Independent research projects for Archosaurs (nee Ornithology)

We started school 45 minutes ago and my first class is less than 24 hours away. I used to call it Ornithology but I changed it to Archosaurs. Partly because I was lecturing on dinosaurs and crocodilians anyway and partly because it sounds cooler. 

The lab section starts tomorrow and this year I'm having them do group research projects. In the past I made these simple - too simple. So I'm upping my game and giving them a few options

1. molecular detection of blood parasites in birds in the fall

• catch birds at a local park (Kirby Natural Area)
• take blood samples
• use PCR and gel electrophoresis to determine if blood parasites are present
• use microscopy as validation (to detect false negatives for the molecular techniques)

2. seed dispersal across urban gradients

• set up seed traps (flat window screens)
• visit and check for bird crap
• compare seeds to knowns (we need to build our library)

3. ?  Would love to do something with ectoparasites or diet (if we did next generation sequencing). 

PNAS Avian malaria paper: It's out!

Two years ago I sent off a number of blood samples from birds we were capturing to a post doc at University of Missouri - St. Louis in Dr. Robert Ricklefs' lab. 

The next thing I knew was that there was a manuscript. I made a few recommendations (and they're in the paper!) and then it was accepted. 

Here's the link. 

Here's the short story: avian blood parasites largely ignore their hosts' taxonomy and where they are. In Pennsylvania, our birds were loaded with parasites - hmm. That needs clarification. I have no idea of the intensity of parasitism (# parasites within an individual) but the prevalence (portion of the population that was infected) was very high: about 60% of samples. 

Which strongly suggests that when you get bit by a few mosquitoes you're being injected with avian malaria. Be thankful these species don't like mammals. 

6th International Barcode of Life Conference

I believe the International Barcode of Life Conference is held every other year. The first conference was held in 2005 and had some 50 attendees. This meeting had over 500 delegates from 68 countries. 

A barcode, in most cases, is a segment of DNA that is conserved within a species and variable among species such that each species has an identifying marker. For animals, the mitochondrian cytochrome oxidase I (COI) is typically used and in the plant the chloroplast gene rbcl is often used. However, in plants you may require several genes to nail down a particular species. The method was popularized by Paul Hebert of the University of Guelph. See here for seminal paper. 

Our discovery of new species has exploded with DNA barcoding; mostly of very tiny things (< 2 mm). For example, Mark Blaxter of Edinburgh, found a remarkable number of nematodes in a small plot behind one of the university buildings. One thing I learned was that the explosion of discovered species with taxonomic assignment (they haven't been named) has created the need to come up with a term that describes populations that probably are species. They are discovered by running a phylogeny and looking for tight clustering. A cluster is called a barcode index number (BIN) - not very sexy but it allows for easy reference. 

Below are three images from the conference from Hebert's talk that I though were particularly thought provoking. The first is the number of pubs over time and the power of barcoding as a new tool pushing science. The second shows an estimate of $250 billion to describe all the species that he estimates to be 8.7 million. 

It is going to be a while before I can wrap my head around the BIN thing as a stand in for species but it appears to work. The graph below shows the relationship between BINS and species. There seems to be a 1:1 relationship which suggests that BINS are a good approximation of species. 

Dr. Melania Cristescu, of McGill University gave a great talk on invasive species. Her specialty is aquatic ecosystems and gave a nice graphic of shipping density. The result of all these invasions (including terrestrial ecosystems) is biotic homogenization.  Species are spread throughout the globe such that the same species are found everywhere. 

There were a few food web talks and I found this experiment exceedingly cool. One angiosperm dominates the tundra and Tomas Roslin and his team set out fake sticky flowers to collect the pollinators. 

If you think, like I did, that food webs are just hawks that eat mice that eat plants. This bipartite graph shows that they are anything but simple.

I also learned about next generation sequencing (NGS). The younger generation will giggle but I had no idea what NGS was. This is my understanding: NGS allows for the sequencing of multiple genes or gene variants in one run. You can use NGS to do things like identify a number of plants in fecal sample of some herbivore. This is essentially running multiple barcodes at once and it has led to rampant species discovery. 

There were great talks, I made great connections and our goal is to present at the next conference. It's a challenge that will be difficult: I have yet to get a single barcode to run. But the uses of barcoding for conservation are numerous and I should learn it. 

The best part of the meeting? Barcoded beer: 

Got plague will travel

Guy goes on a hike in California and encounters plague on a hike and returns to his home in Georgia. Story here. 

Mumpy college kids

There's a quick survey to this short article but here's the link: 

http://www.kcrg.com/subject/news/health/as-mumps-cases-increase-in-johnson-county-officials-push-vaccination-20150819

Barcoding meeting: reception

I'm at the 6th Annual Barcode of Life Conference held at the University of Guelph, pinched between Lake Eerie and Lake Ontario. 

Left Wilkes-Barre at 1030 AM and arrived here around 5. Check in our townhouse (think of a classic dorm room but bigger). It's home for a week. One problem: no coffee maker. 

The reception was packed. Posters were set up, the buffet and drink lines were full but moving quickly. Met a number of people and even may have found someone to collaborate with on an urbanization study in the tropics. 

One very cool aspect of the reception: custom beer that had one element of the beer barcoded. Below shows the barcode for the hops (on the left) and the yeast (right). 

2015 Summer research week 13 (8/10/15 - 8/14/15)

8/10/15 State Game Land 205 

Two vehicles and four of us went down to SGL 205 to measure vegetation at two of the grassland sites. It rained for an hour and a half so we tucked our tails and made it back to Wilkes-Barre and celebrated CS's birthday with sushi. #fieldworkfail

8/11/15 Day off 

8/12/15 Ecological Society of America

Met up with some Auburn U folks that I adore. Helen and John are entomologists and Christina is an invasive species biologists that specializes on invasive herps (reptiles and amphibians).  I was there for one day and took a page and a half of notes and all research ideas. What is clear is that we need more work on urbanization. 

8/13/15  

Office day. Would have liked to have gone out to the field but the lab was a mess and needed help. Still way behind on emails.

8/14/15  Francis Walter Dam

There to do vegetation measurements and met up with a herpetologist from East Stoudsburg University. Already picked up two amphibian specimens for the food web study. No snakes today but a bunch of other interesting critters including a Northern Harrier, Broad-winged Hawk, belostomatid, Gray Treefrog tadpole, American Toad, and Red-spotted Newt.