Paraphyletic Problems

Adding more individuals from populations that were already represented in the dataset, two more populations not previously represented and outgroup taxa did not resolve any of the paraphyletic problems. Two morphological species are reprsented in this treee'll call it the "T" group and the "B" group. Neither are monophyletic. There are two problem populations. The first is from the "T" group and is located in the Sierras. This could easily represent a cryptic species. This is the only population I was able to collect (despite widespread searching in the northern Sierras) in 2007. Therefore more collecting may provide additional resolution. Alternativley, there are approximately 90 basepair differences (out of 1424bp) between this population and the nearest relative which leads me to think of things such as pseudogenes. I'm investigating the pseudogene possiblilty by reexamining the chromatograms and translating the sequence to amino acids and looking for stop codons. None of these methods are foolproof, but when combined, may provide some indication of a pseudogene.

I still cannot get COII to amplify/properly sequence for the three individuals I have DNA for in the Sierra population. I get multiple bands and when using gel extraction techniques, do not get clean sequences. I'll try the entire process of amplification, gel extraction and sequencing again for these three individuals.

Field Season Approaches

People are abuzz in the lab, getting ready for their various field projects and trips to meetings. The undergraduates are scarcely seen, likely preparing for their finals and summer work elsewhere. I myself am also frantic to get ready for the field season. In preparing for the field some serious decisions need to be made. To help me make those decisions I extracted DNA from more individuals from the populations that are causing the phylogeny to be rather paraphyletic at this point with regards to the two "species" I currently have samples for. One population is from California (Sierra Nevadas) and the other is from Idaho in Boise National Forest. Both wonderful places, but far from where my other collecting needs to take place. I would love to return to these places, but if more individuals added to the phylogeny brings more resolution and allows for monophyletic groups among the "species", then all will be well and I can concentrate on collecting in the east. If not, then I will have to try to get to at least one of these localities.

I've been working on scouting potential locations to travel to in the east. Among these are places really near our house. By being so close to these sites, hopefully I can collect some adults and rear them to get larvae to be able to describe the larvae of this genus, which has never been done. Matt and I went to Zurrick Bog to look for Neophylidorea. We came up empty handed, but found one adult Axymyia furcata flying around. Here are some photos of the pitcher plants and potential Neophylidorea habitat at Zurrick Bog.



I should get sequences back from these new individuals on Monday, align them and run some quick analyses to see whether a trip to the west is warrented. Stay tuned.

Specify 6 Launched

We are truly living in a remarkable time where information technology is evolving extremely rapidly. The result of this progress is an explosion in data. As of April 10th, Specify 6 was launched. Specify 6 is an open source computing program made freely available for download. With Specify, institutions such as natural history collections will be able to better manage their data and make it freely available to others around the world. Hopefully it will catch on and become a valuable tool for georeferenced collections as well as a multitude of other uses I'm sure.

Daddy Long Legs?

People in Europe generally refer to crane flies as daddy long legs. Now, that may come as a surprise to some because you may know daddy long legs as a spider with long legs.
This becomes a problem with people don't know the difference, biologically. The problem here in case you don't know is that the article is referring to crane flies (Tipulidae) as plover food but the picture is of a spider (Pholcidae). The authors of this article likely googled daddy long legs, took some image they found and stuck it on their publication. This only perpetuates the problem of course of not knowing the difference. Another common mistake people make is between mosquitoes and crane flies. Watch out for those giant mosquitoes!! This article displays a photo of a crane fly (likely Nephrotoma: Tipulidae) but is discussing the blood sucking flies, mosquitoes (Culicidae).

There are two issues here in my opinion. The first is of confusion surrounding common names. It is difficult to communicate when we don't have a common language. I don't have the answer here as to how to solve this problem. The second issue however may solve the first. The larger issue here is that people don't recognize a morphological difference between biological organisms. In both of these cases of mistakes, knowing about the biology being able to accurately identify a mosquito or crane fly would have avoided the mistakes. This does not only apply to non-biologists. I was having a conversation with a biologist that studies birds and made some mention of mosquitoes as flies (which they are). They were amazed to learn that mosquitoes are flies.

Insects are everywhere and even biologists that don't study them tend to overlook insects and their morphology, ecology and biology. Obviously education can help here and offering more insect information at the introductory biology levels is important.

More on Darwin

Even this clip on Richard Milner shows how we can change our language when speaking about evolution. We didn't "come from apes" as he and others suggest all the time when speaking about evolution. We share a common ancestor with apes, chimps monkeys etc. and a relatively recent one at that.

On a somewhat related note, I was listening to the Science podcast (January 9 episode) when they starting talking about a new series they are having on evolution. This is interesting for two reasons. 1). 6 months ago I asked a friend of mine "what is the deal with these podcast things? I don't get the hype or the utility of them?" Then I bought myself an ipod and soon discovered the joy of podcasts. Besides the Science one, the geeky podcasts I listen to are NPR: Environment, NPR: Science Friday and WNYC's Radio Lab. Non-science ones I enjoy are The Story with Dick Gordon and of course Wait, Wait Don't Tell Me and This American Life. If you have other nerdy podcasts or otherwise, that I'm missing out on, let me know. Now for the second reason this particular story was interesting. 2). I was asked by one of my committee members during my preliminary oral exam, "Is life monophyletic?". Granted, that is a pretty crazy question, but not unexpected for me. Some of my other committee members were a little astonished, but I proceeded to attempt to answer it. I likely said some blabbering things and didn't really answer it. I think I said something like, maybe but we'll never know. Now to the point of this story, in this episode of Science they were talking about this very question. I hadn't connected the idea of understanding the origin of life with the question posed during my prelims, but it seems like they are very similar. One prevailing theory on the origin of life is that of the RNA world hypothesis where RNA was the precursor to DNA. This is important to the idea of monophyly because all cellular life has DNA and some viruses have RNA. It follows that if we are going to consider all life on Earth today to be monophyletic, RNA would be one of the "all life" group defining characters. As I suggested, this was not something I discussed (to my knowledge) in my answer to the question "is life monophyletic" and this was a way to redeem myself slightly.

Celebrating Darwin

This weeks issue of Science is devoted to speciation! The review articles are good historical accounts of different common topics revolving around speciation, written by well known researchers in the field. It's nice to see speciation take a place in Science during this year of Darwin. At the Museum of the Earth in Ithaca, NY they are celebrating Darwin Days by inviting the public to listen to scientists and philosophers discuss and present on different topics of evolution. I wish I was in Iowa to see E.O. Wilson speak in Iowa City for their Dawin Days event. What a thrill that would be. I have seen his office door, but that is as close as I have gotten to the great ant researcher. Hopefully these types of activities for the pubic will help people understand evolution better. It's not likely to change the opinion of those who deny evolution, but may heighten the awareness and understanding of those those accepting. I think it's extremely difficult to change peoples opinion. A better approach is to target the youth through education.






In the same state that invites E.O. Wilson to speak at Darwin days, also proposed the "anti-evolution" bill, the Evolution Academic Freedom Act . This bill would allow teachers to teach whatever they want, and students to answer however they want on exams with regards to evolution/creationism/intelligent design. The following sections of the bill provide that teachers in the state's public schools and instructors in the state's public community colleges and state universities may "objectively present scientific information relevant to the full range of scientific views regarding biological and chemical evolution in connection with teaching any prescribed
curriculum regarding chemical or biological evolution" and that they "shall not be disciplined, denied tenure, terminated, or otherwise discriminated against" for doing so. Also, the bill adds, although students "shall be evaluated based upon their understanding of course materials through standard testing procedures," they "shall not be penalized for subscribing to a particular position or view regarding biological or chemical evolution." One step forward, two steps back. The Iowa State Education Association is against the bill, all regents are undecided. Currently the only support comes from the Iowa Christian Alliance.

It still amazes me that the majority of Americans don't "believe" in evolution. Evolution and religion are not diabolically opposed. I don't believe in evolution. I know that evolution is a real, biological phenomena. I think we need to change our verbiage away from belief of evolution. Hopefully things can change through education of evolution in creative and new ways. It won't happen overnight, but it could happen faster with some work. Harvard is hiring new PhD graduates to teach some of their courses. This kind of push to fill the classrooms with new vigor is one way new ideas can move through the education system faster.

I would like to know what people that deny evolution think about the Neanderthal genome being released soon. What do you make of Neanderthals? There are so many questions that could be raised here. Virus evolution; why must we get new flu shots every year? How can people accept some aspects of evolution and yet claim not to "believe" in evolution?

I digressed from my original intentions. My point is, Darwin was amazing and he deserves to be celebrated. Happy 200th Chuck.

Evolution Meetings

Just a plug for the upcoming (well, in June) meetings in Moscow, Idaho.  Moscow is great for anyone who hasn't been there before.  It's a fantastic little community with lots of spirit.