Recently in Copepod Modeling Category

A dynamical systems link between traits and ecosystems

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Over the past few decades, ocean ecosystem modelers like myself have gone from a Nutrient-Phytoplankton-Zooplankton picture of the ocean that looks like this:
NPZ.jpg one that looks more like this:


The motivation, I would say, has been that the simple paradigm misses important processes, like species life history, or important properties, like diversity and its consequences. (Not to mention the myriad of Z that do not consume P.) The more complex picture, although impressive looking, comes with baggage. Among others, there is also the problem of parameterizing these models. Lots of boxes and arrows means lots of rates and properties to be measured--increasing roughly with the square of the number of species (or state variables).

One approach to simplifying this mess is to organize the ocean according to certain traits. Trait-based perspectives are not new, and I think they might be able to clean up the NNNNPPPPPZZZZZZZZZZ spider web we're tinkering around with these days. For example, we can approximate the distribution of a trait across species with a curve. With some analysis, we can then look at the effect of the shape of this curve on the structure of the community. In the example below, a Gaussian distribution of growth rates (gamma) produces realistic rank-abundance curves in a zooplankton population. Different curves produce different community-level patterns.


This is an idealized analytical model. The real world is messier. Still, as long as we are modeling species by using collections of ecologically important traits, we can use the distributions of those traits to inform the model. 

As a messier example, I'll draw from a more complex copepod model. We included a number of traits, such as activation energies, development times, and diapause strategies (many copepods go into dormancy during certain stages). These traits have been painstakingly tabulated across many species by people who I assume have lots of coffee and live in cold, cloudy places. By drawing from these distributions in a sort of stochastic way, and plugging the model into different parts of the ocean, we get very different communities emerging at different places.


The next image shows preliminary output from a North Atlantic model. These are the results for the diapause trait. Basically, in northern latitudes, species that diapause make up the majority of the population. Closer to the equator, they don't fare well. On the right you can see an image of what the population looks like in terms of the size of the animals, and a distribution of the diapause trait as a function of life stage. In the north, there are large diapausing species with long development times. In the south, the opposite.


If you know the North Atlantic well, you'll recognize that this map is not perfect, and we are still a ways from describing the whole ecosystem this way. Still, by shifting the perspective away from the individual species, and towards properties of the community, we are able to make some more sense out of the NNNNNNPPPPPPPZZZZZZZZZZZZ spider web.

Nick Record, signing off

Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography (MPB-32) (Vol. 32). Princeton University Press.

Record NR, Pershing AJ, Maps F (2013) Emergent copepod communities in an adaptive trait-structured model. Ecol Model

Record NR, Pershing AJ, Maps F (2013) The paradox of "the paradox of the plankton". ICES J. Mar. Sci. 


Over-wintering (or -summering)


Autumn is a nostalgic time. The days grow shorter and the nights grow longer. The narrow angle of the sun casts long shadows, and the dry frigid air sucks the moisture from my breath. It's this time of year when the copepod in me starts to think about packing on fat stores, reducing my metabolic rate, and descending into dormancy for the long winter.

Myself, I've never actually diapaused. But lots of copepods do it--not just in the winter, but in some parts of the ocean, when conditions are unfavorable, some species diapause at other times of year. One thing that I do, however, is fill the dark autumn hours mining databases to answer questions about copepods. For example, check out this map:

(click to enlarge)

Can you guess what it is? You might need to squint. It's a little map I put together showing all of the places (according to the OBIS database) where oceanographers have recorded a species that undergoes diapause. You can see right off the strong bias toward where people have done more sampling (the North Atlantic). You can also see that most of the action is near the poles--but there are a few other interesting spots, such as upwelling regions around Africa and the Arabian Sea, as well as the Black Sea. 

The map isn't quite complete, but all this talk of diapause has made me sleepy.

Nick Record, signing off

The Wonders of Copepods

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SeascapeModeling is still waiting for copepod jokes to hit the mainstream.  In the meantime, here's a short video produced by UMaine featuring my views on why copepods are important.  The video was featured on NSF's news site last week.  The video was produced about a year ago and foreshadows some of the work going on in the lab, notably, Karen's work on copepods and carbon and Walt's work on bluefin tuna condition.  

Dr. Record

Nick successfully defended his Ph.D. yesterday, and as the photo below shows, he is now Dr. Record*.
Not that kind of doctor.

The general assessment of Nick's committee was that his thesis was one of the best they've read.  It covered a wide range of topics, from computational methods, to copepod life history, to biodiversity theory.  The Kraken, though, seemed a bit skeptical, and had posed one of the harder questions:

I thought Nick handled the question well, but the Kraken seemed to have more he wanted to discuss.  Still, Kraken did decide to give Nick a bottle of something to help him celebrate.  Congrats Nick!

*assuming he turns in his thesis.

Give the gift of copepods

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Holiday greetings, fellow scientists!

Panicked with last-minute shopping?  Not sure what to get for that special copepodologist in your life?

Well, you've come to the right place.  Here is a link to a website where you can buy sterling copepod pins, complete with eggs (made of freshwater pearl).  Yours, for the low price of $75.

Don't want to splurge for sterling?  How about bronze, for just $65!

It's nice to know that there are artists out there who appreciate the beauty of copepods.

Enjoy your diapause everyone.

-Nick Record, signing off.


A copepod and a right whale walk into a bar...

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So I realize that my 10th and final week at GMRI is a bit late to be writing my first EML blog post, but as they say, better late than never!

To briefly introduce myself, I'm Jane, the ecosystem modeling lab summer intern.  My summer project has been to work with the "compupod" model, trying to model the biogeographical limits of four copepod species: three Calanus species, as well as Pseudocalanus newmani.  It's been a fun journey (though not without its trials and tribulations), and I've learned a lot along the way.

Having never programmed before this summer, at the beginning I faced some frustration while working with Matlab. Andy and Nick may have as well when I asked them questions like, "So how do I limit the latitude and longitude ranges again?" and "Why are my figures coming up as lime green boxes?"  Eventually, however, I got the hang of Matlab and learned how to create pretty maps such as this:
(This figure shows the predicted lifetime egg production for Calanus finmarchicus). 

My learning experience this summer has not been limited to expanding my knowledge about copepods and improving my Matlab skills, however.  I've gained a better understanding of the process of conducting scientific research, and of what it's like to work in a research environment.  Flexibility is key; if your project starts to lead you in a different direction, exploring it instead of sticking to your intended plan may lead to some interesting discoveries.  I also appreciate the importance of persisting in spite of roadblocks.  It was discouraging when my model runs led to unrealistic predictions...but I realized that revisions are an inevitable part of the process.

I've also experienced what it is like to work with intelligent, engaged, hilarious people, not just in science but in every department at GMRI.  I have to say, it has set the bar high for my future jobs.

I am sad to see the summer come to an end, but will end this post on a happy note; since today we realized that "copepod jokes" returns zero hits on Google (shocking, right?!), here is the best one I could come up with:

   Why didn't the bank let the copepod withdraw money from his account?

   They knew he was a Pseudocalanus.

And when I said it's the best copepod joke I could come up with, I really meant the only one...but don't worry, the lab is working on it. :)

Provincetown Eco-cast

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Some time ago, I wrote an entry philosophizing on the idea of an eco-cast -- that is, an ecosystem forecast delivered like a daily weather forecast, complete with a debonniare newscaster.  This ... was my vision:


Sadly, our copepod / right whale forecasting project has all but wrapped up by now.  We did produce a few forecasts over the years (e.g. here, here, here, here...), both online and in print, but we never did the movie-star version.

A couple of days ago, on a ferry ride to work, I threw together a whimsical video of what such an eco-cast might look like.  The quality (including the newscaster) is not what you would find on cable TV -- you'll notice the amateur nature of it right away -- but it does start to make tangible the idea of an eco-cast.


-Nick Record, signing off


(Mathematicians) (Oceanographers) sin θ ?

Something about a "sine wave"?

I'm sure there's a punchline there somewhere.

At any rate, I recently returned from a great workshop where a subset of mathematicians and a subset of oceanographers intersected in the same pool.  It took place at the Mathematical Biosciences Institute at Ohio State.  The mix of people and perspectives was great, and the atmosphere was one of learning and brainstorming.  There is certainly a need for more integration of these two fields.

The talks spanned a range of topics, ranging from mathy to oceany.  Many of the presentations were live-streamed, and can be downloaded here.  My talk, "Toward a Grand Unified Theory of Copepods" is posted here:
Before you click, be warned: it's nearly an hour long.  Make certain you have some time--you might not be able to tear yourself away.

-Nick Record, signing off.


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What maintains diversity in ecosystems?  How is diversity structured?  What facilitates coexistence?

Indeed, these are the questions that plague me in the wee hours of night.  I think to myself, "if only I could pare down those ecosystems to their fundamental properties, and tinker with them."  But alas, the biosphere is far too complex.

Instead, I build simplified ecosystems like the one shown below.  If you have Java 5 or higher enabled in your browser settings, you can play with this system of "simpupods".  These simpupods bounce around randomly within this artificial ecosystem.  Different species are denoted by different colors.  Each species has an assigned egg size, and an adult size.  When two individuals encounter each other, after an implied struggle for survival, the larger one dispassionately consumes the smaller one, and grows accordingly.  Once an individual reaches its adult size, it divides its mass into new individuals.  "Adult size" and "egg size" are traits that are passed on to offspring.

You'll notice from the histograms below that some species (i.e. egg size / adult size combo) go extinct quickly, while others persist.  You can add species by clicking the "add species" button.  You can also adjust the speed of the simulation, making it easier to watch.

Nick Record, signing off.


5th International Zooplankton Production Symposium

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Population connections, community dynamics and climate variability. 

Those were the main themes of the 5th International Zooplankton Production Symposium held in Pucon, Chile this March 2011.  The meeting has just ended yesterday (03/18).



Jeff Runge called those meetings occurring every four years the "Olympics of zooplankton studies".  This wit expresses both Jeff's subtle sense of humour and that those meetings are not your regular science meetings.  They are unique occasions to assess the current status of our discipline in terms of techniques and brain power.  The attendees presented the state-of-the-art in zooplankton science, which declines itself nowadays in a multitudes of specialized topics like molecular techniques, multivariate statistics, in situ observation and of course, numerical methods.


This specialized nature of the modern oceanographic science implies that we all are rare birds in our respective fields.  Hence the importance of meetings like this to gather the community of modelers in order to give our field a concerted direction for the few years to come.  And I had the feeling that all the participants of the modeling workshop I was participating in were genuinely trying to build bridges between our contrasting approaches where they meet their respective limits.  The common aim was to commit ourselves to design our respective models as a suite of numerical tools that could interact together in order to speed-up the understanding of marine ecosystems' complex mechanisms.


At the moment of ending this effervescence of ideas and good energy, the usual assessment was made by Roger Harris, the one oceanographer in the assembly who was present at the very first meeting in 1961!


It was definitely worth it!  I would like to finish on a personal note, by telling to any "young career scientist" fellow that those events are key.  You should never let any analysis, thesis redaction or stubborn supervisor stand between you and the keys to your future.  I had constructive chats, welcome marks of recognition for the work done mostly alone in front of an irksome monitor, and even serious job offers.

To finish the advice section, I'll let you on a video tutorial on how to instantaneously carve oneself a place in the hall of fame of your field...

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