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!

The Birds Across the Bay

You may not have heard me mention the white-crowned sparrows of the East San Francisco Bay much because, well, there aren't that many. At least not the year-round Nuttall's white-crowned sparrow residents.

Subspecies Review

Remember the three subspecies we get here on the California coast? There's the Puget Sound white-crowned sparrow (PSWS or lovingly, "piss wiss"), the Gambel's white-crowned sparrow (GWCS) with its "candy-corn orange" beak, and of course, my focal subspecies, the Nuttall's white-crowned sparrow (NWCS). The Gambel's are easy to tell apart from the others because of their Crayola-colored beak. The Puget Sound and the Nuttall's are a little more tricky though. Both have black streaks on their upper beak extending from the base to the tip of the nares, as seen in the picture below.

(Really just an excuse to show my favorite of Pete's photos) 

Not seen in the picture below but also a distinguishing characteristic of the PSWS and the NWCS are the yellow wash to the feathers in underside of their wings (in the "shoulder" area if you will.) According to Peter Pyle and his banding bible, Identification Guide to North American Birds: Part I, the only way to confidently tell the difference between a Puget Sound and a Nuttell's is by an equation that is of course escaping me at the moment but it is something like the wing length divided by the lean weight (weight in grams minus the fat score) and if that result is less than 2.3 (ish) then it's a Nuttell's and if it's greater than 2.3 (ish) then it's a Puget Sound.* Nuts right? 

*I'll come back to this post and put in the real equation when I am reunited with my version of the Identification Guide, which banders just call "Pyle." As in, "Have you seen my copy of Pyle?" or "Lame, this bird just pooped all over my Pyle."**

**UPDATE 10/25/15

Here's a photograph of part of the page from Pyle.

The equation is: wing ÷ lean weight where lean weight is the weight minus the fat score
If it's >2.6 you've got yourself a PSWS
If it's ≤ 2.6 you're holding a NWCS 

The songs of all three subspecies are different as well but the biggest behavioral difference is that the Nuttall's white-crowns like to stay put. They are the only non-migratory subspecies and are year-round residents of the Bay Area. 

White-crowned Sparrows of the East Bay 

When I was originally planning out my project I was going to band all over the San Francisco Bay in every public park I could. This plan got toned down a bit when I started asking local birders where I could find Nuttall's white-crowns in the East Bay.

Turns out that to the East of this beautiful Bay Bridge here, there aren't too many resident Nuttall's. There was an odd mysticism surrounding these sparrows whenever I would ask about them. I would get answers like, "I heard there were a few of them down in Oakland." or "I thought I heard one singing the other day in the Emeryville Home Depot parking lot." After inquiring among birders and taking a few scoping birdwatching hikes myself in among the East Bay Regional Parks I was able to find only two tiny populations at Eastshore State Park and Albany Bulb. 

Of these two sites I only ever did any banding at Eastshore because at the time Albany Bulb was home to a massive homeless encampment and while there were many wonderful birds and art pieces there I did not feel so safe arriving alone in the pre-dawn hours of the morning. [The encampment has since been removed and the city is working on what is being called "The Albany Bulb Transition" - you can read all about it here.]

I didn't have much luck over at Eastshore either. The habitat is brushy and low and the nets are just too exposed for any sensible bird to fly into. At the time of my attempts the weather was also incredibly temperamental and I got caught in the pouring rain. 

I did manage to catch two males there though before I got rained out: KRW/S and OS/GB. These two males ended up being quite special. Of all the birds I caught over this two-year study period (103 individuals) only 5 were infected with avian malaria. This is fantastic news for the birds, terrible news for my study. There is just no way to make any solid statistical conclusions with an infection rate of 4.9%. But these two wayward birds holding it down as some of the sole white-crowned sparrow residents of the East Bay were BOTH infected. That means they accounted for 40% of the infected birds in my study.

Don't Stop Believin'

A testament to the toughness of these Easterly birds. Not only are they in the minority and isolated from their fellow subspecies flock, they are also battling intracellular blood parasites that are reproducing and rupturing their red blood cells. But do you think all of that could keep them down? 

Not a chance. 

I just got this email and photo from birder John Kenny of OS/GB alive and well!

It thrills me to see him alive and I want to extend a thank you to him for harboring so resiliently the parasite DNA that served as many a positive control in so many otherwise frustrating lab studies where sample after sample turned up negative. 

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 ;)