Thesis Defense!

The day is finally here. After two years of learning and data gathering and statistical analyses and writing and BIRDS - so so many BIRDS 😁 - I am finally ready to defend my thesis.

If you happen to find yourself by the San Francisco State University campus on Tuesday December 8 at 2:10pm, stop on by!

The project has morphed over time to be not quite the thesis I had originally intended but that is the beauty of science. Today I gave a practice talk for my advisor and lab mates and they helped me find my story amidst all the things I want to share. You know that phrase, "can't see the forest through the trees"? That's how it was feeling prior to this morning. It was the first time I had stepped back and looked at the project as a whole.

I feel so grateful at this moment to everyone who has helped me along the way. Financially, emotionally, gastronomically, and beyond. I will not name everyone's name here but please know you are thanked a million times over.

By my next post I'll be Dena Emmerson, M.S.

?????

What is this weird bird doing????

He trills first AND has a blender ball buzz in his trill AND has a complex note after the trill. Very very bizarre...

This is a San Francisco State bird: "S6" or "GO/OS'
He is an older bird, which surprises me because it is often the younger birds that will test out different forms before settling or crystalizing their song. This guy is just weird.

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 ;)

Checking in on Lake Merced

This Thursday Pete and Linda (awesome birders and extraordinary banding assistants) and I went out birding at Lake Merced. Amongst the diverse avifauna we spotted the familiar faces, or legs rather, of our color-banded Nuttall's white-crowned sparrows.

It was much quieter with the passing of the breeding season but I was surprised to still hear some songs here and there from the local males. The songs were, however, noticeably shorter and often lacking the trill. I didn't get a good look at the singers but it's quite possible there were some hatch-year males testing out their vocal abilities for the first time. 

In total we were able to identify 10 different banded individuals. That's not to say there aren't more out there - we birded only a small segment of the lake! The breeding territories have all broken down and most of the white-crowns were spotted grouped together in foraging flocks. Below are some photos Pete was able to snap of some of the color bands:

I love this action shot:

This young bird puzzled us a little because of its plumage - it looks like it just fledged from the nest. Most of the hatch-years we saw had the same characteristic brown-and-tan crown but had gone through a molt to grow in smoother feathers. This guy/gal still has the characteristic "fluff" of a bird fresh out of the nest, which is odd given how late it is in the year.

Some other feathered friends spotted in the morning: 

 

Clark's Grebe

Fox Sparrow

Townsend's Warbler

The rest of Pete's photos from the morning can be found at his Flickr account!

And then happiness of seeing the banded white-crowns foraging about was topped off by this unexpected graduation present from Pete and Linda: 

A toast to the birds!

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!

Audio Analysis Phase!

Had to toggle over to Blogger as I'm here in the lab analyzing these bird songs to share a weird looking sonogram:

Check out that weird buzzy ball in the middle of the trill! I like to call it the "Blender Bottle" note.

Here's what the above sonogram sounds like - you can hear the "Blender Ball" buzz in the middle of the trill:

This is from "SFSU 6" aka "GO/OS" aka this guy:

American Society of Parasitologists

Hello from Omaha, NE!

From June 25-28, 2015 I attended the annual meeting of the American Society of Parasitologists. In February I presented at the regional branch of this society, the North American Society of Parasitologists and was awarded a travel grant to attend the national meeting.

The conference was a great opportunity to meet colleagues in the same field and even catch up with some old friends! Woody and Jeff, fellow participants from the Avian Malaria Workshop, were also in attendance. Below is a photo of just some of the winners from around the United States who were able to attend this year's meeting thanks to a travel grant:

Outside of the conference I explored downtown Omaha, did some Couchsurfing, and checked out the city's burgeoning craft beer scene. I had a great time adventuring around the Heartland!:

I've been horribly slacking in this blog but I'm back in the lab after some vacation time and have set up a regular update schedule now so get ready for hot-off-the-presses (thermalcycler) results!

Sharing the Science!

An important part of being a scientist is disseminating your results. This happens through a variety of outlets including scientific publications, presenting at conferences, and popular science articles, among others.

While my research is still in progress I do have some preliminary results from the birds I caught and recorded in 2014. So far this year I've presented at three different conferences. These are great opportunities to not only share results but also to meet scientists - both professionals and students - in different disciplines.

Northern California Parasitologists Winter Meeting - February 2015

Depending on how you look at it my project can fall into many different categories - ornithology, conservation, bioacoustics, ecology, and in this case, parasitology. Calvin Lee (pictured at the left) and I also both won student awards! As part of this award I also won travel funds to attend the annual meeting of the American Society of Parasitologists, which will be in Nebraska this June.

San Francisco State University Graduate Student Showcase - April 2015

This showcase was an opportunity for graduate students to share the research they've been conducting with the San Francisco State community. We filled the whole gym! Immediately following the showcase there was a dinner and raffle where I luckily came away with two gift cards to Burgermeister!

16th Bay Area Conservation Biology Symposium - May 2015

This conference was a quick one-day symposium but provided the opportunity for those of us who are researching and interested in conservation biology to share are work and meet each other. I presented in the Organismal Ecology & Conservation Section along with Silas, a fellow grad student from SFSU. 

Upcoming Conferences

American Society of Parasitologists - June 2015 - Omaha, NE

This is the annual meeting of the national society and the conference I won travel funds to at the Northern California Society meeting. I've never been to Omaha so decided to travel via CouchSurfing to get a local introduction to the city.

American Ornithologists Union/Cooper Ornithological Society - July 2015 - Norman, OK

I've applied for a travel grant to present at and attend this conference so it's still a pending option but this is the BIG bird conference of the year. It's filled with all sorts of exciting ornithological talks and birding field trips!

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: