For anyone out there who read our Evolution paper last year, Rich Glor, Michael Turelli, and I are putting together a web site to host the software we made for that study. It's got a bunch of other little bits and bobs in development as well, mostly revolving around different resampling procedures for use with environmental niche modeling. You can find it at www.enmtools.com. I'll post any major developments here as well.
Until recently, sticklebacks were thought to be pretty closely related to seahorses and pipefish. At first glance, it seems reasonable: both groups of fish have bony armor plates, male parental care, and species with elongated bodies and snouts. Many of the species also share a mode of swimming called "labriform" that I'll be talking about more in a later entry.
So, the pipefishes and sticklebacks share parental care, bony armor, elongation, swimming mode - seems like a slam dunk, right? Wrong.
Things are rarely that simple when you're dealing with the incredible diversity of teleost fishes, particularly within the Percomorpha, often referred to as the "bush at the top of the tree of life". Fish are just too diverse for simple morphology-based relationships - you need genetic data to really see what's going on, and you need a lot of it, because there are so many groups.
In a paper published early last year, Kawahara et al used 75 sequenced mitogenomes to generate a phylogeny of the Gasterosteiformes and related species, and...bam, there goes the neighborhood!
Gasterosteiformes(bolded in the figure above) was split into three pieces: seahorses, pipefishes and their relatives ended as sister to the gurnards, the weird indostomids were sister to the weird synbranchiformes, and finally, the closest relatives of the Gasterosteidei(sticklebacks) were eelpouts and pholids.
Obviously, there's still a lot of work to be done with these fishes - nuclear genes need to be sequenced to back up the mitochondrial genome data, and given the number of species in the presumed stickleback sister group, it's conceivable that there could be a paraphyly issue as well.
Either way, it looks like the sticklebacks are in for a wild ride!
KAWAHARA, R., MIYA, M., MABUCHI, K., LAVOUE, S., INOUE, J., SATOH, T., KAWAGUCHI, A., & NISHIDA, M. (2008). Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts Molecular Phylogenetics and Evolution, 46 (1), 224-236 DOI: 10.1016/j.ympev.2007.07.009
This is the first installment of a weekly feature on the Wainwright Lab blog.
First, a little introduction: My name is Matthew McGee, and I'm a graduate student in the Population Biology program at UC Davis with Peter Wainwright.
(For those wondering, Peter is the derived fish on the left.)
The species I'm primarily interested in is the threespine stickleback, Gasterosteus aculeatus (which I generally refer to as just "stickleback", because they're much more commonly used in research than the other stickleback species).
My research deals with stickleback functional trophic morphology and evolution; or put another way, how the food sticklebacks eat shapes their appearance and how they change over time.
Threespine stickleback, Gasterosteusaculeatus (Image courtesy of Wikimedia Commons)
So why sticklebacks in particular?
Clearly, because sticklebacks are awesome.
They're awesome because they have a few key qualities that make them an excellent model system for evolutionary biology. Sticklebacks are marine fish that can tolerate freshwater, and populations of stickleback will often colonize lakes and streams from the ocean, then diverge from the marine population in interesting ways.
From a functional perspective, they've got a great assortment of interesting traits: lateral "armor" plates, serrated pelvic spines instead of fins, different mouth shapes, and they produce their own form of glue!
Stickleback are also a great genetic system, because they have a fully sequenced genome, and it's easy to cross different types of stickleback with each other, which can help us locate the genes involved in particular traits.
As if that wasn't enough, stickleback are also a model system for behavior, toxicology, and development.
In short, sticklebacks = awesome.
Every week, I'll be blogging on a different aspect of stickleback biology, which will usually involve a discussion of a stickleback-themed peer-reviewed research publication.
Join me next week, when I talk about phylogenetics and the stickleback family tree!
As many of you know, Rita and Peter found a surprising and unique use for the raptorial set of second jaws in moray eels. This set is used to grab and insert the prey to the mouth. Click here to hear Rita describing the research to NPR science correspondent, Joe Palca.
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?
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.
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!
Until recently, sticklebacks were thought to be pretty closely related to seahorses and pipefish. At first glance, it seems reasonable: both groups of fish have bony armor plates, male parental care, and species with elongated bodies and snouts. Many of the species also share a mode of swimming called "labriform" that I'll be talking about more in a later entry.
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?
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