Well, it’s been nearly 9 months since we returned from Russia. We ended our field season on a triumphant note: standing ankle-deep in the Sea of Japan, 5,600 miles from where we’d started in Moscow. We made it overland the whole way, caught more birds than we’d hoped for, ate more ramen noodles than any healthy person ever should, and met some fantastic people. When we reached Vladivostok we had a celebratory feast at a restaurant called Pyongyang, which was sponsored by the North Korean government, staffed by recent (young female) immigrants, and featured amazing food and karaoke. It may or may not also be involved in espionage and money laundering, but that’s neither here nor there.
We enjoyed two days of rest and some rainy sightseeing in Vladivostok before making our respective ways home: Matt straight back to Boulder for a conference; Georgy on a flight back to Krasnoyarsk, with his trusty car following a week later on a truck; and me back home via Moscow, where I spent a day at the Natural History Museum, checking out the collections for clues about what barn swallows look like in Mongolia and China.
So then what? What do scientists do when the fieldwork ends? The answer: we keep working. A lot. And it’s not very glamorous or photogenic.
So then what? What do scientists do when the fieldwork ends? The answer: we keep working. A lot. And it’s not very glamorous or photogenic.
We returned from Russia with tons of data: blood samples, feathers, data sheets, GPS points, and photos. Each of type of data contains bits of critical information that we piece together to learn about the evolutionary history of all those barn swallows we caught. But each type of data also requires a lot of processing before we can get to the good stuff.
First, data sheets need to be entered into the computer- we have one data sheet per bird, each of which contains information on the location of capture, the band number for that bird, whether it’s male or female, plus all the different measurements we collect on body size, feather lengths, and parasite counts. To make sure we don’t have any typos, data entry is a two-person job: one person reads out the data sheet while another types into Excel, and then the typist reads the entries back to check against the hard copy. It’s really boring, but needs to be done before we can analyze trait differences among different populations.
First, data sheets need to be entered into the computer- we have one data sheet per bird, each of which contains information on the location of capture, the band number for that bird, whether it’s male or female, plus all the different measurements we collect on body size, feather lengths, and parasite counts. To make sure we don’t have any typos, data entry is a two-person job: one person reads out the data sheet while another types into Excel, and then the typist reads the entries back to check against the hard copy. It’s really boring, but needs to be done before we can analyze trait differences among different populations.
Then there’s the feather samples. From each bird, we collect feathers from the throat, breast, belly, and vent. We use these feathers to analyze the color of different feather patches for each individual. Documenting color variation is really important in barn swallows, since the subspecies vary in color, and females of some subspecies use color in mate choice. However, we can’t just call birds “orangeish” or “whitish” - we need to quantify color in an objective way for it to be useful in analysis. We therefore use a spectrophotometer, which pulses a beam of light at a feather and then measures the reflectance curve that bounces back, providing a quantitative measure of color. To use the spectrophotometer, we first carefully tape the thousands of feathers we collect in the field on to index cards, and then measure reflectance of each feather five times. We take the average of those five measures as the color measure. This process is also very time consuming, and ever-less-enthusiastic undergraduates are still plugging away at taping and spec-ing the Russian feathers.
We also brought back hundreds of blood samples, which we use in genetic analyses. Eventually, these samples will be a treasure trove of information: they can tell us how long different subspecies have been separated from each other, if they still hybridize, whether differences between subspecies are due to adaptation, and even which parts of the genome are involved in that adaptation. However, before we can ask any of those interesting questions, we first have to get the DNA out of the cells.
This is done via a process called DNA extraction. We store the blood samples we collect in a preservative solution that preserves everything- red blood cells, white blood cells, water, salts, parasites, and all kinds of other junk. But for our analyses, all we want is the DNA- the raw genetic material- which is trapped inside the nucleus of the red blood cells. By adding different types of chemical reagents to our samples and then carefully warming them overnight, we can make the blood cells burst open to release the DNA. We then wash the samples several times using special solutions and filters and a centrifuge, which gets rid of everything except the DNA. It takes 4 or 5 hours over two days to process 24 samples, and in the end we have a little tube of clear liquid containing purified DNA.
This is done via a process called DNA extraction. We store the blood samples we collect in a preservative solution that preserves everything- red blood cells, white blood cells, water, salts, parasites, and all kinds of other junk. But for our analyses, all we want is the DNA- the raw genetic material- which is trapped inside the nucleus of the red blood cells. By adding different types of chemical reagents to our samples and then carefully warming them overnight, we can make the blood cells burst open to release the DNA. We then wash the samples several times using special solutions and filters and a centrifuge, which gets rid of everything except the DNA. It takes 4 or 5 hours over two days to process 24 samples, and in the end we have a little tube of clear liquid containing purified DNA.
But DNA extraction is only the first step for molecular analyses. For the genomics work that we do, we then have to chop the DNA from each bird into lots of little fragments; bind individual identifiers, or “bar codes”, to each of those fragments so we can keep track of them; and then replicate the fragments a bunch of times and clean out the bits we don’t want (i.e., bits that are too long or too short). Then we sequence the correct-sized fragments- this means we find out the order of base pairs (A’s, C’s, T’s, and G’s) for each piece of DNA. This process, called RAD (restriction-assisted digest) sequencing, is what allows us to examine genome-wide differences among birds from different. We use these short sequences of DNA from tens of thousands of different locations in the genome to identify differences between individuals, populations, and subspecies.
So, we’ve been doing all that for the last nine months. Plus, we’ve been writing a lot. I published several papers, Matt wrote (and defended!) his thesis and is now. Writing is pretty much the most important thing we do as scientists: there’s no point in collecting all these data if we don’t explain what they mean, and then publish papers in journals that the rest of the scientific community can read. Reading and writing papers is how we share our results, find out what questions are interesting, and move our fields forward.
So, we’ve been doing all that for the last nine months. Plus, we’ve been writing a lot. I published several papers, Matt wrote (and defended!) his thesis and is now. Writing is pretty much the most important thing we do as scientists: there’s no point in collecting all these data if we don’t explain what they mean, and then publish papers in journals that the rest of the scientific community can read. Reading and writing papers is how we share our results, find out what questions are interesting, and move our fields forward.
And last but not least, there’s my favorite use of non-fieldwork time: preparing for the next field season. I began planning for summer 2014 two weeks after returning from Russia. A lot of logistics go in to these field seasons: I need to identify where we need to go, find scientists in other countries willing to collaborate with us, figure out the specific locations where we’re most likely to catch birds, find out how long it will take to get the sample sizes we need, obtain permits, make a budget, order equipment…it takes a lot of time. But it’s fun, because once all those logistics are organized, I get to go explore a new place, meet new people, and learn new things.
And now, after 9 months, I’m ready to go again. We’ve got a serious itinerary this summer, perhaps even more ambitious than last year. I’m leaving tomorrow for China, where I, along with University of Colorado alum Caroline and Queen Mary University PhD student Liu Yu, will spend 7 weeks traveling all over the country looking for barn swallows. Caroline and I will then fly to Japan for 10 days to catch birds in Hokkaido and Tokyo. We’ll part ways in Sapporo, with Caroline flying to South Africa to start fieldwork for her graduate research- she begins a PhD the fall. I will head to Mongolia, where I’m meeting up with Georgy (of 2013 trans-Siberian road trip fame) to spend another month searching for barn swallow hybrid zones. The continuing crisis in Ukraine forced us to scrap a late-summer trip to Kamchatka, so we’ll be finished some time in mid to late July. It’s been a stressful few weeks of preparation and last minute planning, but now I’m packed, organized, and super excited. We’ll be blogging and posting photos again, so check back here regularly. This summer should be a pretty great adventure.
-Liz
And now, after 9 months, I’m ready to go again. We’ve got a serious itinerary this summer, perhaps even more ambitious than last year. I’m leaving tomorrow for China, where I, along with University of Colorado alum Caroline and Queen Mary University PhD student Liu Yu, will spend 7 weeks traveling all over the country looking for barn swallows. Caroline and I will then fly to Japan for 10 days to catch birds in Hokkaido and Tokyo. We’ll part ways in Sapporo, with Caroline flying to South Africa to start fieldwork for her graduate research- she begins a PhD the fall. I will head to Mongolia, where I’m meeting up with Georgy (of 2013 trans-Siberian road trip fame) to spend another month searching for barn swallow hybrid zones. The continuing crisis in Ukraine forced us to scrap a late-summer trip to Kamchatka, so we’ll be finished some time in mid to late July. It’s been a stressful few weeks of preparation and last minute planning, but now I’m packed, organized, and super excited. We’ll be blogging and posting photos again, so check back here regularly. This summer should be a pretty great adventure.
-Liz