. And silly statistics videos? Well, that’s like catnip to me.

But today my postdoc Alison introduced me to Dancing Statistics. And it is lovely.

In short, this troupe of dancers illustrates a wide variety of statistical concepts using naught but movement.

Now I just can’t wait until they get to p-values and Bayes’ theorem.

Wanna Join My Department? Tenure Track Job Posting in Disease Ecology/Evolution!

So, rolling into year two here in the Biology Department at UMass Boston, I have to say I’m having a delightful time. Fabulous colleagues (who I’m already co-authoring papers with – that’s just how we roll), a easy access to multiple field sites and stations, a deliciously nerdy intellectual scene throughout Boston, a brand-spankin’-new School for the Environment, and a nice waterfront setting.

Yep, this is us!

Yep, this is us!

So, I’m pleased to announce that we’re hiring a disease ecologist/evolutionary biologist type in our department. And by disease, we’re talking broadly – microbes, viruses, parasites, you name it! Into chytrid fungus? Awesome. Coral disease? Cool. Evolution of echinoderm wasting diseases and their interaction with ocean warming? Bueno. Crazy theoretical modeling of multi-host disease dynamics in wild arboreal cow and wolverine communities? Fantastico! (also, where can I find these wild arboreal cows?)

The text of the ad is below, and can be found here. The application form is at http://umb.interviewexchange.com/candapply.jsp?JOBID=42747&jobboard=148


The Biology Department at the University of Massachusetts, Boston seeks applicants for a full-time tenure track Assistant Professor in the Ecology/Evolution of Diseases in natural or domesticated populations starting in September 1, 2014. Successful applicants will be well versed in evolutionary and ecological theory of host-pathogen relationships, and engaged in research on the ecological circumstances and evolutionary processes associated with epidemics and their impacts on natural populations. Applications will be particularly welcome from candidates who are working on some aspect of global change, biodiversity, or evolutionary genomics and who utilize creative experimental approaches that investigate how host-pathogen interactions affect the structure, dynamics and function of communities and ecosystems (marine, terrestrial or aquatic). The successful applicant is expected to establish an externally funded research program, direct the research of students at the undergraduate, masters and doctoral levels, and interact with a dynamic group of ecologists and environmental biologists.

Excellence in teaching at the undergraduate and graduate levels is expected. A Ph.D. and postdoctoral training (or equivalent professional experience) in population genetics, ecology or evolution is required.

The University has a strong faculty with substantial research and doctoral programs in Environmental Biology; Molecular, Cellular and Organismal Biology; and Environmental Sciences. Excellent opportunities exist to collaborate and engage in multidisciplinary research on campus, across the five UMass campuses and at UMass Boston’s Nantucket Field Station.

Application materials must be submitted online. Please include a statement of teaching and research interests and goals, curriculum vitae, and 3-5 representative reprints. Applicants should also arrange for three letters of reference to be sent to Ecology/ Evolution Pathogens Search, Biology Department, University of Massachusetts, 100 Morrissey Blvd., Boston, MA 02125.

For further information, visit the Biology Department website at http://www.umb.edu/academics/csm/biology, or contact Ron Etter, Chair of Search Committee, at ron.etter@umb.edu or (617)-287-6613. Review of applications will begin on November 15, 2013 and will continue until the position is filled.

The application can be found at http://umb.interviewexchange.com/candapply.jsp?JOBID=42747&jobboard=148