Monday, August 31, 2015

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). 

Monday, August 24, 2015

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. 

Saturday, August 22, 2015

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:

Tuesday, August 18, 2015

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). 

Friday, August 14, 2015

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. 


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.

Thursday, August 13, 2015

Eagle vs. drone: hell yea!

This is really cool but I really hope this doesn't inspire people to harass wildlife.  

Monday, August 10, 2015

Using natural predators in agriculture

Here's a blog post related to a paper in the Journal of Applied Ecology that demonstrates the ability the ability of natural predators to control pests when the natural predators are provided suitable habitat. 

Their study was in South Africa and predation on pests was highest near natural habitat and declined with increasing distance. The pests are identified (two insects and a fungus) but the predators were not (at least not in the abstract) and that's a little frustrating. 

Looks like an interesting paper. 

Friday, August 7, 2015

Summer research week 12

Monday 8/3/2015

Finished off edits of the State Wildlife Action Plans. I volunteers to cover 6 early successional (grassland and shrubland) species of birds and I called for more fire to maintain habitat for these species. Will be interesting to see how that is received.

Tuesday 8/4/2015

Went to Nescopeck State Park to catch birds and set up small mammal traps. Was bloody hot and only captured three birds: 2 Song Sparrow and a Rudy-throated Hummingbird. 

We also need to do tons of vegetation measurements for birds. For me that means structure more than composition (I hope!). Did the first one today with only a few goof ups (like measuring a transect out from the radius and not the diameter so after 10 points there were still 10 to go outside of our plot area). 

Wednesday 8/5/2015

Went toNescopeck State Park for vegetation sampling, small mammals, and birds. The crew has picked up on how to do vegetation sampling so I'm happy with that. We have some 20 small mammal traps out and captured a female meadow vole. We only had two nets out but we captured a Yellow-throated Vireo and a flycatcher that was either an Alder or Willow. 

Thursday 8/6/2015

Last day at Nescopeck State Park. Goal was to finish vegetation sampling at two fields. Done. No small mammals in the small mammal traps. Better luck with the birds. Picked up another hummingbird and we were able to use feathers from the breast that sloughed off. Captured a Field Sparrow at the silo field (there's an actual silo), American Goldfinch, and a Common Yellowthroat. Overall a good day.

Tuesday, August 4, 2015

Great podcast from the CDC on pre-vaccine measle epidemics

Here's a link to a CDC podcast that reads excerpts from the journal of an colonial American physician in Massachusetts whose town was besieged by a measles epidemic. 

How the anti-vaxers could prefer epidemics over vaccines is beyond comprehension. 

Photo of a boy with measles rash

Monday, August 3, 2015


OK, that's a horrible title. This year we've had over 200 cases of Chikungunya in the US but none locally acquired as reported by the CDC.  

The largest number (40) was in NY and I suspect we'll have another story similar to West Nile virus that was also established in the US in NY. It does seem like it's just a matter time given we are surrounded by it. 

Sunday, August 2, 2015

It's that time of year again: West Nile virus

Pennsylvania is reporting large number of WNV positive mosquitoes and a few positive in sentinel (chickens set out in various places to see if they get WNV). There was even a recent case in humans; a Venango county woman tested positive without hospitalization. The location was a surprise. Venango county in the northwest corner of the state not far from Allegheny National Forest. I would have expected it to come from the Philly area (they have in the past). 

WNV is more common in the suburbs where breeding sites are a plenty and the WNV super-spreader American Robin is also abundant. 

I suspect WNV did in this young robin below and I wish I had the lab material to detect it. Bird was healthy - at least the muscle was not receding from the sternum/keel.

UPDATE 8/3/2015  State released its weekly WNV report with 61 mosquitoes being positive. That's far more than I've seen... ever

It's plaguing cats and dogs

There have been several waves of mortality due to infections of Yersinia pestis, the most famous wave being the Black Death. Most of us think of this as a Medieval disease but plague persists and even smolders in the US. In the American southwest, plague is of conservation concern since it can obliterate prairie dogs and their predator, the endangered Black-footed Ferret. 

Transmission to humans is rare but happens and I remember seeing warnings of plague on a reality survival show. Fleas are the primary vector and jump from host to human and spread plague. 

I remember reading about a human-dog case of plague here from last year. Now there's a case of plague in a cat from Colorado.

Saturday, August 1, 2015

Getting my smart ass on... more Confederate flag flack

Made this on  Made me feel juvenile but this is partly how I see the argument.