16 posts · 7,264 views
A blog about ecology, invertebrates, kelp, statistics, and the marine world.
jebyrnes
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- July 20, 2010
- 05:05 PM
- 103 views
“Privatizing” the Reviewer Commons?
by jebyrnes in I'm a chordata, urochordata!
Let’s face it. The current journal system is slowly breaking down – in Ecology if not in other disciplines as well. The number of submissions is going up exponentially. At the same time, journals are finding it harder and harder to find reviewers. Statistics such as editors contacting 10 reviewers to [...]... Read more »
Fox, J., & Petchey, O. (2010) Pubcreds: Fixing the Peer Review Process by “Privatizing” the Reviewer Commons. Bulletin of the Ecological Society of America, 91(3), 325-333. DOI: 10.1890/0012-9623-91.3.325
Stefano Allesina. (2009) Accelerating the pace of discovery by changing the peer review algorithm. arXiv.org. arXiv: 0911.0344v1
- June 17, 2010
- 07:28 PM
- 199 views
Do Not Log-Transform Count Data, Bitches!
by jebyrnes in I'm a chordata, urochordata!
OK, so, the title of this article is actually Do not log-transform count data, but, as @ascidacea mentioned, you just can’t resist adding the “bitches” to the end.
Onwards.
If you’re like me, when you learned experimental stats, you were taught to worship at the throne of the Normal Distribution. Always check your data and [...]... Read more »
O’Hara, R., & Kotze, D. (2010) Do not log-transform count data. Methods in Ecology and Evolution, 1(2), 118-122. DOI: 10.1111/j.2041-210X.2010.00021.x
- April 1, 2010
- 07:48 PM
- 131 views
My Dissertation in Under 7 Minutes
by jebyrnes in I'm a chordata, urochordata!
I recently attended the DISCCRS symposium for recent PhDs of a wide variety of disciplines whose work (past or present) deals with climate change. The week-long meeting was phenomenal, seeding me with thoughts, ideas, and basically making me feel quite good about the work I’m doing (if also very pessimistic about how society is [...]... Read more »
Byrnes, J., Reynolds, P., & Stachowicz, J. (2007) Invasions and Extinctions Reshape Coastal Marine Food Webs. PLoS ONE, 2(3). DOI: 10.1371/journal.pone.0000295
Byrnes, J., Stachowicz, J., Hultgren, K., Randall Hughes, A., Olyarnik, S., & Thornber, C. (2005) Predator diversity strengthens trophic cascades in kelp forests by modifying herbivore behaviour. Ecology Letters, 9(1), 61-71. DOI: 10.1111/j.1461-0248.2005.00842.x
Byrnes, J., & Stachowicz, J. (2009) The consequences of consumer diversity loss: different answers from different experimental designs. Ecology, 90(10), 2879-2888. DOI: 10.1890/08-1073.1
- March 31, 2010
- 10:55 AM
- 222 views
Our Future: Hot n’ Tasty?
by jebyrnes in I'm a chordata, urochordata!
Climate change. It’s going to wreak no small amount of havoc on mother nature (and if you’re reading this but think all of this climate change stuff is poppycock, please visit Skeptical Science and then come back). How good of a guide is our intuition for what will happen?
This is a great question [...]... Read more »
O'Connor, M., Piehler, M., Leech, D., Anton, A., & Bruno, J. (2009) Warming and Resource Availability Shift Food Web Structure and Metabolism. PLoS Biology, 7(8). DOI: 10.1371/journal.pbio.1000178
Beveridge, O., Humphries, S., & Petchey, O. (2010) The interacting effects of temperature and food chain length on trophic abundance and ecosystem function. Journal of Animal Ecology, 79(3), 693-700. DOI: 10.1111/j.1365-2656.2010.01662.x
- February 15, 2010
- 04:41 PM
- 338 views
Viva la Neo-Fisherian Liberation Front!
by jebyrnes in I'm a chordata, urochordata!
p≤0.05
Significant p-values. For so many scientists using statistics, this is your lord. Your master. Heck, it has its own facebook group filed under religious affiliations (ok, so, maybe I created that.) And it is a concept to whose slavish devotion we may have sacrificed a good bit of forward progress [...]... Read more »
Hurlbert, S. H., & Lombardi, C. M. (2009) Final collapse of the Neyman-Pearson decision theoretic framework and rise of the neoFisherian. Annales Zoologici Fennici, 311-349. info:/
- January 20, 2010
- 07:07 PM
- 203 views
The Conservation Horizon
by jebyrnes in I'm a chordata, urochordata!
Every so often, a conservation problem rears its head that, upon reflection, we realize we had some inkling of even decades ago. Global warming, biofuels, overfishing, etc. The information was there, but scarce, buried in obscurity, or seemingly counterintuitive. Why not try and recognize the crucial questions early, before the lobster is [...]... Read more »
Sutherland, W., Clout, M., Côté, I., Daszak, P., Depledge, M., Fellman, L., Fleishman, E., Garthwaite, R., Gibbons, D., & De Lurio, J. (2010) A horizon scan of global conservation issues for 2010. Trends in Ecology , 25(1), 1-7. DOI: 10.1016/j.tree.2009.10.003
- September 10, 2009
- 02:50 PM
- 366 views
Sea Stars on Acid
by jebyrnes in I'm a chordata, urochordata!
As an ecologist working in temperate climes, I’ve been following the ocean acidification field with some interest. It’s always been obvious to me how acidification has enormous ramifications for coral reefs and other tropical marine ecosystems. They exist in warm waters already, often close to their thermal maxima. Acidifying the water [...]... Read more »
Gooding, R., Harley, C., & Tang, E. (2009) Elevated water temperature and carbon dioxide concentration increase the growth of a keystone echinoderm. Proceedings of the National Academy of Sciences, 106(23), 9316-9321. DOI: 10.1073/pnas.0811143106
- July 11, 2009
- 09:59 PM
- 473 views
Lytechinus: Pack Wolf of the Sea
by jebyrnes in I'm a chordata, urochordata!
So, you know, I’m cruising along, trying to determine the diet of the white urchin, Lytechinus anamesus, from the literature. There’s your usual “It eats kelp” papers, a few red algae papers, and nothing else special and then - A PAPER ON LYTICHINUS EATING OTHER SPECIES OF URCHINS.
That’s right, baby, urchin on urchin predation. [...]... Read more »
COYER, J., ENGLE, J., AMBROSE, R., & NELSON, B. (1987) Utilization of purple and red sea urchins (Strongylocentrotus purpuratus Stimpson and S. franciscanus Agassiz) as food by the white sea urchin (Lytechinus anamesus Clark) in the field and laboratory. Journal of Experimental Marine Biology and Ecology, 105(1), 21-38. DOI: 10.1016/S0022-0981(87)80027-8
- July 1, 2009
- 07:45 PM
- 680 views
Mapping the Sasquatch
by jebyrnes in I'm a chordata, urochordata!
I love modeling! I love modeling! Modeling will solve everything!
Let’s model the spatial distribution of Bigfoot!
WAIT, WHAT?!
Figure 1 from the paper. Foots denote sighting of Sasquatch footprints. Circles for just visual/auditory sightings. I ask, how does one know what Bigfoot sounds like?
Yes, it sounds silly, but in the current issue [...]... Read more »
Lozier, J., Aniello, P., & Hickerson, M. (2009) Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling. Journal of Biogeography. DOI: 10.1111/j.1365-2699.2009.02152.x
- May 10, 2009
- 02:41 PM
- 550 views
New Ideas in Ecology and Reviewing
by jebyrnes in I'm a chordata, urochordata!
Recently on ecolog-l, there has been a thread going around about journal publishing - open access v. pay-for access, impact factor, elitism, reviewing, etc. The central question seems to be, is the publication system somehow broken? Do we need to fix it? Is the model of journals such as PLoS Biology or [...]... Read more »
Aarssen, L. (2008) Ideas in Ecology and Evolution – A new open-access model dedicated to the rapid release of creativity in peer-review publication. Ideas in Ecology and Evolution, 1-9. DOI: 10.4033/iee.2008.1.1.e
- April 24, 2009
- 02:58 PM
- 748 views
snails going nom nom nom = productive diverse tidepools?
by jebyrnes in I'm a chordata, urochordata!
The “gold standard” experimental design for asking how do changes in biodiversity change ecosystem function has been to randomly assemble communities of varying species richness, but equal abundance, and examining differences in function from one level of richness to the next.
But let’s be honest. Changes in diversity due to impacts by man will not [...]... Read more »
Altieri, A., Trussell, G., Ewanchuk, P., Bernatchez, G., & Bracken, M. (2009) Consumers Control Diversity and Functioning of a Natural Marine Ecosystem. PLoS ONE, 4(4). DOI: 10.1371/journal.pone.0005291
- March 9, 2009
- 12:48 PM
- 798 views
when NOT to MANOVA
by jebyrnes in I'm a chordata, urochordata!
And now its time for a multivariate stats geek out.
The statistics that we use determine the inferences we draw from our data. The more statistical tools you learn to use, the more likely you are likely to slip on a loose bit of data, and stab yourself in the eyeball with your swiss-army-knife of [...]... Read more »
H. J. Keselman, C. J. Huberty, L. M. Lix, S. Olejnik, R. A. Cribbie, B. Donahue, R. K. Kowalchuk, L. L. Lowman, M. D. Petoskey, J. C. Keselman.... (1998) Statistical Practices of Educational Researchers: An Analysis of their ANOVA, MANOVA, and ANCOVA Analyses. Review of Educational Research, 68(3), 350-386. DOI: 10.3102/00346543068003350
- February 3, 2009
- 02:55 PM
- 836 views
Rum, Sea Squirts, and the Lash!
by jebyrnes in I'm a chordata, urochordata!
“But assuming that the would-be scientist managed to avoid, or survive, the potentially dire consequences of scurvy, dysentery and malaria, that his ship was not sunk in bad weather or driven onto an uncharted rock or reef, and that his journals and specimens were not destroyed by shipboard fungus, insects, rodents or cow or sheep [...]... Read more »
Anthony L. Rice. (2009) Marine science in the age of sail. Zoologica Scripta, 25-31. DOI: 10.1111/j.1463-6409.2007.00305.x
- January 27, 2009
- 07:00 PM
- 682 views
the light! the heat! the feedback!
by jebyrnes in I'm a chordata, urochordata!
Sometimes, the devil IS in the details. I’ve been thinking about feedbacks between community community structure and function lately, and run into a few curious roadblocks, as well as one very very interesting story.
First, the roadblocks. Just what do we mean by structure and function, particularly in reference to a [...]... Read more »
S. V. Ollinger, A. D. Richardson, M. E. Martin, D. Y. Hollinger, S. E. Frolking, P. B. Reich, L. C. Plourde, G. G. Katul, J. W. Munger, R. Oren.... (2008) Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks. Proceedings of the National Academy of Sciences, 105(49), 19336-19341. DOI: 10.1073/pnas.0810021105
- July 21, 2008
- 02:48 PM
- 453 views
Algae fight on the side of light. Inverts, not so much...
by jebyrnes in I'm a chordata, urochordata!
So, given my recent transition, it gives me great pleasure to talk about a paper that kind of sums up both halves of my split personality these days. Inverts and algae - who will win! The recent Miller and Etter paper in Ecology I think is not only a great piece of experimental ecology - careful, painstaking, and thorough - but it's also just a nice piece of natural history looking at the New England subtidal.
Oh, and maybe I worked on this project as an undergrad tech, and, well, maybe one of the authors is my current office-mate.
When I head out on a dive, I tend to do two things. The first is to hover above the surface, and take in the grandeur of the rocky benches below - ah, me, the beautiful algal bed, swaying two and fro, teeming with life. I run my hands through the fronds, examining their texture, peering at the life within.
The second is to head right for the nearest vertical surface, even if it's a tiny boulder just poking up above the substrate. I stick my nose close to it, and peer at all of the encrusting invertebrates duking it out for space. If there are no rock walls, I peer into the cracks and crevices to see where squirts, sponges, and bryozoans have managed to eek out a bit of life, safe from their algal foes.
A sampling of some invertebrates from a New Zealand Fjord. Photo credit Franz Smith, from Treasures of the Sea
But why are the foes? Why do vast walls of ascidians and the like tend to only occur on walls, and why is this a DMZ as far as many algae are concerned?
Of course, one of you will shout, flow is better on walls - haven't Witman, Sebens, and others taught us anything? Well, maybe. But someone else may say that it's light - I mean, obviously, those walls shade algae, so only the inverts can survive. And then someone else pipes up - No! Predators! It's hard out there for a crab - and it may not have access to those big walls. Or maybe it's sedimentation - more on the horizontal than the vertical - or maybe...
Yeah, you get the point.
So Miller set out to see just what's going on. What are the local factors that mediate algal-invertebrate competition? In Maine and Massachusetts, he set up a detailed series of manipulations of each of these factors within cages on horizontal substrates, attempting to add in varying levels of light limitation and predator restrictions. For each manipulation, there was a series of controls that also ruled out differing hydrodynamic regimes that were artefacts of the initial cage design. Then he measured changes in each and every variable, and sampled the heck out of the cages over time (including in the winter...in Maine! It had just finished snowing, for chrissakes!)
Basically, we dove, chipped out a bunch of divots in the substrate, z-sparred in a series of blank granite tiles, and slapped an dizzying array of caged, each slightly different than the others, over a series of weeks. This is the experiment that taught me to stop worrying, and love the z-spar.
(Note, to test the light idea, we also tried bolting mirrors to rock walls. Then a storm came, and lo, the mirrors, they acted like airplane wings...and were found days later scatter all about the seafloor.)
The take-home is that it's pretty much all light. Cages with clear or no shades were dominated by algae. Cages with shades were dominated by what you'd expect to find on walls, with the exception of a few species which (maybe) were excluded due to sedimentation. That, and inverts are often negatively phototactic, preferentially setting where it is darker.
Bray-Curtis dissimilarities (how I dislike them...mostly) showing the clustering of different community types. Note that the shaded treatments and the actual wall samples overlap, while the unshaded treatment cluster way off to the other side for the most part
Predation by urchins may play a role - insofar as it can exclude algae, but that can only really be seen in looking at past work in the system and comparing it to the results here. That, and, heck, urchins can climb walls. So, really, their distribution matters only insofar as the periodic pulses that can wipe out algae.
A conceptual model of subtidal coexistence from this paper. Light plays the key role in mediating the competitive relationship between these two groups, although sedimentation and heavy grazing may play a role at different points in time
What I find most interesting here is that it really explores the major types of niche differentiation that occur due to landscape heterogeneity, and finds just which ones can mediate coexistence on a regular basis. Sure, sedimentation and herbivory/predation/flow will play their role, but the irregular landscape really matters by setting up light gradients. These types of gradients are all over the natural world, but they can easily and flippantly be ascribed to the wrong reason. Heck, one can even look at things like just where MPAs are placed and see all sorts of correlations with pre-existing human behavior and political concessions rather than straight-up biology. It takes a careful eye and an exacting design to really teases apart these correlated differences to find the mechanism behind the pattern - even in the icy waters of Maine.
With your tech shivering due to inadequate drysuit underwear.
Miller, R.J., Etter, R.J. (2008). SHADING FACILITATES SESSILE INVERTEBRATE DOMINANCE IN THE ROCKY SUBTIDAL GULF OF MAINE. Ecology, 89(2), 452. DOI: 10.1890/06-1099.1... Read more »
Robert Miller, & Ron J Etter. (2008) SHADING FACILITATES SESSILE INVERTEBRATE DOMINANCE IN THE ROCKY SUBTIDAL GULF OF MAINE. Ecology, 89(2), 452. DOI: 10.1890/06-1099.1
- March 10, 2008
- 08:51 AM
- 482 views
The Dim Sum Principle: Resource Complementarity Increases in Importance with Density
by jebyrnes in I'm a chordata, urochordata!
In order to have a fun time at Dim Sum, you need a lot of people so that there's lots of plates to try from. But, if you went, and everyone wanted Char sio bau (Pork Buns), how boring would that be? And how many fights might break out over that last little bun?
This is the kind of science I think about - only, in the ocean.
And for this reason, I just about plotzed with joy when I saw the opening paper by Griffin et al in this month's issue of Ecology. The paper, Predator diversity and ecosystem functioning: density modifies the effect of resource partitioning, really shows how interactions between predators can change how food webs work, as well as the interaction between predator and prey diversity. It's a truly beautiful synthetic study, showing that high diversity of its multiple species of crabbies being progressively more important in determining the sterngth of predation at higher total density, as consumers parition prey types, and intraspecific interactions are lessened. It shows that there are can be some real consequences of deleting the number of species in nature, even if the density of those that remain is elevated. It also gets at why different experimental designs in the diversity-function field produce different answers.
Crabs (from left) Necora puber, Carcinus maenas, and Cancer pagurus are important coexisting predators in rocky intertidal habitats. Photo credit: P. Moore.... Read more »
John Griffin, Kate L de la Haye, Stephen J Hawkins, Richard C Thompson, & Stuart R Jenkins. (2008) Predator diversity and ecosystem functioning: density modifies the effect of resource partitioning. Ecology, 89(2), 298-305. http://www.esajournals.org/perlserv/?request
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