From Coast to Coast

My crane fly collecting this summer for the most part was spent solo, in the car, out in the woods alone with the friendly mosquitoes and black flies to keep me company. This summer was exceptionally bad for these blood sucking flies (well, I guess good if you look at it from their perspective). The weather was wet and rainy, something I hadn't really experienced collecting in the west the last two years. Dragging out a wet tent every night, putting on wet gear was exhausting. Looking back on it I wouldn't have traded any of it for the sights I saw and the experiences I had.

Bradford Bog

Near the very beginning of my trip, on the first leg I was greeted by my good friends and fellow EEB folks Daelyn and Dave. As new faculty members at Central Michigan, Daelyn and Dave are settling in to a new life, much improved from the poverty stricken graduate student life. They were great hosts and the visit was much appreciated on both ends. We swapped stories about the field and living out of tents, caught up on knowledge of mutal friends, remembered our dear friend Ron and fantastic biologist that had passed away, had some great food and drinks, a much needed shower (for me) and then headed off on Memorial Day to do some collecting of flies and unionids alike. We came up successful on both accounts. Daelyn and I spent some time collecting in the nearby Au Sable State Forest. We successfully found one population of adusta after checking at a few locations. The habitats were forested swampy areas with white oak, hemlock and ferns as understory. We then headed off to do some muscle scouting. The highlight of this for me was seeing a female display her glochidia. I was able to take an underwater video.

I then headed to the western edge of Michigan, then northeast to the edge of Lake Huron, south near the "thumb" and home through Canada for a few days rest. Overall this trip to Michigan was sucessfull; approximatley 8 populations of adusta and more importantly the only population of caudifera I found all summer. Here is a map of some of the places I visited.

View summer 2009 in a larger map

I headed north to Canada, collecting at a few places along the way. The Canadian government took away my means of bear and backwoods dangerous humans protection that they themselves insisted on me carrying into National Parks in Canada. Luckily I never felt like I needed it, but never the less was sorry to see my security blanket taken. Fenja Brodo and others had collected adusta from areas surrounding Ottawa. I was fortunate enough to be welcomed in by Fenja and her husband for the weekend, despite their busy schedules. It was a joy to meet her and discuss all things crane flies. Fenja was a great help in reassuring me that my work is worthwhile and prudent. We had a great time collecting. This was the first place where I started seeing flies with some kind of fungus. At this point I have the genus narrowed down, but work still continues on the mystery of the fungus. No fungus of any kind has been reported in these flies and it was very common throughout the remainder of the season, likley rendering the females infertile, which begs so many interesting questions.

Myself and Fenja Brodo in her home.

After a nice restful night I headed back to the homeland, passed through the border without problems and headed to the Adirondacks. Collecting was lack luster, only finding adusta in a few locations. Then I traveled south towards the southern end of the Green Mountains and collected in various places throughout the mountains. The weather was cold and rainy, likely extending the flight season further into June. I was only successful at a few places in Vermont. Next I went east into the White Mountains of New Hampshire. I didn't find any populations there, but found many suitable habitats. Maine offered a plethora of bogs and collecting was much easier. By this time the weather had warmed considerably, although I continued to get rained on daily. My rain pants became a permanent feature. I took shelter at Acadia National Park where they provide temporary housing for researchers. I had some human contact, much needed rest and relaxation in an actual bed and time to recover from the black fly bites covering most of my head. I headed into Canada one last time traveling along the Bay of Fundy through New Brunswick and into Nova Scotia. Finding areas to collect was more difficult than in the US, but luckily adusta was quite abundant. Matt met me in Halifax where we spent one luxerious night in a bed and breakfast, then headed back to the wilderness. We collected along the way as we drove back through Maine, New Hampshire, Vermont and the Adirondacks.

On the Fourth of July I took a redeye flight to California. I was welcomed by many family members, some of which I had never met, in Modesto where I spent the night. I then headed to the Sierra Nevadas where nightly temperatures were around 38 degrees. I was ill prepared to say the least. Crane fly collecting in general was terrible. Very few flies were out at this time here. I did a lot of hiking and driving many miles in search of at least one population of flavapila in hopes of resolving my currently paraphyletic and confusing phylogeny of this genus. At the very last stop, after a week of searching, at a place where Matt and I had looked but collected nothing in 2007, but where Joseph Speed Rogers had collected columbiana many years ago, after spending 30 minutes finding nothing, I walked back to the car, defeated. I gasped and saw what was obviously Neophylidorea. I caught her easily, sat down and sighed. My trip was not wasted. (Not to spoil the story, but I have since analyzed the data and this population was only columbiana and did not provide any resolution to my tree).

One last trip was to the Adirondacks in search of neadusta in late July. This time I was accompanied by our golden Radar and Matt. The weather was great and the area was beautiful. We hiked up to Marcy Dam the continued further towards Avalanche Lake. Again, defeated we hiked back to camp with our nets folded up. My motto (adopted from Matt's somewhat tongue and cheek saying) for the summer has been ABC* Always Be Collecting. This was the epitome of ABC. Matt caught a single female with his hand after Radar and I had already passed her. The habitat was nothing that I would have expected. She was full of fungus and not flying well at all. (Again, not to spoil the story, but because this was a female it's difficult to say whether morphologically she is neadusta, but molecularly she matches adusta well). We had a good hearty breakfast the next morning, did some additional collecting at Browns Tract Bog where I had hoped to get enough specimens to take back to Cornell to culture the fungus, and headed home. We were only able to find a single male and he didn't survive the two hour trip home.

Since then I have collected locally having some success. I haven't been able to find any individuals locally that are infested with the fungus, and therefore have had no luck culturing it.

Microsoft Molecular Patent?

An update on my summer research will have to wait. The most recent issue of Science included an article about Microsoft and a patent application they submitted having to do with using molecular data to infer phylogenies. From the article it sounds like the patent was written to be too broad encompassing and simple to be approved. However, if such a patent were to pass it would have huge affects. I have to wonder what the rules are for patent applications to pass. Do they take into considerations such as slowing down the progress of scientists when making their decisions? Who makes such decisions and how knowledgeable about they about molecular phylogenetics? This is a world of which I am unaware.

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.

PCR is Magic

Over the summer I attempted to sequence COI from a few samples of the genus I'm working with.  I had little to know luck doing this on my own in an abandoned lab at Iowa State.  Although I had various friends helping troubleshoot, I was taking away their time and supplies and spending limited funds on a seemingly endless struggle to sequence what is often considered a relatively easy gene to sequence (well know, "universal" primers are published, etc.).  So, I headed east to a lab at the Cornell Lab of Ornithology, the Evolutionary Biology lab to work with Irby Lovette and his army of students and lab managers.  They offered open arms.  I continued to have minimal success, then had help developing primers from the success I did have.  I went gang busters yesterday finishing the PCR on the remaining samples using these new primers only to continue to have minimal luck (23 out of 36 samples showed promising results after running a gel).  I guess this is par for the course and something that people perhaps don't always talk or write about in the literature.  It's frustrating for sure.  PCR is really magical to me.  Not that I don't understand the basic process, but that there seem to be complexities beyond what I can understand.  Why some samples work and some don't under the "same" conditions (or at least as humanly possible) is amazing.  That it even works at all is amazing.  So I've progressed and I'm moving on to other genes, narrowing down the
remaining COI samples, aligning and analyzing what few sequences I do
have and learning a lot.