Friday, October 30, 2015

Your halloween treat: acorn weevil larvae!

Students have been cutting up acorn larvae and gathering data for a 20 year data set. These larvae would normally chew their way out of the acorn and go into the soil for a year (or two or three - nobody really knows). We just started looking at soil type to see if that affects survivorship and we're going to start barcoding to see if there are new species out there and to see if there is some sort of specialization out there. 

Wednesday, October 28, 2015

Home economics: II

One downer about being a graduate student for so long is that you become behind financially - not all of us - but many of us. So, by the time our friends are thinking about a second home or retirement, I'm thinking about living like I have a job. 

The home we live in was flooded in 1972 with Hurricane Agnes and water reached the second floor. We just removed all the paneling and random pieces of wood and were down to the studs. Then the electrician came and the inspector after that. Initially they said two weeks for the whole project but we're in the third week already and we just finished putting up the insulation last night - then immediately went to bed. Who knew insulation became so heavy after three days of installing it. 

The guys are at the house to put up the sheet rock and that is supposed to take three days from start to finish. Exciting just to start the next phase. 

Here's what it looks like with insulation (and you can still see mud on the studs). 

Monday, October 26, 2015

Pin oaks and birds

I remember seeing a bird talk that dissed pin oaks as being a trash species because it was not important to birds. This was in the southeast and pin/willow oaks are super abundant when you don't have fire. So, for some time, I just didn't like them.

But I've made a 180 on pin oaks and I realize they are hugely important to a number of birds in the northeast US (and probably elsewhere pin oak occurs) and probably host a number of invertebrates and other unpopular but crucial species. 

Today I spent an hour on the roof of Cohen and had three species come by. Blue Jays were there grabbing and flying off with several acorns in their crop. The one group of jays was coming from the other side of the Darte Center, which is 500 m away. They're flying over open areas where they could cache. Perplexing!

Crows ignored me and came by and ate a few acorns and took off. A titmouse looked be pounding an acorn to open it - not sure if it was successful. Last year there was a Red-bellied Woodpecker carrying off acorns. So pin oaks are not the fig trees of the tropics (which are known to be eaten by anything that can make up a tree) but they must be crucial to many birds.

Sunday, October 18, 2015

Archosaurs class at home

Yesterday [last week.. not sure why this didn't post] we had class at the house and the goal was to get kids to handle wild birds and show them how to get blood, make blood smears, turn blood smears into slides to look for blood parasites and observe different cell types, and get blood in capillary tubes that get centrifuged and we measure hematocrit. 

We ended up catching three house sparrows, a song sparrow, and two white-throated sparrows. Best part of the day was watching the kids I've trained work with the kids in the class. 

DNA barcoding: a road map

I went to a DNA barcoding meeting a few months ago and I've been more inspired to integrate this technique into my own research. I've been working on a food web project but I could also use this to identify parts of birds and the bits in a bird's diet. 

The first application would be to identify the invertebrates we've been catching for our grassland food web project. My idea was that we just needed to get a bit of tissue, amplify the DNA using PCR, send it off, get the sequence, ID the species, and DONE.

If I have gone through with this I could get our critters identified but with lower confidence and the work with be of little use for other researchers. A shame and near waste of work.

At the barcoding meeting, we met up with a Smithsonian scientist, Caroline, that agreed to come up and discuss with us barcoding issues. So, last week, she came up and gave a two day workshop for Ned and I and a number of students. It was incredibly enlightening. We found (many) issues with our protocols and we were pointed to a number of resources to help us with technical issues. More importantly, we were given a work flow that greatly expands on the flow I outlined above. The biggest missing piece is building a library of local organisms that are identified independently of DNA barcodes. These organisms you barcode and then use a reference. This seems a bit circular (and it is) but you can use your reference collection to identify bits of organisms or organisms in other stages, such as larvae and eggs. This sounds simple but it means getting specimens and organizing them. Organizing them. That is completely new to our lab and will be a challenge. But it's a challenge I'm willing to take up. One of the first things to do is to create an outline for the whole project and I'm doing it here

So, the workflow is this, get specimens (mostly, go out and collect insects), give them a number, get them identified, pin them in an organized way (presumably by order), bar code a small bit of them, link the barcode to the specimen. Now unknowns can either be ID'ed through the vouchers are barcoded. Everything is organized through BOLD Systems.

It was a hugely useful workshop and Caroline was a blast. She stayed at the Hillard House, which has an awesome breakfast menu. Students enjoyed the workshop as well and I hope they're inspired as well. 

Monday, October 12, 2015

Home economics

We're gutting our downstairs. This means tearing up the carpet, tearing down the panels, the plaster, and the plaster backing. It's mess. 

Our house was flooded in 1972 during Hurricane Agnes and you can still see mud from the flood on the supports. We're going to tweak the electric, insulate, sheet rock, and paint. Looking at a finish date of Thanksgiving. 

Friday, October 9, 2015

Music to write research papers to

I was introduced to the music of Marissa Monte in Brazil in the early 1990's. Great stuff. 

Thursday, October 8, 2015

A trip to the American Museum of Natural History: Part 3. Dinosaurs

Last Tuesday I spent the day at the American Museum of Natural History and had my Archosaur students in for some of it. Technically, I think we spent most of our time on the bus and if I'm going to do this again I think I'll take a van. I did this once and, except for the Holland Tunnel, it want very well. This was both expensive and time consuming. Live and learn. 

I posted on the type specimens and other birds and I ran through to get pictures of dinosaurs to integrate into lectures. Never enough time. 

Here are some of the better pictures. If I had a complaint about the museum it would be this - so much glare. So it goes. 

Acanthostega - nice intermediate between fish and amphibians

Allosaurus manuss

Archaeopteryx - close enough to dinosaurs!

Deinonychus manus - note the reduced number of digits and carpels

Deinonychus skull - built for ripping your face off

Diatryma - a bird, taller than me and three times as kick ass

Plateosaurus - an early quasi-bipedal sauropod - note the reduced outer digits
Prestosuchus - early archosaur

Gallimimus - very bird-like dinosaur
Temnospondyl - early amphibian
T. rex!

A trip to the American Museum of Natural History: Part 2. Birds

I've been in the suboscine section of the bird collection several times and it never gets old. This isn't the largest section but it does contain several of my favorite birds: the flycatchers (not looked at), manakins (not looked at), treecreepers (not looked at), antbirds, contingas, and Old World pitas. So I'd like to get back again and check out many more specimens. I'm just taking pictures but these collections are invaluable to science and there are many many publications out there demonstrating this. What is wonderful for me is to simply be in their presence and to look at them. I have used collections though to see if blue jays have easily recognizable characters that would indicate their geographic origin - they don't. If they did, then I would be able to observe jays in the winter and tell if they're migrants or not. Without a collection, I would never know either way. I also wanted to know if relative eye size varied by habitat in South American antbirds - I was scooped a month after I collected data. Again, you couldn't answer these questions without a collection. 

Batara cinerea - I didn't know this bird was so kick ass. Most thamnophilid-type antbirds are sparrow-sized. I could see this thing quickly and painfully removing the flesh from an ornithologist's hand. Putting this on my bucket list. 

Cephalopterus ornatus - greatest doo ever

Umbrellabirds are large cotingas and not related to crows 

Continga cayana - I'm in love. 

Cotinga cotinga

Cymbalaimus lineatus - I love critters that are striped like this

Cephalopterus penduliger. This species doesn't just have a great doo - check out the feathers coming from the breast. Remarkable! 
Formicarius colma - I have several papers on this bird. You're basic bird but so damn interesting

Two Grallaria species: G. excelsa in the front and giganta in the back. Antpittas are not so exciting as specimens but in the field they are really cool birds.

G. varia - a species I worked with in the Amazon and one of the most elusive, despite their abundance. They sing before sunrise and are able to move in the forest in almost complete darkness. 

Crimson Fruitcrow - another continga and this one restricted to the Manaus area. Love them. I a recording of one them giving a "BOCK" call

Hypocnemis cantator - a small antbird and there showing three subspecies (that are probably different species)

Myrmothera campanisona - an antpitta species I worked with in the Amazon.
This is most certainly a large canopy gap specialist.

Pithys albifrons - one of the showiest antbirds. Commonly caught and rarely seen. A specialist of army ant swarms. 

Pitta erythrogaster - Old World pitta. 

Pitta maxima - any questions??

Pitta sordida

Procnias averano - another amazing cotinga 

Procnias tricarunculta - a continga on my must see see before I die list. You can listen to them here

Pyroderus  scutatus - another amazing cotinga

Rupicola peruvian - Andean Cock-of-the-rock. Gorgeous.

Tuesday, October 6, 2015

A trip to the American Museum of Natural History: Part 1. Extinct and Type Specimens

The AMNH is, by far, my favorite place under a roof. Today, I brought my Archosaur class and I was immensely please by their attention and excitement that the brought to the collection. We were greeted by and given a tour by Dr. Paul Sweet, the curator of birds at the museum. This is probably my fifth trip to the collection but he took us to the section with type specimens and extinct birds. Totally awesome! The bottom pictures are Ivory-billed Woodpeckers, an extinct species of the American southeast. 

I was then left alone in the suboscines.