Recently in Copepod Modeling Category

Apparently, the concept made its way into the mainstream scientific journals. The art resides in the numerous educated guesses and assumptions an ecologist faces when building and (as importantly) assessing the validity of his model. From the conceptualization of the scientific question addressed, to the choice of the numerical method(s), the amount and level of precision of the processes to represent, their mathematical formulation, and the determination of the parameters of the equations etc. At each step, some subjectivity, some instinct, some serendipitous success, maybe...

The highest level of certainty an ecological modeler knows is that there are some apparently unavoidable pitfalls. One is mortality (any biological modeler reading this will nod in spite of himself). Sooner or later, in a meeting like the one I am this week, you'll hear something spirited like "...but your mortality function is not based on any mechanism, so what the ... are we (non-modelers) supposed to do with your results..."

Mortality rates of the small plankton are notoriously difficult to measure in the field, and thus, this term is one of the most difficult to constrain. Most single species copepod models have developed empirical relationships with temperature and/or food (for seasonality purpose) and many include some form of density dependence (for numerical purpose). Those choices arise from the trade-offs between the availability of data and the necessity to move forward and do actual modeling.

The case of temperature-dependent functions illustrates this situation: the Gulf of Maine time series suggest that herring predation may limit Calanus finmarchicus abundance. Predation by herring is the highest in the summer and the seasonal changes could then be approximated as a function of temperature. If spring conditions were warmer, we might expect that herring would begin feeding earlier, and thus, the temperature dependent mortality would adequately reflect interannual changes in a mechanistic way. However, it seems unlikely that herring predation would respond to a temperature anomaly of a few days, and it is unclear whether a warming throughout the year would correspond to higher mortality.

A novel approach of mortality in copepod models requires a mortality function that reflects some aspects of the dynamical response of predator populations to copepod abundance. This requirement becomes essential to enable realistic projections under climate variability and change. Our knowledge of copepod predators remains limited, and attempting to model the populations of all of the major predators of the life stages of our copepod would just be unfeasible. Following the "middle-out" framework, in future iteration of our models we want to use a compromise mortality function. This new function will make use of several populations of predators, each representing predation by progressively larger animals preying on progressively larger copepods. We will use classical size-dependent feeding behavior for the predators, namely a type II ingestion function (rapid increase at low food concentrations) for small predators and type III function (depressed feeding at low concentrations) for large predators. The result will be that on one hand, the predation rate on smaller copepods (early life stages) will increase largely through changes in the abundance of the predators, while on the other hand predation on larger copepods (later life stages) will respond to changes in their own abundance through the variable ingestion rate of the larger predators. That, is a bold move!

This picture has nothing to do with what I just talked about... I just feel that the pictures on the blog are discriminatory toward the earthly mammals ! And raccoons are cute (at 3pm, not 3am, though...).

I think these videos speak for themselves.

the presentation:

fancy snack from peter stetson on Vimeo.

the naming:

copepod sur la petite four from peter stetson on Vimeo.

just how good is it?

One for me, one for the birds from peter stetson on Vimeo.

Our lab has had a good month for publications.  Fred's paper on C. finmarchicus diapause, and the role of lipids, finally made it to press.  The paper appears in the Marine Ecology Progress Series, and can be found here.  The paper was submitted for review on the 4th of November, 2008--roughly 17 months ago.

Not all review experiences are as lengthy or arduous.  Our lab had three other papers accepted for publication this month.  Two of them were submitted earlier this year.  We will post an update when they make it to press.  Meanwhile, a list of our publications can be found on our welcome page, here.

The official meeting started at 8AM this morning.  Meetings like this are the intellectual equivalent of drinking from a firehouse.  At any given time, there are 15 different sessions in progress.  Each session is organized around a particular theorem, and the themes at this meeting cover the full gamut of oceanography.  About a year ago, groups of scientists submitted proposals for sessions.  Once the sessions were selected, the oceanographic community was asked to submit abstracts.  An abstract is a brief (~one paragraph) description of a study, and when you submit an abstract, you select which session you think is most appropriate for your work.  Then, one of three things happens.  1. The session rejects your abstract, possibly passing to another session, 2. The session accepts your abstract and invites you to give a talk, or 3. The session accepts your abstract and asks to you prepare a poster.

Usually, breakfast is spent looking over the titles of the talks, and figuring out which ones you'll try to see.  One talk was easy to add.  Our very own Frederic Maps gave a talk at 8:30 in the morning on his work modeling copepods.  Depending on the talk and the session, you can have anywhere from a few people to more than 50 (remember, you're up against 14 other talks).  As you an see from the picture below, Fred's talk was quite popular:

Andy's concerns about discriminating wisely between trend and noise, between low-frequency and high-frequency signals in time series of environmental variables (Air temperature in his example), apply as well to measurable quantities in ecosystems. Particularly relevant is the phenology of the species, which defines the timing of crucial recurrent events of their life cycle, like the date of first arrival to the nesting ground, the date of germination, the date of mating, the date of blooming etc. You may have noticed that I used examples related to birds and plants. Well, while phenology is a general concept, an empirical knowledge patiently accumulated by bird lovers and Sunday gardeners of the 19th and 20th centuries was first to be translated into systematic scientific surveys. And following rigorous statistical analyses of those long time series of observations, it has been firmly established that changes in the phenology of most species accompanied trends in temperature. The strength of the correlation is all the more important as the seasonality (latitude) of the ecosystem and the dependance of the species to their environment increase. The connection with climate change issues is straightforward. And it is not just about how one species or another will cope with changes of its environment, but rather about the interlocked interactions between all those species.

If you can easily think at a beautiful tulip as a species embedded in its environment, it is the same, in a more dynamic way, for planktonic marine species. Now oceanographers begin to benefit of the fruits of several long lasting monitoring programs. Unfortunately, the ever increasing pace of global climate change means that oceanographers are required to draw firm conclusions about the impact of environmental variability on ecosystems and develop predictive capabilities in the meantime ! And this will remain an elusive target as long as the mechanisms gearing those changes are not understood properly. Daunting task, as the changes in timing of such major event as diapause entrance and exit emerge form several layers of physiological and behavioral processes obeying their own dynamics while interacting with each others. But impossible is not known at the EML, so we decided to model the mechanisms behind the diapause of the dominant copepod Calanus finmarchicus. We already know that even if it can produce several generation a year, this critically important species thrives in its seasonal environment (Northern half of the North Atlantic) thanks to its diapause strategy, which means killing time at depth in order not to be killed by the detrimental conditions prevailing at the surface in winter. For this purpose, it makes a feast on large phytoplankton cells (mainly diatoms) during the short period they are available, and build up impressive amount of energy rich lipid reserves. Those swimming droplets of lipid are in turn the basis for the rest of the upper trophic levels.

And what about changes then ? Things are more sparse there... Records of physiological properties related to the diapausing strategy are about a decade old now. Not enough really to study trends on climatological scales, but enough to understand that interannual variability is high (see figure). But abundance data are enough to see changes, especially in areas localized at its biogeographical fringe. In the North Sea for example, the ecosystem shifted from a copepod population dominated by 80% of C. finmarchicus before the 60's to a present state dominated by 80% of its southern congener C. helgolandicus. What is the role of diapause in that ? Not known yet. One thing is certain though: changes occur at an ever accelerating pace, and the unforeseen consequences for the ecosystems are likely to appear before our eyes while we are still racing to improve our understanding. I strongly wish that Copenhagen "talks" will end up with agreements as legally constraining on our leaders than the climate changes will be actually constraining on us.

Superimposed to the climatological (2004-2008) relative abundance of the different copepodid stages are box plots of the estimated dates of initiation (late winter) and termination (summer) of diapause in Calanus finmarchicus in the Gulf of Maine. Data from UNH COOC WB-7 station. Figure from James J. Pierson.

Okay, it's been a while since I wrote about the topic of diapause in our preferred species around here, the famous Calanus finmarchicus (Take no offense, right whale...it's your favorite food anyway). But I promised model results and, hey, it takes a while to write a bunch of equations that make sense and, on top of that, without bugs ! I can ensure you, numerical bugs are no more pleasant than the one you would fight franticly while fishing the trout during a nice day of June on a Maine river...
So here is a presentation taking the issue of the control of diapause by the lipid metabolism in Calanus finmarchicus where this blog entry left it. Enjoy it !

lipid_and_dormancy_Calanus.pdf

Did you ever wonder, attentive reader, why our model results only span the late winter / spring season? Well, first most of the modeling effort developed in the EML aims at a better understanding of the timing of arrival of right whales in the Gulf of Maine area, and this occurs around spring. Second, our beloved copepod Calanus finmarchicus (the most delicious meal for the right whales!) disappears for most of the year from the surface waters. They escape and survive unfavorable environmental conditions (which is between fall and winter, everybody in New England will acknowledge that...) by staying at depth in a dormancy (diapause) state right before their final molt into adults. Dormancy means that every function of the organism is slowed down, no feeding takes place, and the only active behavior is, perhaps, a sluggish swimming to remain at depth.

Maybe you will be skeptical while you read me stating that little is known yet about the triggers controlling the entrance into and the exit from dormancy in C. finmarchicus. But... well, so it is !  Hence, as this species spends routinely more than half its life cycle down there, the EML has to broaden its interests to include the dormancy issue. And a promising approach to better understand dormancy makes use of the lipids stored in the so called "oil sac" of the copepods. The rationale is that lipids are a very efficient way of storing energy. Remember that while C. finmarchicus does not feed during dormancy, it spends most of its life cycle in that state. Thus, dormant individuals need huge amounts of energy reserves, which are in the form of lipids. Entrance into dormancy must be linked with the amount of lipid storage an individual managed to build up during its development. Indeed, you can see on this picture of a copepodid 5 of C. finmarchicus (the stage during which dormancy takes place) the impressive body volume occupied by the oil sac. When the diapause period approaches its end however, most of the lipid storage is used. Nevertheless, a certain amount of lipid still need to remain, in order to produce the gonadic tissue and the final molt. Exit from dormancy must be linked to the minimal amount of lipid required by these different steps of the final maturation.

Following these observations and deductions, the EML is now resolved to tackle the diapause issue. So be prepared to see soon model results during winter time !


Photo by Phoebe Jekielek.

       For the past two months, I have been interning with the EML. Mainly focusing on getting our Calanus finmarchicus model to work better; an investigation into the relationship between our model and the whale data revealed an interesting phenomenon. Below is a figure showing arrival dates (red line) versus departure dates (blue line) for Right Whales in Cape Cod Bay (CCB). 

From Nick:

Here's our first LOPC cast, by the side of the dock.  Splice held.  Phoebe is here safely, after rowing this morning from Witch Island.  Plan is to test the weather tomorrow at 6 am, and hopefully begin sampling, though it could be rough.  If things go as planned, I won't be in internet contact after tomorrow morning.  Maybe next time we dock, I can get a signal and do another post.

The figure is the output from the LOPC test cast.  Each bar on the left indicates the number of particles passing through the unit that had a particular "equivalent spherical diameter".  As you can see, not a lot of big stuff.