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. 

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!

Avian Malaria (& Relatives) Workshop - Part 3 - Indentifying Blood Parasites

This post brings me to my third and concluding update on the Third Annual International Workshop on Malaria and Related Haemosporidian Parasites of Wildlife (whew - that title is epic!) [Here's Part 1 and Part 2]

The first two days of the four day workshop focused on blood smears and identifying parasites by their physical characteristics. The second two days focused on vectors and genetic techniques.

Vectors

Malaria, as we all know, is a vector-borne disease transmitted by mosquitoes. Insect vectors are the sites of sexual reproduction for haemosporidian parasites; without these vectors the parasites would not be able to complete their life cycle.

Therefore, as avian parasitologists, it is important for us to know how to identify vectors that could potentially spreading infectious agents to our birds. It's not just mosquitoes we need to be concerned about either. Each of the three parasite genera, Plasmodium, Haemoproteus, and Leucocytozoon, are transmitted by different types of insects.

The following vector images are from Avian Malaria Parasites and Other Haemosporidia by Gediminas Valkiūnas. 

Plasmodium is transmitted by mosquitoes:

Haemoproteus is transmitted by biting midges and hippoboscid flies:

And Leucocytozoon is transmitted by black flies:

Each vector has its own unique set of habitat requirements. Combined with the habitat requirements of the bird hosts and the parasites, understanding these insect-vectored diseases quickly becomes quite complex.

For the purposes of this workshop we focused on mosquito vectors. We learned how to trap, identify, and dissect mosquitoes. This last skill in particular was difficult to master. Mosquitoes seem pretty big when you're swatting them on your arm but when you're actually trying to keep parts of them intact as you sever them with a small knife, believe me they seem very small.

Mosquito Traps

Photo by Francisco Ferreira

This trap is called a gravid trap. It attracts gravid ("pregnant") female mosquitoes looking for somewhere to lay their eggs. In the bottom bucket there is a putrid liquid called (very technically) "smelly water" - a lovely mixture of cow feces, water, and yeast left to rot in the hot sun for a couple of months. The vertical contraption contains a fan at the top to suck up female mosquitoes as they come to lay their eggs.

Ellen Martinsen explaining the inner mechanism of the gravid trap - Photo by Francisco Ferreira

Photo by Francisco Ferreira

This trap is a CDC Light Trap. Developed by the Centers for Disease Control, this trap uses both carbon dioxide and light to attract in mosquitoes. You may know this already but it is only female mosquitoes that bite you. Ingeniously but frustratingly, females use your exhaled breath (CO2, carbon dioxide) to find you. This trap works in much the same way - in the dark thermos there is dry ice that sublimates to release CO2 gas. Mosquitoes fly towards it and are sucked into the mesh bag by a fan at the top of the trap. Unlike the gravid trap the CDC light trap is also equipped with a flashing light that draws in both males and females. 

Identification and Dissection

One thing that is important to note at this stage is the importance of keeping your mosquito alive prior to dissection. A dead mosquito is a squishy mosquito and impossible to dissect properly. For this reason the traps are set out at night and checked the following day. Any trapped mosquitoes are brought back to the lab and kept alive in a mini habitat, such as this bug tent:

Just like parasite identification, mosquito ID was difficult at first but once we knew what to look for it became much easier. We used various physical characteristics including wings and palps to tell species apart:

From our Malaria Workshop handout materials (unknown source beyond that)

Once we knew our species and whether it was a male or a female (no use dissecting the males - they don't bite birds and therefore wont carry parasites), we moved on to dissection. We targeted both the salivary glands and the midgut of our insect vectors.

Presence of parasites in the salivary glands indicates the mosquito is a suitable vector - when mosquitoes bite they also inject an anticoagulant to keep the blood flowing. Parasites in the salivary glands will be injected into the host along with the anticoagulant. 

The midgut is the site of parasite reproduction. The "male" and "female" gametes fuse to form a zygote, which then implants in the gut lining of the mosquito and proceeds to divide and divide and divide. Eventually these divisions burst out and make their way to the salivary glands.

Carter Atkinson demonstrates mosquito dissection.

Below is a video from the 1980's that we watched in the workshop. Despite its age, it is an incredibly helpful video to reference technique.

I really cannot reiterate this enough - mosquitoes are small. It was absolutely essential to use a dissecting microscope just to see what we were doing. These were the tiny tools we used:

Initially we chopped off a lot of mosquito heads and lost the glands and guts into a boogery mess of mashed mosquito. But with some fine tuning of our large (comparatively) human hands, we were eventually able to isolate our organs of interest. 

Genetic Techniques

The last half of the last day focused on the use of genetics to determine the species and lineage of parasite as well as their phylogenetic relationships. We looked at several genetic sequences and became familiar with a couple different computer programs used to manipulate this kind of data. 

This picture is a little difficult to see but this is what a genetic sequence looks like read out on a computer screen. Peaks of different colors correspond to specific nucleotide bases - A, G, T, or C. Mutations unique to different parasites help to determine the specific infection present in a bird. These can then be pooled to create a phylogenetic tree, which helps to visualize relationships and evolutionary patterns. 

Saying Goodbye

It was so tough to say goodbye to everybody the last day. An early morning shuttle sent some students to bed early but not before a final round of "selfies" from the 2014 Malaria RCN Student Cohort:

Photos by Adam Krupski

Thank you to the Malaria RCN for this amazing opportunity. I am so grateful to have participated in this workshop and meet all these amazing biologists from around the world! 

Avian Malaria (& Relatives) Workshop - Part 2 - Indentifying Blood Parasites

Here I am one year into my Master's program at San Francisco State University. Time has flown by so fast it's hard to believe a whole year has gone by already. But at the same time when I look at where I was at this time in 2013 I realize how much my skills and experience have progressed.

One year ago I didn't know how to handle a bird or set up a mist net - now I can handle and take a blood sample from a bird. I have a formal training course under my belt and work at a bird banding station.

One year ago I didn't have a single wildlife permit - now I have three (and IACUC approval from my school.)

One year ago I barely knew how to run a gel or do nested PCR or sequence a DNA segment - now these are integral pieces of my research project.

And one year ago I didn't know a thing about avian blood parasites. Now it's the focus of my project and I've participated in the International Workshop on Malaria and Related Haemosporidian Parasites of Wildlife.

Meet this year's "Haemosporidian Workshop" participants! pic.twitter.com/ui2YKOn5Nk

— Malaria RCN (@MalariaRCN) August 1, 2014

In a graduate program you pick up a lot of your knowledge and tips from your advisor and fellow lab mates. That being said, nothing beats an intensive, concentrated training experience. That's what the Malaria Workshop was - after four packed days of content, I felt that my knowledge about blood parasites had taken a giant leap forward. I even gained skills that I never dreamed I would have... believe it or not, I can now dissect out the salivary glands of a mosquito.

Blood Sampling and Parasite ID

The first two days of the workshop emphasized identifying parasites in blood smears under a microscope. In a past post about Avian Malaria I went into a little detail about the causative agent of malaria, Plasmodium (different species within this genus cause malaria in humans, birds, reptiles, etc.) In addition to Plasmodium there are two other genera of blood parasites within the order Haemosporidia we are concerned with: Haemoproteus and Leucocytozoon.

These three genera each have unique methods of reproduction and are spread by different insect vectors. Once you know what you're looking for, they're quite easy to tell apart under a microscope. Here's what the first two days of the workshop looked like:

First we caught some local birds:

Gray Catbird - Photo by Elin Videvall

And took some blood samples:

Strahil taking a blood sample from the brachial vein of a flycatcher - Photo by Strahil Peev

And made some blood smears - sometimes using the "Polaroid method":

Dovile blotting and drying a smear

But preferably with a fan:

Gediminas Valkiūnas fan drying blood smears - It is important to dry the slides right away because soon as they are exposed to air the parasites begin to change form. Fan drying suspends that transformation and preserves their current form.

Then we fixed the slides in methanol: 

Photo by Elin Videvall

Then we stained the slides with Giemsa stain: 

This process stains the cells purple - the nuclei (bird red blood cells have nuclei) and parasites are stained dark purple while the cytoplasm stays clear - Photo by Elin Videvall

Then we looked under our microscopes!:

Photo by Elin Videvall

We did this for several afternoons, looking at both our local bird slides and some "known positive" slides to practice our parasite ID. Our course instructors were very helpful when we inevitably got stuck:

Photo by Elin Videvall

This is what we saw:

Most of what you see here are avian red blood cells, which are nucleated. Right at the tip of the pointer is a Haemoproteus parasite. There are many many species of Haemoproteus that infect birds but they can be differentiated if you know what to look for. 

We would look for defining morphological characteristics such as:

• Location of the pigment granules (in this picture the small dark dots scattered throughout the cell)
• Location of the parasite nucleus (light pink spot in the top right corner)
• How much of the host cell the parasite takes up and what membranes it touches (in this case the whole cell and both the nucleus and outer cell membrane - this isn't always the case!)
• General size and shape 
• And more

Gediminas Valkiūnas' book has a very helpful key - we used it (as well as his direct instruction) extensively:

And this is Leucocytozoon:

Leucocytozoon parasites are much larger than the other two genera. They're the Jabba the Hutt of the parasite world:

To the untrained eye (us before this workshop) Leucocytozoon looks suspiciously like white blood cells so we had a special lecture on that as well:

Interspersed with all these parasites we also each gave a 5 minute presentation of our research projects. It was so interesting to see the different pieces of the blood parasite world that people had carved out internationally. 

Paulo gives his 5 minute presentation - Photo by Strahil Peev

And this was just the first two days! Stay tuned for the third and final installment - Vectors and Summary

The Third Annual International Workshop on Malaria and Related Haemosporidian Parasites of Wildlife - Part 1 - Facilities

This year I've have two different but equally amazing training opportunities. The first, for the bird banding portion of my master's research, you can read about in Braddock Bay Bird Observatory Spring 2014 Bander Training.

The second, for the blood parasite portion, was a workshop organized and funded by the Malaria RCN, a collaborative network of researchers around the world all working on haemosporidian blood parasites of wildlife. This July was their annual International Workshop on Malaria and Related Haemosporidian Parasites of Wildlife.

Participants in this workshop hailed from all different parts of the world. Represented countries included Lithuania, Mexico, Brazil, Sweden, Australia, India, Bulgaria, Poland, Spain, Colombia, and all corners of the United States.

I broke this update into a couple different entries because it was such a fantastic experience and the content so rich that it deserves an extended post. Between all the people I had the wonderful opportunity to meet and the beautiful campus it was hosted at, it has been a major highlight of my graduate experience so far.

The first installment will cover the gorgeous grounds and facilities. Picture heavy!

The workshop was hosted at the U.S. Fish and Wildlife Service's National Conservation Training Center (NCTC) in Shepherstown, West Virginia. The NCTC is a network of facilities located on a 533 acre property along the Potomac River.

The grounds of the campus were beautiful. Full of wildlife and so green. Coming from California, a state in a severe drought, the green was especially noticeable.  

Some wildlife more intimidating than others. Note the pencil for scale.

The facilities themselves were also beautiful. I stayed in the Rachel Carson Lodge, where every room had a copy of Silent Spring, a seminal book in the environmental conservation movement. 

The Rachel Carson Lodge.

The view surrounding the Rachel Carson Lodge - the green!

Another building we spent a lot of time in was the Commons, where all our meals were held and the location of a beer and wine bar where we would hang out after "class."

The food was another highlight of the accommodations. Each day for both lunch and dinner the entree selection would change; at the deli you could build any desired sandwich; at the grill you could order anything from a grilled cheese to a bison burger; the salad bar was stocked with fresh veggies; and the dessert station served frozen yogurt and a rotating selection of cakes and pies. I have to say as a graduate student living in the pricey Bay Area (ie having very little money) this was a really nice break from ramen noodles and peanut butter.

Stay tuned for Part 2 - Blood Parasite Identification.