Just returned from two weeks on the road, so I've got mounds of work to catch up on. In the meantime, check out this interesting post over at Thomas' Plant Related Blog. Its about Neutral Theory and why there are so many species distributed the way they are. The ecology of diversity is one of my pet research areas, or at least, I like to think about it a lot (see earlier DTF posts about it here and here)
Entries in species accumulation curves (4)
Morato, T., Hoyle, S., Allain, V., & Nicol, S. (2010). Seamounts are hotspots of pelagic biodiversity in the open ocean Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0910290107
A little while back I wrote about how we can use Species Accumulation Curves to learn stuff about the ecology of animal, as well as to decide when we can stop sampling and have a frosty beverage. There’s a timely paper in this month’s Journal of Parasitology by Gerardo Pérez-Ponce de Leon and Anindo Choudhury about these curves (let’s call them SACs) and the discovery of new parasite species in freshwater fishes in Mexico. Their central question was not “When can we stop sampling and have a beer?” so much as “When will we have sampled all the parasites in Mexican freshwaters?”. They conclude, based on “flattening off” of their curves (shown below, especially T, C and N), that researchers have discovered the majority of new species for many major groups of parasites and that we can probably ease up on the sampling.
Trying to wrap your arms (and brain) around an inventory of all the species in a group(s) within a region is a daunting task, and I admire Pérez-Ponce de Leon and Choudhury for trying it, but I have some problems with the way they used SACs to do it, and these problems undermine their conclusions somewhat.quadrats deployed or (in this case) animals dissected, not a time series of years. The second problem is that sequential years are not independent of each other, as units of sampling effort are (supposed to be). If you have a big active research group operating in 1995, the chances that they are still out there finding new species in 1996 is higher than in 2009; just the same as the weather today is likely to bear some relationship to the weather yesterday.
OK, so what do the graphs in this paper actually tell us? Well, without an actual measure of effort, not much, unfortunately; perhaps only that there was a hey-day for Mexican fish parasite discovery in the mid-1990’s. It is likely, maybe even probable, that this pattern represents recent changes in sampling effort, more than any underlying pattern in biology. More importantly, perhaps, the apparent flattening off of the curves (not all that convincing to me anyway), which they interpret to mean that the rate of discovery is decreasing, may be an illusion. I bet there are tons of new parasite species yet to discover in Mexican rivers and lakes, but without a more comprehensive analysis, it’s impossible to tell for sure.
There is one thing they could have done to help support their conclusion. If they abandoned the time series and then made an average curve by randomizing the order of years on the x-axis a bunch of times, that might tell us something; this would be a form of rarefaction. The averaging process will smooth out the curve, giving us a better idea of when, if ever, they flatten off, and thereby allowing a prediction of the total number of species we could expect to find if we kept sampling forever. Sometimes that mid-90’s increase will occur early in a randomised series, sometimes late, and the overall shape for the average curve will be the more “normal” concave-down curve from my previous post, not the S-shape that they found. After randomizing, their x-axis would no longer be a “calendar” time series, just “years of sampling” 1, 2, 3… etc. There's free software out there that will do this for you: EstimateS by Robert Colwell at U.Conn.
The raw material is there in this paper, it just needs a bit more work on the analysis before they can stop sampling and have their cervezas.
Perez-Ponce de León, G. and Choudhury, A. (2010). Parasite Inventories and DNA-based Taxonomy: Lessons from Helminths of Freshwater Fishes in a Megadiverse Country Journal of Parasitology, 96 (1), 236-244 DOI: 10.1645/GE-2239.1
Tom and I wrote our paper after many nights in the field spent dissecting coral reef fishes to recover new species of parasitic worms - a time consuming and sometimes tedious process (sometimes thrilling too, depending on what you do or don't find). We were often motivated by another far more important factor too - when can we stop all this bloody sampling so that we can go and have a beer on the beach?!? Species accumulation curves therefore have a very practical aspect to them - they tell you when its OK to stop sampling because you've either sampled all the available species, OR, you've sampled enough to extrapolate a good estimate of how many species there might be.
Back to Eric Seabloom. He and his colleagues wrote a paper about the diversity of aphid-borne viruses infecting grasses of the US Pacific northwest and Canada. While the environment that they sampled was about as far away as its possible to be from the coral reefs that Tom and I looked at, the patterns of saturated and unsaturated communities they observed were the same. I get a huge buzz out of that, and that out of the morass of published science out there, Dr. Seabloom found a scientific kindred spirit who had had the same thoughts and ideas about nature, however different the specific areas of study. While Tom and I sipped beers on the beach and watched the sunset over the reef, I wonder if Eric and his colleagues blew the froth off a few while they watched the wind waves spread across the grasslands. There's something so unifying about science; it can give you common ground with someone you never would have otherwise known, and that's just one reason why I love it so much.
*The tendency for a continuing application of effort or skill toward a particular project or goal to decline in effectiveness after a certain level of result has been achieved. Answers.com
DOVE, A., & CRIBB, T. (2006). Species accumulation curves and their applications in parasite ecology Trends in Parasitology, 22 (12), 568-574 DOI: 10.1016/j.pt.2006.09.008
ERIC W. SEABLOOM, ELIZABETH T. BORER, CHARLES E. MITCHELL, & ALISON G. POWER (2010). Viral diversity and prevalence gradients in North American Pacific Coast grasslands Ecology, 91 (3), 721-732 (doi:10.1890/08-2170.1)