Sabrina Taylor on unlocking messages in genes
Coyotes versus wolves: how do we know which animal dominated the southeast U.S. 1000 years ago? Historic DNA of course! Dr. Sabrina Taylor, Associate Professor from the School of Renewable Natural Resources shares how she uses historic DNA to unlock the mysteries surrounding century old changes in species population size, range, and disease susceptibility. Her lab not only answers these puzzling questions, but directly implements them into conservation management for endangered species. (Transcript below.)
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Transcript
Becky Carmichael
[0:00] This is Experimental, where we explore exciting research occurring at Louisiana State University and learn about the individuals posing the questions. What answers can be derived from 200-year-old Gopher Tortoise bones? Dr. Sabrina Taylor from the School of Renewable Natural Resources shares her lab's research examining the genetics of historic remains from threatened and endangered species to unlock the genetic changes populations in the past and connect those changes to present management needs.
Sabrina Taylor
[0:33] Over the past few hundred years, collectors have been depositing animal and plants specimens from thousands of species into museums all around the world. These specimens have traditionally been used to educate visitors and researchers about the organism's physical features and the ecosystem where it lives, but these specimens can share more. Did you know that today scientists are recovering DNA? The genetic code from these animals and plants or that scientists are recovering DNA from even older thousands year old samples on Earth are the archaeological sites. DNA analysis of this historic and ancient DNA can help us to understand changes in the genetic composition of organisms answer your questions about the evolutionary history of species and provides important information for management and protection of both species in their ecosystems. My lab at Louisiana State University studies the genetics of several threatened and endangered species. We use DNA from historic remains to find out how species have changed genetically over time, which can serve as important baseline information for management. Although I often focus on birds, DNA and genetic theory applies to all species. So along with my graduate students, I have the freedom to study other groups. A freedom I really appreciate because my interests are wide ranging. I'm currently using genetics to understand population changes when a species expands their habitat. One of my master's students is using historic DNA from Bachman's Sparrows to see whether their turn of the century range expansion from southeastern United States all the way north to Canada was responsible for the genetically uniform population we see today. A genetically uniform population is surprising to see because three subspecies were initially described on the basis of differences in feather color. If populations were historically structured it means that the birds were probably adapted to environmental differences across the range, adaptations that were probably lost from large scale changes and habitat. I'm also using genetics to understand disease susceptibility and threatened species. For instance, one of my PhD students is using 200 year old gopher tortoise bones to see whether immune genes have changed over time in areas where tortoises contract a sometimes fatal respiratory disease. DNA analysis can also help answer questions about the geographic range of a species. A former PhD student used thousand year old teeth samples from the southeastern US to figure out whether wolves or coyotes occupied the area in pre Columbian times. Finally, DNA analysis can tell us about population size, a key piece of information used in management and recovery plans. For example, one of my Master's students is using historic DNA to look at endangered small tooth sawfish. Sawfish have noses like hedge trimmers projecting out above their mouths, and these saws have been collected for a long time as trophies by fishermen. We can get DNA from the saws today and estimate how big the population size was in the past. This gives us an idea of how many fish we should aim to have to consider the population recovered. Sawfish are one of the only fish species with usable historic DNA because most fishes were preserved in formalin, which makes DNA recovery difficult if not impossible. So the sawfish study will provide us with information that's pretty unique in the fish world. Overall, historic DNA is giving us rare insight into the diversity, evolution, and connectivity of genes and populations, an opportunity that isn't available in many other fields. Those bygone museum collectors left a very important and unimagined legacy when they began to systematically deposit specimens into museums all of those years ago, one that we benefit from enormously today.
Mark DiTusa
[4:14] So I'm here with Dr. Sabrina Taylor. A professor here at LSU. Thank you very much for being with us.
Sabrina Taylor
[4:19] My pleasure. It's great to be here.
Mark DiTusa
[4:22] Okay, so tell us a little bit about your research here at LSU.
Sabrina Taylor
[4:25] I think of myself as a conservation geneticists, which means I'm very interested in the conservation of endangered and threatened species and how you can use genetics to do that.
Mark DiTusa
[4:35] Okay, so how exactly do you study that?
Sabrina Taylor
[4:40] Well, you need to get a DNA sample from whatever you're studying. So typically, that's blood in birds, or a fin clip from a fish, for example, if it's alive, or you can take a small tissue sample from mammals. Usually blood is the way we go. And with birds, you get a ton of data DNA from a very small blood sample. You know, like a drop, which is about 50 microliters. And so you can do a ton of different things with that blood once you have that sample.
Mark DiTusa
[5:11] So what interests you specifically about birds?
Sabrina Taylor
[5:13] Birds have a very long history. Ornithologists have been around for hundreds of years. So a lot of the very basic natural history has been figured out for the common species in North America and Europe, for example. Which means that you can ask more in-depth theoretical questions about evolutionary changes, conservation biology, how population sizes have changed over time, ecological questions, whereas newer fields, like some of the amphibians and reptiles, for instance, there isn't that baseline natural history that's as available as it is for birds.
Mark DiTusa
[5:50] Okay, so give me an example of some of the research that you're doing right now or just finished?
Sabrina Taylor
[5:56] Well, I've got one PhD student who's looking at Gopher Tortoises. He's looking at the relationship between genetic variation and disease susceptibility. I have a second PhD student who's actually looking at the effects of the oil spill on marsh rice routes. So she's looking at a gene that begins to express messenger RNA and protein when it's exposed to polycyclic aromatic hydrocarbons, which is one of the toxic components in oil. So when rat, it you know, experiences exposure to PAHs, that gene starts working and making copies, basically to help metabolize those PAHs and get them out of the body. So you can look at oil than no other sites and look at these differences in gene expression. And I have another student who's also working on the oil spill. She's a master student who's looking at diet in birds. So some of the volatiles in oil are naphthalenes which is basically what's in mothballs, right. So when you have high temperatures and low tides, you can get a lot of naphthalenes volatilizing, which, you know, might knock off quite a few insects in the area. And so you might expect to see a change in diet at higher trophic levels, like the sparrows because they're having to hunt for and eat different kinds of prey. So she'll look at fecal samples from birds on oil then on oil sites. And you can extract the DNA from the fecal samples, and then match those sequences up to a big repository, called Genbank, and see what species are there, which can be a little bit easier than trying to identify all of those insect parts which have gone through the digestive track.
Mark DiTusa
[7:39] Yeah, that does sound like it'd be a little bit easier to do, hopefully. So how did you get into this? So like, it's all well and good that you have gotten to this point, and you're doing some amazing research on all different kinds of animals, but how did you even make the first step towards doing that?
Sabrina Taylor
[7:57] Well, I always wanted to be a biologist. I would say my biggest struggle was deciding what type of biologists because insects, plants, animals, you know, they all really interest me. And at least doing genetic research, you have a little more flexibility to look at lots of different groups, because most organisms have DNA, right. But I would say in terms of genetics, what happened was that I was doing my Masters on Humboldt Penguins in Peru, and we were using radio tags to see where they were and time depth recorders to see when and how deep the penguins were diving so we could look at foraging behavior. And when I finished that project, I kind of felt like this is a project that anybody could have done. It didn't require any special skill set particularly. So when I went on to do a PhD, I wanted to acquire a skill that you know, you can bring to the table when you're collaborating with other scientists. And I was kind of hesitating between GIS based studies, you know, which use Geographical Information Systems and GPS data in order to look at, for example, how animals are using habitats or going into genetics. And there's just so many other questions that you can ask with genetics in terms of how birds are behaving, how things have changed over time. You can look at some of those interesting evolutionary questions. And so that's really what drove me to pick genetics for PhD.
Mark DiTusa
[9:25] Hmm... And how long have the tools been available to study genes in the way you've been able to?
Sabrina Taylor
[9:33] Oh, pretty recently. I would say, you know, it was in the 1960s that people started looking at chromosomes, you know?
Mark DiTusa
[9:43] Right.
Sabrina Taylor
[9:43] And then later in the 1980s, people started looking at mitochondrial DNA, which is a small organelle outside of the nucleus. And there's a lot more copies of mitochondrial DNA than nuclear DNA. And then with the invention of a process called Polymerase Chain Reaction, where you're basically making lots and lots of copies of DNA, you can start to examine other parts of the genome. Well, actually... Let's cancel that. You need that for mitochondrial DNA too so that's not quite right. But basically, people started looking at chromosomes first, mitochondrial DNA in the 1960s, and then later in the 1980s they started looking more at nuclear genes. And it's really only been, I'd say, in the past 5-10 years when people have been looking at genomes, you know, they've had that kind of sequencing capacity become available.
Mark DiTusa
[10:38] So you said that you already knew you wanted to be a biologist? How early did you kind of like figure that out? And just again, what kind of brought you to that decision?
Sabrina Taylor
[10:50] I'd say it's because my dad used to take me and my three brothers out camping and hiking all the time when we were little, you know? I can remember being pretty young, probably eight or nine, and flipping through National Geographic and seeing people off on all these amazing, you know, adventures and thinking... Oh, well, if there are people out there getting paid to do this there must be a way to get a job in that kind of area. Yeah.
Mark DiTusa
[11:18] I mean, getting paid to... I mean, do you do field work?
Sabrina Taylor
[11:21] I do. Not as much as I used to. But when I was a master's student and a PhD student, and also in between my degrees, I spent probably most of the year out in the field.
Mark DiTusa
[11:31] Wow.
Sabrina Taylor
[11:32] Now the only time I go out in the field is to see what my graduate students are up to. And I also have a little side project in New Zealand on Fern Birds. So I go to New Zealand every year for a month and a half or so and collect blood samples from Fern Birds.
Mark DiTusa
[11:49] Wow. I mean, I brought this up with my interview with Dr. Chakrabarty, which may or may not be out at this point, so either look forward to it or go back and listen to it. Either way. He does a lot of fieldwork when he's studying his fishes. And I just find it interesting as a physicist, like, I don't do field work while I'm at work. I do a lot of wrench torquing in making instruments in the lab. And that's interesting, but it's not as... I don't know. A lot of people seem very inspired by kind of being able to go out into nature and do their field work and kind of explore things that have not been explored as much. And I guess that's kind of the... For a lot of biologists, that's really the Siren call of biology. I find that really interesting. Because, you know, whenever I was kind of picking a discipline between physics and chemistry like that, that was just never something I considered. So and you know... For people who don't necessarily want to be shut ins, but also want to be a scientist, congratulations! There's an option! So kind of... This is a difficult question, but what has been your best mistake? This could be something in research. This could be something in childhood, for whatever reason. You know just what do you think has been your best mistake?
Sabrina Taylor
[13:01] I would say it's been more of what was the little side project you tried that you didn't think was going to be a major part of a research question that eventually turns into it. So during my PhD, my original project was actually to look at the genetic characteristics of Saddlebacks, which is a species of bird in New Zealand. So the genetic characteristics of these birds that make them more successful in the reintroduction programs. So in New Zealand, there's a lot of introduced mammals that aren't native. In fact, New Zealand has no native mammals, except for bats and seals. So when things like weasels and rats and mice were introduced, the native species just had no way to cope with them and it caused many extinctions. And so what the New Zealanders do started to do was to find islands, clear them of introduced species like weasel, rats, and mice, and then move endangered species on to those islands where those populations could grow without being, you know, totally extirpated by predation, basically. So there was a translocation occurring for Saddlebacks, and I was taking genetic samples of the birds that were to be moved. And then I was following those birds around to see which ones survived, which ones had more nests, which ones had more chicks, to see whether there were particular genetic characteristics that were associated with success. And in fact, that translation didn't go particularly well because all the birds died. It looked actually to me like New Zealand Falcons were taking them out.
Mark DiTusa
[14:45] Oh, wow.
Sabrina Taylor
[14:46] Yeah, and there weren't that many birds there. But in the meantime, I'd also been talking to somebody about using museum DNA to look at genetic variation in the past. I was really excited about this possibility, but very nervous that it wouldn't work. But I decided to try it just as, you know, a little side project. And in fact, that turned out to be the major focus of my thesis. And probably where my best papers came from. It was very interesting because those museum samples were available because New Zealand has unique fauna. Those museum collectors in the 1800s were basically traveling around the world, collecting unique plants and, you know, mammals and birds and then selling them to big museums in Europe. So you could be a professional collector. And because New Zealand has such a distinct fauna that's found nowhere else in the world, these collectors would go down and collect samples. So SaddleBacks, which formally ranged all across the South Island of New Zealand, went extinct in the late 1800s on the mainland, and they were relegated to just one island in the south called Big South Cape Island. But that island is traditionally used by the (inaudible) to harvest shearwaters, or mutton birds as they're called. So rats, unfortunately, came along on one of these trips to the island, and basically just decimated the birds there. So someone from the New Zealand Department of Wildlife, I think it was called at the time. It's now the Department of Conservation. They took 15 birds to (inaudible) Island and 21 birds to Big Island, and that basically saved the species because all the birds on Big South Cape after that went extinct. And those populations grew and then they'd catch birds and transfer them to other islands and allow those populations to grow, and so on. So that species is now secure with about 2000 birds or so and birds on probably around 20 Islands now, but collectors had been there all along the way. So there were those museum specimens from the mainland, and there were museum specimens from Big South Cape Island before the rats arrived. So you could look into how genetic variation changed over time, right. And it turns out that the South Island of New Zealand had a massive amount of genetic variation. And when birds were relegated to Big South cape Island, they lost about 75% of their genetic diversity. On the other hand, that big bottleneck caused by the invasion of rats onto big South cape didn't have a large effect on genetic variation because it was already so low. And they managed to capture enough birds and translocate them to safe havens that enough variation was left. So you can kind of track that process over time.
Mark DiTusa
[17:39] Wow. That's really cool. Yeah. So if somebody wanted to get into biology... Like, I mean, whether they're, you know, maybe they're in middle school, and just kind of excited to hear this, that you can study animals or fauna, or even just anything alive this way. How would you suggest they go about becoming a biologist and getting excited about that?
Sabrina Taylor
[18:02] I would just get involved. You know, there are naturalist groups in Louisiana and and in Baton Rouge. There's the Bluebonnet Nature Center. There's people who are out catching and banding birds every other weekend, you know, and you might be able to help with that if you're interested in doing that. They often take volunteers. There's tons of research projects that particularly high school students can do with university professors, you know, for science fairs and things like that. So if you have a real interest, hunt around on the web, and see who has a similar interest to you, and see if he can maybe team up somehow on a science fair project or on some sort of research project. But I would, you know, I would really recommend that you are engaged, you know. Like you take the project by the horns, because it's your baby and run with it. Don't rely on other people to do that for you, because that's what in particular a university professor would be looking for.
Mark DiTusa
[19:03] Yeah, it's funny because I never really saw science fairs as a kind of way to or an excuse to get involved in actual science. It's just never occurred to me and really a lot of, especially LSU professors, love getting involved in science fair and helping students out. And so I'm hoping that it helps inspire people and get them, even for science fair, kind of thinking about different things they can do. So that's fantastic. Well, thank you very much for coming on the program, Dr. Taylor.
Sabrina Taylor
[19:33] Thanks very much for inviting me.
Mark DiTusa
[19:35] Of course.
Experimental Podcast
[19:36] Experimental was recorded and produced in the KLSU Studios here on the campus of Louisiana State University and is supported by LSU's Communication Across the Curriculum and the College of Science. Today's interview was conducted by Mark DiTusa and edited by Bailey Wilder. To learn more about today's episode, subscribe to the podcast, ask questions and recommend future investigators, visit cxc.lsu.edu/experimental