Project Phases - Where are we now?

If this project were to be broken down into phases it would be as follows:

Field Work Phase
Lab Work Phase
Data Analysis Phase
Writing Phase

Field Work Phase

The Field Work Phase was wonderful. It was full of sunrises, bird banding, and sound recordings. Easily my favorite among the Phases. I got to work with wonderful people and learn so much about the white-crowned sparrows of San Francisco.

Lab Work Phase

Not my favorite but a lot was learned in this phase - both about laboratory techniques and about the parasites. It was in this phase that my thesis took on a new direction. After extracting all of the parasite DNA from my blood samples and running PCR, it turned out that only 5 total birds were infected. Of the 103 individuals captured over the two field seasons only 5 were infected! Statistically speaking this is not a large enough sample size to come to any solid conclusions about the effects of parasites on song. Unfortunately I had to put this portion of my investigation aside.

The good thing is I have plenty of other data to work with to investigate the factors influencing song performance in Nuttall's white-crowned sparrows. These factors include things such as morphology, weather, proximity to competitors, and anthropogenic noise.

Data Analysis/Writing Phases

While these phases are heavy on the indoor/computer work, they are critical to any scientific study. It is important to get the results of a study published and accessible to the scientific community and the public at large. From there the results are added to the general body of knowledge and can inspire future work so that the inertia of learning is carried on.

For me these phases have encompassed becoming familiar with several new computer programs. Here's a few that I have relied on most heavily lately:

Audacity

viewing and analyzing song spectrograms

This program allows me to visualize and annotate various features of a bird's song. It is how I generated song performance measures such as song rate, song length, trill number and trill rate.

ArcGIS

creating maps and analyzing relationships among various features

This program is fantastic! I took a course at SFSU called "Intro to GIS" (GIS = Geographic Information Systems) where I just scratched the surface on all the features this program has to offer. I'll write a separate post about all the cool analyses I did with ArcGIS.

RStudio 

statistical analysis

RStudio is a really helpful graphical user interface for the R statistics program, which is just raw coding. I am using this program to compare song performance between different study sites and attempt to tease out which factors seem to be most significant in influencing performance.

Mendeley 

storing and organizing primary literature

This program is an essential organization tool during writing. It stores all relevant publications and allows one to highlight, annotate, tag, and extract citations. Every professor I've had in graduate school has recommended this program or something like it.





Stay tuned because I have some exciting things to share in upcoming posts! I'll share some of the maps I've created and interesting differences I've seen in the sonograms of the white-crowns within and among the study sites. For now it's back to the statistics!

Honing Banding Skills

My project is officially in the "data processing" and not the "data collecting" phase. I'm reading a lot of primary literature, analyzing recorded songs, and preparing my thesis for defense. These are all extremely important aspects of a scientific project but I have to admit, they're not as enjoyable as being out in the field collecting the data and working with the birds first-hand.

Luckily I still have the opportunity to get outside banding birds as a volunteer with the San Francisco Bay Bird Observatory. Since beginning as a "Predator Patroller" (keeping an eye out for foxes, feral cats, etc.) there nearly two years ago now I've gained skills first as an "Extractor" (able to get birds out of nets) and finally as a full fledged bander (code name E7!) 

Fall migration is in full swing and we've been busy the past few weeks.This past Sunday we had so many birds come in I didn't leave the banding table once! It was a great day to practice my skills identifying, quantifying fat, determining degrees of skull ossification, and aging different species of birds. 

Here's just a small subset of the birds that came through. 

A really tough Townsend's warbler.

Fox sparrow. I am quite partial to these birds - These were some of the first birds I learned how to handle. They also kick up leaves like crazy while forraging. Reminds me of how a dog kicks up grass with its back legs after it poops.

Lincoln sparrow - These have just a smooth clean look about them. They're a treat to see up close.

Black phoebe. These birds are not caught too often - they're extremely agile flyers and usually dodge the nets. 

Bushtit. These birds can be sexed by eye color! A light eye, like this lady here, indicates she's a female. Bushtits are some of the tiniest birds we catch but also the spunkiest. They travel in flocks, constantly twittering back and forth to each other. 

Ok I'm not going to label this one. I would hope you could recognize it by now ;)

The Buzz Dive

Today I am annotating the birds of Golden Gate Park. It is fascinating how each bird is just a little bit different from the last, even though they are all the same species, and within close proximity to each other too!

This bird has what I've dubbed the "buzz dive" on his second note. Whereas other birds just have a straight buzz he plunges in:

It's little nuances like this that make me love being able to look at the sonograms - the visual representation of the songs. This dip is very difficult to pick out in just the audio version of the recording. Here's the sonogram above at full speed:




It's only with the recording slowed down that the "buzz dive" is audible. Here's the same clip at 70% of it's original speed:




This song belongs to "G31" or "GS/GY"

He's being a little shy in this picture and turning his head away but you can see that he's a younger bird because of his brown and tan (as opposed to the adult black and white) crown.

I'm looking forward to comparing all the songs across my study sites and seeing how much variation there is between sites and between individuals. So far there's a TON of variation!

Birds of the Day - Monday April 27, 2015

Lake Merced

Sunrise is getting earlier and earlier. Today Charlie and I got started at 6:15am at Lake Merced. My goal was to catch two birds that have been eluding me this season. Unfortunately I think it just isn't going to happen. They respond well to the playback but the net locations just aren't ideal.

The perfect situation is to set up a net between two stands of tall vegetation so that the bird gets caught flying from one stand to the next. Unfortunately at Lake Merced there are isolated clumps of low brush separated by relatively large open spaces. The birds I've been trying to catch have hopped down by the speaker but remain protected in their bushes. Alas, these two continue to be elusive.

I did, however, catch three birds this morning. Two previously unbanded individuals and one recapture from last year.

The first one was a second-year male halfway grown into his black-and-white crown. He became "RS/RY" today:

Then there was this recapture male from 2014, "S/YOB":

And in the same net we caught a female who became "OGO/S":

Banding is in Full Swing!

The 2015 banding season is off and running! (flying?)

As of today (Saturday April 25, 2015) I've processed 41 birds this season. I'm using the word "processed" instead of "banded" because some of these birds have been recaptures from last year! It's been pretty exciting to see some of 2014's birds again - both for my study and for my own personal interest in seeing them survive another year.

One thing I've noticed this year is that the birds don't seem to be responding to the playback in the same way as last year. At first I was using the same set of songs I used last year but the birds seemed much more hesitant to charge the speaker. I would get some counter-singers and some full-fledged [bird humor] abandonment. I changed up my tactic and added site-specific songs to my iPod. These were much more successful!

Another interesting difference this year is the amount of females I've been catching along with the males. Last year yielded mostly male captures but this year I'm getting a lot more pairs co-defending their territory.

I also have to take a moment to thank Charlie, Erika, Pete and Linda - thank you so much for your help so far!!

Here are some birds from my four field sites this year:

San Francisco State University

Thanks to David Emmerson (aka Dad) for help on this first bird! He's been resited and recorded.

Not too many second year (brown-and-tan crowns) this year but this male is an avid singer from South campus:

Golden Gate Park

San Francisco Zoo

This bird is a recapture of the very first bird I caught at the Zoo. Dubbed very elaborately (sarcasm) "Zoo1" or "S/WYW", this male had a brown-and-tan crown when I first caught him - now he's all grown up!

Lake Merced

I cannot make any claim to these amazing photos. They're all from Pete - check out his other amazing bird photography (including many of Lake Merced's banded white-crowns) at his Flickr.

And my personal favorite:

Solving the Mystery of Songbird Migration

This June I had the privilege of helping out my friend and fellow lab mate, Allison Nelson, with her research project. She's studying the migration of hermit thrushes. Described by the Cornell Laboratory of Ornithology as an "unassuming bird with a lovely, melancholy song," these birds are well known for their beautiful metallic songs. Despite their popularity, the migration patterns of these birds are not well understood. Different populations with overlapping ranges travel in completely opposite directions - and we have no idea why. Allison aims to answer some of these questions.

To fund this research trip, Allison ran a successful Kickstarter campaign. Kickstarter is a crowd-funding website for creative projects where individuals donate funds at different levels in exchange for small gifts such as a picture or sound recording of a Big Basin hermit thrush.

With the money she raised through Kickstarter Allison was able to purchase 20 tiny geolocators that use light levels to determine the approximate latitude and longitude of the bird. The video below from her Kickstarter campaign describes out the aims of her study:

We spent a week in Big Basin Redwood State Park target netting hermit thrushes and harnessing them up with geolocators. Big Basin is California's oldest state park - the sites we were working in were full of lush trees and undergrowth.

The hermit thrushes here spend the summer in Big Basin and migrate south for the winter. They have high site fidelity, meaning they return to the same sites year after year. Allison color banded birds in Big Basin Park last year and we recaptured 9 of her birds from last year! That means those birds spent the summer of 2013 in Big Basin, flew all the way down to the southern United States or Mexico for winter, and then flew back to the exact same spot in Big Basin for summer of 2014.

Next year we'll return again to try to recapture the geolocator birds to download the data and see exactly where they spent the winter. Given our recapture rates from this year we're confident we'll get quite a few of the geolocators back.

We set up most nets back in the brush but in the final day when we needed to catch the last few stragglers we set up a long net lane along the path - it ended up being successful! Thrushes are ground feeders and took advantage of these walking paths - we caught five birds as they made their way onto the path.

Allison determining the age of a thrush by looking at its feathers and molt pattern.

One indicator is the shape of P10 (the 10th primary flight feather) - pointed (vs. rounded) indicates an older bird.

A geolocator and harness - the loops tucked around each leg with the geolocator extended above the feathers on the thrushs' backs. Each one weighed about a gram or less. 

Ready to go!