Published and more

5ii 2012
0116- playing WoW
0310- playing online
0444- sleeping
2036- watching the super bowl

Random Fact- The Giants set a record of having the poorest season record of any Superbowl champion

Lunch- rice and sausage 
Dinner-burgers and brownies 

Brad and I went to Lowes to buy the supplies we needed for our various bird encloses.  We had to race home at 2 so I could do the WoW study I had signed up for, only to discover it had been canceled due to technical difficulties.  So instead we cut the lumber and assembled the long sides and decided we could start a custom budget construction company if the whole academia thing didn't work out.  About 1730 we went over to Chris's to watch the Super Bowl and have dinner.  I was happy the Giant's won and thought it was a great game- its always fun when a game where you don't have strong feelings about who you want to win goes down to the wire like that...

6 ii 2012
0434- sleeping
1057- on my way to campus
2024- at Mad Hatters with Eric
2233- setting up a quick BEAST analysis

Random Fact- Newfoundland didn't become part of Canada until 1949

Lunch- Freebirds steak, cheese, and sour cream burito 
Dinner- rice and sausage  

Eric and I had decided to meet up and make Ira take us to lunch which worked out quite nicely.  I found out Eric is considered a faculty member, a fact I find frightening.  I managed to get a tray of Xyphon databased, I'm getting close to the end finally.  The only really exciting thing I did today was some basic BEAST analyses with the new data.  I split out the Hecalus and so far it looks like there are two clades of Hecalus- a New World and an Old World group. 

7 ii 2012
0317- sleeping
0454- sleeping
1420- driving around trying to trap hawks
1950- dinner with Eric

Random Fact- You have to be on the graduate faculty to be on graduate committees, just being a faculty member isn't enough.
 
Lunch- Sausage plate and potato salad at J Cody's 
Dinner- chunky steak at Pho John's  

Had an unsuccessful trapping trip- saw a bunch of birds but they were all either uninterested or interested enough to come down but not hungry enough to land on the trap- rather they would land next to it and foot it from the side.  It was a really pretty day out though, with the sun shining it was a typical Texas spring day.  The big news though was that The Wildlife Techniques book is officially published, can't wait to actually get my copy of it.  I had a momentary scary though at dinner- since Eric is a faculty member now maybe he could also be on graduate committees, so I texted Ira and found out luckily that he can't.  As Ira said, the world is still safe. 

8 ii 2012
0159- reading a Victoria Thompson book
0240- sleeping
1539- databasing leafhoppers- 1 more drawer left
1720- at home watching TV

Random Fact- DIVA tends to infer ancestral ranges to include all the daughter taxa ranges because it treats vicariance as the null model (with a 0 cost) while disbursal and extinction have costs of 1.

Dinner- a pastry with ground beef and potatoes that Kira made  

Today I led the systematics discussion group meeting on Bayes-DIVA.  It went pretty well, and the fact 1/3 of the paper was spent bashing one of the profs who was in the group made it pretty amusing.  I think the paper was a bit advanced for some of the students, but it went well overall.  Amazingly, I found out the Jen in the group was the same Jen I went to High School with- she recognized me when I came in and I had been wondering about it myself...  Other than that spent the evening playing worms with Brad and Kira and doing some work in the lab.

Back to Warcraft

24 i 2012
1845-  Driving back from picking up quail
1906-  eating
2116-  reading the paper for tomorrow's discussion
2134-  playing with Boo

Random fact- The first pinewood derby was held on 15 May 1953 in Manhattan Beach, CA.
 
Lunch- chili 
Dinner- tamales  

My major accomplishment was picking up the quail from out near Bloomington.  It's apparently pinewood derby season, which brought back memories of having a track stretching from one side of the house to the other.  Other than that, I'm happy to report John finally trapped his bird using a different BC and a pigeon.  He's now out of town so I'm watching the falcon and dog.  I also spent the evening fighting with Blizzard- by the time I was able to get into my account they decided I was a hacker and locked it down so now I have to call them tomorrow...

25 i 2012
0220- bout to go to sleep
0759- sleeping
1206- meeting with chris to get some leafhoppers IDed
2240- playing with Boo

Random fact- to unlock your Battle.net account you have to call them and practically verify your life or mail them copies of your drivers liscence, passport, or some other legal document proving you are who you say you are.  People take this game pretty damn seriously...
 
Lunch- steak 
Dinner- fish sticks  

I had my A&M systematics discussion group today- Skype went much better this time, I could hear most everyone talking and there wasn't the strange background humming going on.  I also got my WoW account reactivated so spent a few hours wandering around the forest.  Massimo and I went to the gym, ran our mile in 8 minutes 50 seconds and lifted for a while also. When we got done I was starving so I had Brendan throw my fish sticks (turned out to be a bad choice since I'd burnt my tounge on today's hot chocolate) in the oven while I went to take care of Boo.  Shes so much clamer than Dumas, its crazy to watch her in comparision to him.

26 i 2012
0219- bout to go to sleep
0856- sleeping
1216- rereading the paper for todays discussion
2132- questing with a new toon I'm playing

Random fact- bird systematists are splitters (which is old news).  What I didn't know is mammal and herp people are lumppers by comparision

Lunch- steak 
Dinner- shrimp and rice  

Systematics discussion group turned out to be quite interesting.  As usual we ended up talking about species concepts, and I got to mention Aubrey and her reaction to species delimination in fish.  I vortexed my 22 extractions throughout the day but otherwise spent it just working on image extractions.  Once I was home I spent a couple hours playing WoW- I started a new night elf hunter to try and remember how to best play my main.  Lastly, Dumas was incredibly sweet this evening, and even managed to sneak up on the couch and stay calm enough not to get thrown off- I skyped Is as proof it happened.

So what do systematists do for spring break?

Thanks to a post on Darren Naish’s blog Tetrapod Zoology about plastic pelicans the taxon of interest was pelicans. For people who actually care how I got the tree hear are the methods. Otherwise just skip it and go check out the tree. I only did a parsimony analysis, but if I get bored I’ll do a Bayesian analysis also. As I’m not a pelican taxonomist I’ll leave the result interpretation to someone who actually knows something about these birds.

Methodology

Sequence data

Due to my inability to get morphological data and the fact I was on spring break so didn’t want to spend the entire time tracking down original descriptions etc to code a morph matrix my analysis is only of molecular data mined off of Genbank. I narrowed the sequence data to genes that had sequences for at least 3 taxa included in the analysis (5 pelicans and 1 outgroup a shoebill, Balaeniceps rex). Genes included in my analysis were cytochrome oxidase subunit 1, ATP synthase subunit 8 and 6, 12s, Fibrinogen beta chain gene, cytochrome b, and ornithine decarboxylase gene. A total of 3893 bases were included in the analysis of which 3409 were constant. Of the remaining characters 313 were parsimony uninformative leaving 171 characters as parsimony informative. Because sequences were not from the same specimen they were combined at random in order to have one sample of each taxa with the most possible sequences for analysis.

Taxon sampling

Data were only available for 5 of the 8 species of Pelecanus. Included taxa were the brown pelican (P. occidentalis), American white pelican (P. erythrorhnchous), great white pelican (P. onocrotalus), Dalmatian pelican (P. crispus), and the Australian pelican (P. conspicillatus). Only a single gene (which was not available for any other species) was available for the spot-billed pelican (P. phillippensis). The remaining two species, the Perunvian pelican (P. thagus) and the pink-backed pelican (P. rufescens) lacked any sequence data.

Data analysis

Data were extracted from genbank, aligned in clustal w (using bioedit) then manually checked by eye. Data were then analyzed using parsimony in PAUP*. A heuristic search was done using 1000 random adition sequences. Next duplicates of taxa were removed and an exhaustive search performed (tree shown below)

Results

A single most parsimonious tree was recovered with a length of 547. CI and RI were 0.956 and 0.870 respectively. The ingroup was monophyletic with a bootstrap value of 95. The Australian pelican was the most basal of the ingroup sampled. I haven't done bremer supports or looked at the Ti/Tv ratios etc if people are curious though it could be arranged.

another month have passed

Well another month has passed and my life can pretty much be summarized with a few brief statements.
1. I defend my first thesis next month, i sank about have the members of the genus, and described a new species. Additionally I'm working on the description of 2 species in a related genus. No names posted so as not to cause confusion.
2. I got a 3 year fellowship to University of Illinois Urbana-Champaign to get my PhD in Ecology, Evolution, and Conservation. Start up there in August doing leafhopper systematics, hopefully some biogeography, and of course still playing in avian ecology
3. My peregrine is molting like its going out of style, if this continues he should be ready to go in September. I flew him in the Texas Sky Trials and learned an important lesson about greedy pitches. My kestrel is still weak from WNV but she is finally flying pretty strongly
4. I go back to africa in May. Will get my plane tickets next week, but it looks like I'll be there for 2.5 months, plenty of time to get the black spar hunting.
5. My pointer is going to be awesome, hes 9 months and already holding point like a pro.

Thats all for now, maybe I'll really start updating this thing now that its spring break and i have time to find cool stories to talk about...