Problems with ANOSIM

What I have been doing of late is trying to work on a revision of a paper I wrote on the subterranean probe. One of the reviewers suggested I use a program called ANOSIM, which is an analysis of similarity which gives you a significance value. Money is always a problem in our lab and apparently the best place to get this program is through a very expensive software package called PRIMER, but we eventually found a free package called PAST that includes it. Great. The thing about ANOSIM is that you can choose which distance measure you want to use -- Bray-Curtis, Jaccard's, Raup-Crick, etc. etc. But we are having trouble finding any sort of discussion about how you choose the distance measure. The one thing we were able to find says that Bray-Curtis should be used for abundance data, not presence-absence data (which is what we have). Bray-Curtis seems to be the default, and most of the published papers we have been able to find use it (including some with presence-absence data), but none of them seem to include an explanation of why they chose it. And the distance measures which appear to be more appropriate for presence-absence data seem to give wildly different results. So we're kind of at a loss. Does anybody out there understand this stuff?

Ants of India Book

Just found this fantastic looking book on the ants of India:

On A Trail With Ants
A Handbook of the Ants of Peninsular India
Ajay Narendra and Sunil Kumar

A primer to the life of ants, introducing the reader to the ants of Peninsular India. The book sets a trend in ant studies by enabling the reader to observe and identify ants at home and elsewhere, in a non-intrusive manner. It is suitable for a varied audience, from students, entomologists, naturalists to photographers. Included in the book are more than 150 colour photographs, almost all photographed in the wild for the first time. A5 size paperback; 208 Pages; 188 Figures.

The blog Ant Visions has some beautiful example pages you can check out here.

For copies contact: antbook.india@gmail.com

Trap-Jawed Ant Video

I saw this study about trap jaw ants when it first came out a few months ago. Frankly, I didn't pay too much attention other than to skim it. I mean, I already knew these guys had wicked awesome jaws. BUT I HAD NO IDEA THERE WAS VIDEO. Holy crap, this video is so fantastic. I really really wish I knew how to edit online videos. I would park a couple of school buses between those ants just hanging out and then add a flaming ring of death that the Odontomachus can hurl itself through on his way to breaking the world ant-jumping record. Or something like that. And the first video with the vertical jump clearly needs The Blue Danube waltz playing in the background. Possibly with multiple copies of the ant slowly spinning and floating by ala the end credits of Wallace and Gromit's The Curse of the Were-Rabbit movie with the floating bunnies. If someone ever does this, please let me know. Or tell me how I can do this.

creative commons license

Rod Page recently left a comment on my blog entry about copyrighting my ant images. I thought I would highlight it here as there is some great information in it that I think others would be interested in:

Rod Page said...

Two thoughts on copyrighting images. The first is why choose copyright © as opposed to a Creative Common (cc) license? With a cc license you get to specify what I can and can't do with the image, without me having to ask you. By sticking "© K. T. Ryder Wilkie 2005" on an image (e.g., your gorgeous picture of Acanthoponera peruviana), I then have to contact you to ask your permission. For one or two images, that's OK I guess, but what it I want to use lots of images? What if you are on holiday?

The second comment is that I can read "© K. T. Ryder Wilkie 2005" but computers can't (at least, not easily). There other other ways to tag images that computers can read this information. Examples include EXIF tags (as used by Antweb, as mentioned on my iSpecies blog) which get embedded in the image file itself (also XMP information added by Photoshop, or Flickr tags (for example, this image of Strumigenys precava). My point is that if people are going to make use of your work on a large scale, using Creative Common licenses and embedding that information electronically in the image in the form of metadata will make your hard work even more useful.

If sharing information on biodiversity is going to take off, then we need to start thinking about how to share, and how to make our information accessible to computers, not just people.

I hadn't really known about this option before, but it seems like a great idea. I will definitely look into it as soon as I get a free moment. Any day now, I'm sure.

Ant identification, comparison microscopes, and digital microscopes

Every time I sit down and try to identify ants, I have the same thought -- if only I could look at a whole bunch of ants at the same time. This seems like such a simple idea. Especially if you have no key and are trying to organize your ants into morphospecies. My identification process often goes something like this:

Okay, the hair on the head seems to be important, so I'll look at that. This ant has really long hair all over the place, we'll put you in group A. This ant also has really long hair all over the place. Great. Group A. This ant has really long hair all over the place, too, but it looks different somehow. Why? Is the color darker? I can't remember what the color of the first two ants were. I'd better go back and check. Okay the first ant's facial hair is kind of a yellow color. The second ant's facial hair is also kind of yellow, but only when you look at it at a certain angle. Maybe I should go back and check that first one again. What color was the third ant's hair? Aaahhh! I wonder if I've gotten any new email in the past ten minutes?

It is a constant exercise in going back and forth, looking at one ant, looking at another ant, going back and looking at the first ant, then looking at the second ant, then the third ant, then back to the first ant, etc. etc. I've seen ant folks put two ants together on a little square of foam and look at them together that way, but I find this difficult and inefficient.

By chance the other day I came across a comparison microscope. I had no idea these things even existed. Basically it is two microscopes connected together with a single set of eyepieces, so that you can (for instance) put an ant under one microscope, put another ant under the second microscope, and then look at both of them together in the same field of view at the same time. Brilliant. Of course I don't think anyone actually uses these things for entomology. They seem to be popular for use in forensics studies. But my question is, why not? How nice would it be to be able to do that? Very nice, is the answer. Of course they are not cheap and I can't afford one, but maybe there are those of you out there who could. Or who are already using this technology. If so, let me know. I would really like to know.

More recently I have been thinking about video microscopes, digital camera attachments, etc. There is great potential there for similar usefulness. Pop each of your (insert generic genus of terribleness) specimens onto the microscope, snap a few images of head, dorsal and side (for instance), and then line up your photos on the monitor and look at them all a once. Group the photos visually into morphospecies. You could quickly see differences that might take you awhile to figure out one by one. Some sort of mechanism to quickly click and drag images from group to group (or make a new group), change views, take notes, etc. would be nice. Obviously you would still have to go back and check stuff under the microscope but I am sure this would be much faster and less frustrating. Are people doing this? I don't really know of any software programs that might facilitate this, but it seems like it would be fairly easy. I don't actually have a way to look at images from my microscope on the computer at the moment, but I am looking into it. There are a lot of options out there, mostly too expensive for me at the moment, and it is all very confusing. Does anyone have any suggestions? I actually just bought a Digital Blue QX5 Computer Microscope, but it has not arrived yet. I'm sure the images won't be super awesome but for $70 bucks it seemed worth the chance that it might be useful. I've read a lot about this microscope online and how even professional researchers are using it (it is marketed as a toy), but I haven't seen anyone actually using it for identifying. Anyone?

When I think about it, it seems crazy to me that myrmecologists are basically using the same technology that Darwin used to identify ants. Am I the only person who thinks this?

Geeky Ant Christmas Cards

By the way, there is one more day left on the 25% off greeting cards and Christmas ornaments sale at The Gigantiops Destructor Store. If you're a super ant geek and really want your Christmas cards to get noticed, they even come with silly greetings inside like Have a Myrmy Christmas! and From Our Colony to Yours. I've already got mine.

Male ants update

So I have been going through all of my male ant specimens and trying to identify them, at least to genus. I have been surprisingly successful. I was able to print out a copy of the 1943 Smith paper on North American male ants. This obviously has a lot of drawbacks, just due to its age. Many genera had not been described yet and some of those that had now go by different names. Plus it is only North American ants, which is also not too helpful. I also ordered a copy of the Japanese male ant paper by Yoshimura and Onoyama (2002). This hasn't yet arrived but I was also pointed to an online key of Japanese male ants, which I have been using. Obviously, Japanese ants are not exactly the same thing as ants from the rainforests of South America, so that is definitely a problem. And the website has some basic problems with broken links and very few actual pictures of male ants.

Despite all of these issues, I have found both of these resources to be very useful. By using a combination of these two resources, combined with my own general knowledge of neotropical ants, I have been able to identify a surprisingly large number of specimens to genus. I am beginning to see patterns in how they look and starting to recognize specific genera without the key. I really want to put up some sort of a key to my male ants but I need pictures first, which is a whole different problem I am still working on. Right now, though, I would like to make the following recommendations to anyone working on a similar issue:

Go to the Taxonomic Keys page of the Japanese Ant Image Database. Many of the links in the online key dead end but you can always go to this page and find the appropriate link. Start with the male key to subfamilies and use it a couple of times on some specimens. Then do the same specimens with the Smith key (but first go through the keys and replace the outdated genera names with their current names -- this will make things much less confusing. You can go to the Hymenoptera Name Server to get current names). Between the two keys, you can get a fairly good idea of how to identify male ants to subfamily. Once you've done that, try the genus keys. It won't be easy of course, since the fauna are so different (and paltry compared to Ecuador!), but I have found myself amazingly pleased with my progress. You know you're on the right track when you start to recognize the worker in the ant with a little Aha! Of course that's what you are!