Month: February 2009

Mysteries in Fish Functional Morphology 1. Unicorn surgeonfish

February 22, 2009 / pcwainwr

Welcome to “Mysteries in Fish Functional Morphology”. From time to time I plan on posting descriptions of some of the most fascinating and perplexing unsolved mysteries in fish functional morphology. My hope is that some of you will find these entertaining, but if you think you might have the answer to any of these mysteries or if you have any comments about them, please feel free to post a comment here. My first installment is the cephalic horn that is found on the forehead of four species of surgeonfish in the genus Naso (N. annulatus, N. brachycentron, N. brevirostris & N. unicornis). The top photo to the left is N. brevirostris (courtesy of Bruce Yates – UnderwaterRelections.com). Below that, a group of N. annulatus. Four species also have a rounded, bump-like protuberance that is less extreme in size and shape (N. tuberosus, N. tonganus, N. mcdadei & N. vlamingii). A picture of N. tonganus illustrating the bump is at the bottom to the left. Remarkably, according to a recent treatment of the phylogenetics of this group (Klanten et al. 2004. Molecular Phylogenetics & Evolution 32:221), the elongate, slender horn appears to have evolved three times among the living species. What is the function of the cephalic horn? One possibility is that the structure is used in mate selection or intrasexual displays – in other words, it evolved as a consequence of sexual selection. For me, this is the by far most appealing hypothesis I have heard, but unfortunately, the structure is not sexually dimorphic, as far as I know. Although this does not rule out the sexual selection hypothesis (sexually selected traits can have equal expression in the two genders), it is a strike against the idea. Nevertheless, Arai & Sato (2007. Ichthyological Research 54:49) observed that the horn of male N. unicornis and the hump of male N. vlamingii were used in quick color-changing displays to females (unicornis) and other males (vlamingii) and these authors favor the sexual selection hypothesis. Many years ago I heard another idea about function – that zooplanton-feeding species use it to help them gauge distance to their prey in the midwater, where there are few positional and distance reference points. This is an interesting idea that has not been tested to my knowledge. But, one complication here is that among the Naso species with the elongate horn, two are benthic herbivores and two feed on plankton and on the benthose. This indicates that a function in plankton feeding is unlikely to explain all occurrences of the structure. So, is this fabulous structure the work of sexual selection or an adaptation for feeding on small plankton in midwater? Or, is there another explanation? What do you think?

Woodchipper – a script for breaking phylogenetic trees into subclades

February 13, 2009 / pcwainwr

Here’s a handy little Perl script I wrote that takes a nexus formatted tree file and breaks down every tree that it finds into the clades that it is composed of (i.e., every node in the starting tree is returned as a new tree). It spits all of these out into a text file, which can then be copied and pasted into a tree block.

Each tree in the original file gets its own text file, named woodchipper_treename.tre, where “treename” is the name of the tree given in the trees block in the input file.

It hasn’t been tested exhaustively yet, so please check the results and contact me if you run into any trouble. No warranty is expressed or implied, your mileage may vary, not valid where prohibited, and all that.

NOTE: If you’re having trouble saving the link above, try right click -> save as instead of clicking on it in the normal way.

Datamuncher – a handy tool for niche and distribution modelers

February 9, 2009 / pcwainwr

Here’s a little tool I whipped together for my own use. I hope it’s useful to others as well. Basically what it does is take .csv files of species occurrences and a batch of ASCII files, and converts them into three output files. They are:

A community presence/absence matrix, with “community” defined as a grid cell in the ASCII raster files.
A set of coordinates for each grid cell that has at least one species present in it, corresponding to the “communities” above.
A matrix of values from the ASCII raster files for each community.

The general idea is to take data in a format that is acceptable for Maxent (.csv and .asc) and convert it into a set of files that are usable with some of the R algorithms. Currently it seems to be working with GDM, but I haven’t tried anything else. You may need to delete columns 1-3 in the environment file, depending on what you’re doing with it.

Here’s the quick and dirty of it:

Where it says “occurrence files”, you just hit the “add files” button and drop in all of the .csv files you want to use. Note that everything in that box is going to be thrown into ONE set of output files!

Second, you add your environmental layers. ASCII raster format is the only one it understands.

Third, pick an output directory.

Finally, name your analysis. If your analysis is named “my_stuff”, the output files will be “my_stuff_communities.csv” (1 above), “my_stuff_community_coordinates.csv” (2), “my_stuff_environment.csv” (3), all dropped into the output directory you chose.

In addition to its original intent, this tool may also be useful to those who want a quick and dirty way to get their data extracted for a MANOVA or other analysis – if you feed it occurrence files for one species at a time, the environment file will contain all conditions occupied by that species. Neat!

You can download it as a Windows executable file here, or as a Perl script>here. Be aware that the Perl script requires that Tk be installed (NOT Tk+!), which you can do from the package manager. Also be aware that it probably won’t work on a Mac because of the way it’s parsing directories. If anyone wants a Mac version, please feel free to email me.

Also let me know if you hit any snags. Testing has been rather limited so far, as I just finished it today. Use at your own risk!