Season 2 |
Episode S2E8: Integrating Genetics and Anthropology with Dr. Anne Stone
[00:00:00] RORI: Welcome to Science-Wise, a podcast where we talk to scientists with years of experience to learn from their wisdom,
[00:00:06] EMILIA: who are not only very experienced, but also really inspiring scientists.
[00:00:11] RORI: I'm Rori Rohlfs, an associate professor in data Science at the University of Oregon.
[00:00:14] EMILIA: And I'm Emilia-Huerta Sanchez, an associate professor at Brown. Our guest today is Dr. Anne Stone. A Regents professor and associate director of the Center for Evolution and Medicine at Arizona State University. Both Rory and I first became acquainted with Dr. Anne Stone's work when we read her papers as graduate students and postdocs at journal clubs. We later had the privilege of attending her lectures at conferences organized by one of our scientific societies, the Society for Molecular Biology and Evolution.
Dr. Ann Stone received her PhD in anthropology at Penn State, followed by a postdoc at University of Arizona, and she went on to University of New Mexico to start her first faculty position and later moving to Arizona State University where she is now. Dr. Stone's work has contributed to our understanding of how humans.
And infectious diseases have evolved over time. Her work is highly recognized in the field, and she has received many awards and honors. For example, she has been a Fulbright fellow, a Catholic scholar, and she received a Guggenheim Foundation Fellowship In 2011, in 2016, she was selected as a member of the National Academy of Sciences, which is one of the biggest honors for a scientist. Her lab is constantly making new biological discoveries that continue to inspire my own work and others in the field. It is my absolute pleasure to have her here today as one of our guests,
[00:01:48] RORI: Dr. Ann Stone, welcome to Science-Wise. Thank you so much for sitting with us, courtesy of our amazing producer, Marita Smith here in person in Phoenix. Your AM ACE paper is something that I presented at Journal Club back when I was a PhD student, and I was like, this is the coolest thing I have ever read. I was so amped about it.
[00:02:09] ANNE: Thank you so much.
[00:02:10] RORI: Well, maybe we'll start by talking about your life a long time ago. Like your kid hood. Can you tell us about your family?
[00:02:17] ANNE: Sure. I grew up in Tennessee, in South Carolina. Oh. And I was a grad school baby, actually. Okay. My dad ended up being a professor at the University of Tennessee, Martin.
[00:02:25] It was a small school actually, while he was still finishing his PhD in chemistry. And you know, Martin Tennessee was a small town and we lived on the edge of a big forest, and so we ran all over the place
[00:02:38] RORI: having like you played in the forest a lot.
[00:02:40] ANNE: Oh yeah, I had a really nice childhood. I was always a big reader involved in scouts, involved in a lot of various art projects.
[00:02:48] My mom was an artisan, a craftsperson.
[00:02:51] RORI: What kind of crafts did she do?
[00:02:52] ANNE: She did kind of a traditional cone craft. Oh. Making wreaths and candle rings and ornaments and things like that. So we went to a lot of craft fairs when I was a kid. Okay. So it was a good kid hood.
[00:03:04] RORI: And then your dad, he was a university professor.
[00:03:08] ANNE: So he finished his dissertation and when I was five years old, he did a postdoc at the University of Zurich in Switzerland.
[00:03:15] RORI: Oh wow.
[00:03:16] ANNE: And so I actually went to kindergarten in Switzerland, which was a great experience.
[00:03:20] EMILIA: Do you have memories of that?
[00:03:21] ANNE: I definitely have memories of that. Some of them are quite funny because now when I go back to Zurich, I recognize things that I realized were very important to a 6-year-old.
[00:03:31] RORI: What was, what mattered to you then?
[00:03:33] ANNE: You know, you'll turn a corner in the old. Part of the city and see a really cool fountain or playground and I'll be like, oh yeah, I remember that. Or the chocolate shop.
[00:03:44] RORI: Yeah. Playgrounds and chocolate shops.
[00:03:45] ANNE: Right. And then I just sort of chuckle 'cause I'm like, oh right. 6-year-old me.
[00:03:49] EMILIA: So how long did you stay there?
[00:03:51] ANNE: A year. Just a year.
[00:03:52] EMILIA: Did you learn some German?
[00:03:53] ANNE: Yeah, actually I became fluent in Swiss German.
[00:03:56] EMILIA: Oh
[00:03:56] ANNE: Wow. I've unfortunately forgotten a lot of, but it turned out to be helpful in grad school when I did a Fulbright in Germany. So some of it kind of came back
[00:04:06] RORI: and you grew up with like understanding how kind of the academy works, how.
[00:04:11] Academic life is, did you picture yourself in that life when you were young?
[00:04:14] ANNE: I think I sort of did.
[00:04:15] RORI: Okay.
[00:04:15] ANNE: Actually, I was a big mystery reader and I loved trying to figure things out and you know, I think that sort of drew me to research. Well, for a while I wanted to be an astronomer. I actually started to make my own telescope lens.
[00:04:29] RORI: Whoa. That's hardcore.
[00:04:31] ANNE: Yeah.
[00:04:32] EMILIA: How old were you?
[00:04:32] ANNE: Was probably when I was in about fifth or sixth grade. Wow. You know, so I got it as a Christmas present, one of those kits where you uhhuh, polish. And then I sort of slid toward biology more and became interested in that. My mom actually had a master's degree in Botany.
[00:04:47] RORI: Oh wow.
[00:04:48] ANNE: So I also grew up. Helping her collect nuts and cones and all these things.
[00:04:53] RORI: When you say cone crafts, you're talking about like, you're like taking pine cones and making beautiful things outta pine cones.
[00:04:58] ANNE: Right.
[00:04:58] RORI: But your mom did this with a botanist perspective.
[00:05:01] ANNE: Yeah. So she had taken a course in Western North Carolina where my grandparents lived.
At one of the community colleges that's actually really well known for its craft and had gotten into it and I think saw it as a way that she could stay home with us, but also, you know, in a small town, kind of the options were perhaps a little more limited, but she could basically work from home. These were the days before Etsy.
So, um, instead we do sort of craft fairs on the weekends and later. In life. She actually was part of the Highland Guild of Craftspeople in Western North Carolina.
[00:05:40] RORI: Mm-hmm.
[00:05:41] ANNE: So I actually learned a lot of botany on the side
[00:05:45] RORI: because you would go with her to collect these,
[00:05:46] ANNE: would go with her to collect uhhuh.
I think sometimes she would pay us like 5 cents a. Cup full or something. Wow. Okay. So there were some incentives there.
[00:05:55] RORI: Uhhuh Uhhuh motivation.
[00:05:57] EMILIA: So when you became interested in biology, was that like in middle school or in high school? I
[00:06:01] ANNE: I think it was toward high school that I kind of got interested in biology.
[00:06:04] EMILIA: And was it your decision or did somebody influence you?
[00:06:08] ANNE: By then? We had moved to South Carolina. Mm-hmm. Uh, because my dad
did a two year stint at NSF and then he joined Clemson.
[00:06:15] EMILIA: So after Zurich, he came back to, he went back to Tennessee. Okay.
[00:06:19] ANNE: And we were there for several years. And then middle school was in Maryland and then high school in South Carolina.
I would say that I became interested in biology maybe despite my bi high school biology teacher. Okay.
[00:06:32] EMILIA: What was that like? He was the soccer coach. Oh. And he was mostly interested in soccer.
[00:06:38] RORI: I see. Okay.
[00:06:39] ANNE: And it was also South Carolina in the eighties, and we completely skipped the evolution chapter,
[00:06:44] EMILIA: which is the best part.
[00:06:45] ANNE: Right. So of course, if people are gonna say, oh, we're not gonna read something, I'm like, well, I'm gonna read that. Oh, right. It's like the whole band book thing. Yeah. You know, Uhhuh. Is this band,
[00:06:55] RORI: Why is this band right?
[00:06:57] ANNE: Of course I read it and uh, I became interested in that and I think like most biology majors, at some point I was like, well, maybe I could be a doctor, but, and I went to college at the University of Virginia and while there I ended up majoring in biology and I double majored.
Actually, I had a. Interdisciplinary major in archeology as well, because I took a human Origins class and thought that was really interesting.
[00:07:20] RORI: Mm-hmm.
[00:07:20] ANNE: They didn't actually have biological anthropology, so Oh, okay. I kind of ended up cobbling together classes that interested me, that turned out to be sort of bi biological anthropology.
[00:07:31] EMILIA: Did you write an undergraduate thesis?
[00:07:33] ANNE: I did not write an official thesis. I did end up doing an independent research project with Paul Adler, who was a. Fruit fly geneticists. And so I spent a whole year with fruit flies and miraculously did find the ISO that we were looking for. And yeah, so I did that for a year. And then I also participated in some archeology projects.
[00:07:57] EMILIA: Did you do any field work?
[00:07:58] ANNE: Yeah, I actually went to Copan, Honduras. Oh, so part of the requirements for archeology. My major was to do some field work. And so a lot of people were like going to Monticello and excavating, you know, Jefferson's Rose Garden or something.
[00:08:12] RORI: Mm-hmm.
[00:08:13] ANNE: And I was more interested in something more further. So I looked at opportunities in Europe, I think I looked at one in Israel and then a couple in the Americas. I actually worked a couple summers at the Grand Canyon.
[00:08:26] EMILIA: Doing what?
[00:08:27] ANNE: Working in a gift shop at the Grand Canyon. Exactly. I applied to a bunch of different national parks and that's the one, and I think I got slotted into the gift shop because I knew some German, so I could talk to tourists badly.
[00:08:42] RORI: That's your little foot in the door. Okay. But then you went to Hon Toura for this field work.
[00:08:46] ANNE: Yep.
[00:08:47] RORI: What was that experience like?
[00:08:48] ANNE: So we were actually in, at the large side of Copan. I mean, there were excavations that were happening all around, but I ended up inside a tunnel that was going into one of the temples.
I actually spent most of my time mapping a profile, so drawing, okay. The excavated wall and making sure all the features were in. This was before all the fancy radar. And everything. So it was a little more old school, you know? So obviously we took a lot of pictures, but there are some things that maybe aren't as obvious in pictures, and so we would draw and annotate.
[00:09:25] EMILIA: Like now there's a lot of collaborations between archeologists and geneticists, for instance. How was it back then?
[00:09:32] ANNE: There was none. And so when I decided to go to grad school, I kind of wanted to marry my two interests of biology and archeology. And my very first year in grad school at Penn State, you know, you're in your first semester in grad school and you're like, oh, I have to write this research paper.
What am I gonna write it on? And my roommate, who's a biology graduate student said, oh, this really cool paper just came out. I just saw it. And she actually said, take a look at this. And it was the hagberg that got all 89 DNA from bone. And so. I thought, wow, that's really interesting. And so I wrote my term paper on getting DNA from ancient remains, and there were not very many papers mm-hmm.
On that at all. And I kind of ended up at the right place at the right time, I would say, because that first year of grad school is when Penn State searched for a geneticist for the. The Anthropology department then hired Mark Stone King.
[00:10:30] RORI: Mm-hmm. Oh, and so, so after you were there, he was hired?
[00:10:32] ANNE: Yeah, so he started my second year of grad school.
[00:10:36] EMILIA: Okay. Penn State was also already really strong in like population genetics.
[00:10:40] ANNE: Yeah. And when Mark showed up, I remember pretty much maybe his first week there, I sort of poked my head around the corner of his office and introduced myself and said, you know, I'm interested in ancient DNA. Yeah. So I sort of had the right background.
[00:10:56] EMILIA: How did you choose Penn State?
[00:10:58] ANNE: Actually, the archeologists that were my mentors at the University of Virginia were like, well read these articles and read the journal, the American Journal of Physical Anthropology.
[00:11:08] RORI: Mm-hmm.
[00:11:09] ANNE: And you know, you start getting ideas and I thought, well, maybe I want to. To be involved in Osteology, I wasn't quite sure.
And so George Milner and, well, Ken Weiss and some other folks, it was just a really strong biological anthropology group within the anthropology department at Penn State. So I kind of knew that I could develop my interests there. And then it just so happened that Mark was hired.
[00:11:35] RORI: So some careful planning and some luck.
[00:11:38] ANNE: Mostly luck.
[00:11:40] RORI: And then once Mark came on the scene. Did you like to develop a formal mentoring relationship with him or a collaboration relationship?
[00:11:49] ANNE: I basically joined the lab, me and, okay. Me and another couple students just sort of decided that we wanted to do anthropological genetics.
[00:11:58] EMILIA: How did it work back then?
You know, like now it's like people ask, do you have funding?
[00:12:03] ANNE: No, it was less. Formal. It just sort of happened organically, I would say. And I ended up kind of doing my own project, right. He would support me in the summers. He usually found funds fortunate for me. He had been at Berkeley and was a graduate student of Alan Wilson's.
[00:12:19] RORI: Mm-hmm.
[00:12:20] ANNE: And he was in the Wilson Lab when he was a postdoc.
[00:12:24] EMILIA: Oh, that's how they met? Yeah.
[00:12:26] RORI: Oh, interesting.
[00:12:26] ANNE: And he was like, oh, okay. I know a little bit about ancient DNA. So then basically it was a discussion of, all right, well, what do you wanna work on within that? And we decided to apply for permission to see if we could test ancient DNA, and it happened to be a site where there was good preservation. However, these were the old days of PCR and Sanger sequencing. Pretty labor intensive. Yeah. And I had to set up my own sort of. Ancient DNA lab. I actually went to the first international ancient DNA meeting in Nottingham, England.
[00:13:05] EMILIA: What were the topics back then? What can you get DNA out of? What meaningful information could you get? Right? And so there were a lot of people trying new methods, trying to make sure that. The results were real, mostly looking at mitochondrial DNA because of the higher copy number, it was really difficult to get any nuclear DNA results.
[00:13:27] RORI: Mm-hmm.
[00:13:28] ANNE: And so by the time of the, the, the first ancient DNA meeting people were, you know, trying to test other bones. So most of the human work was looking at mitochondrial DNA, the folks working on ancient. Human DNA were very much focused on mitochondrial DNA.
[00:13:43] RORI: Yeah, it was both what's available,
[00:13:44] ANNE: So I was interested in the people of the Americas.
How many waves of migration, when did people come over? Mm-hmm. The other thing I was actually really interested in was the spatial patterning of burials at the site and the relationships between individuals.
[00:14:00] RORI: Hmm.
[00:14:01] ANNE: So over the course of my dissertation, I extracted DNA from 150 some odd individuals.
[00:14:07] RORI: Wow.
[00:14:08] ANNE: And I managed to get mitochondrial DNA out of 108.
[00:14:11] EMILIA: Oh, that's pretty good.
[00:14:12] ANNE: But we didn't have the data to, to really look further. I did also develop a method to identify sex, which is easy to do, easy. Ish to do physiologically with adults.
[00:14:24] RORI: Mm-hmm.
[00:14:25] ANNE: But it's very difficult with children. Mm-hmm. Unfortunately, children's bones are also much less dense, and I was trying to only sample ribs, which are not a great source of DNA generally.
[00:14:35] EMILIA: Was it easy to get samples or
[00:14:37] ANNE: It wasn't easy, I would say. I mean, this was really just as NAGPRA was beginning. Right. The whole Native American grave Repatriation act. Mm-hmm. And discussions about the ethics surrounding excavation, skeletal analysis, and ultimately DNA and other types of analyses.
[00:14:54] EMILIA: All this work that you were doing that was part of your PhD thesis?
[00:14:57] ANNE: Right.
[00:14:58] EMILIA: Okay.
[00:14:58] ANNE: So at that first international ancient DNA meeting, I actually met Savante Pabo for the first time. And so I got up the nerve to ask if I could. Try to apply for a Fulbright Fellowship to be in his lab for a year and ended up doing that and getting it. His first position was at the Ludwig Maxil University, which turns out to be probably the most expensive city to in Germany.
[00:15:24] EMILIA: So all of these projects were developed mostly by you, or how was. Mark helping you develop these projects?
[00:15:31] ANNE: He was cheering me on, but he was also definitely helping me think through the different parts. I think what was great was that George Milner and Mark Stone King were my co-chairs. Mm-hmm. And so George was the archeologist and Mark was the geneticist, and I was sort of the person in the middle knowing some of both. And so we would brainstorm ideas of questions to ask.
[00:15:52] EMILIA: That's a really interesting interdisciplinary training.
[00:15:55] ANNE: Yeah.
[00:15:55] EMILIA: And so how was your year as a Fulbright student?
[00:15:58] ANNE: It was great.I spent six weeks in keel learning some German before being in Munich for the year. I took samples to the lab there, got to meet a great group of people, and yeah, it was an exciting lab. There were a lot of things happening. I shared an office with Oliva Hunt who was working on the Iceman. While I was there, I actually got to go see the ice span and we took samples and uh, my other office mate was Mathias K Kinks, who was involved in a lot of the cave Bear kind of work.
So it was a really great experience.
[00:16:31] EMILIA: So when you went to Leipsic, what year were you?
[00:16:33] ANNE: I had just finished my Master's, so I was in the third year.
[00:16:37] EMILIA: Back at Penn State, you had two PhD advisors, and now here you are by yourself in this new institute.
[00:16:43] ANNE: Yep.
[00:16:43] EMILIA: How long did it take you to adapt or to make progress?
[00:16:47] ANNE: I would say I was pretty driven, so I pretty quickly got to work.
You know, there was a good community of grad students. I think I was really fortunate in mentors, you know, and I could always send an email to George or Mark, and they were very supportive.
[00:17:01] RORI: And then as you finished up your PhD, how did you think about your next steps?
[00:17:05] ANNE: So right as I was finishing my PhD, I got involved in the first Neanderthal paper.
[00:17:09] RORI: Okay.
[00:17:09] ANNE: And I think a lot of people thought, oh, you know, she's done this ancient DNA and she's done the Neanderthal stuff. Surely she's going to keep doing ancient DNA, which was something that I planned to do. But I also realized that if I was gonna be a tenure track professor, ancient DNA is really terrible for actually getting things to work, right?
[00:17:29] And as a tenure track professor, you need to produce results.
[00:17:33] RORI: You gotta have your, you gotta papers, a couple of papers a year, all the things, all the things.
[00:17:37] EMILIA: You were thinking about all these things. Yes. As a PhD student. Yeah,
[00:17:41] ANNE: and I also realized that as a postdoc, this was kind of my opportunity to learn something new and some of this is actually because of Mark when you're trying to finish up your PhD and you're kind of in that really intense PhD dissertation brain stage where you're just super focused. He actually pulled me aside about six months before I finished. And said, okay, this week you're not gonna work on your dissertation.
It's what is your postdoc going to be this week? Oh, oh. So I thought, well, it'd be really interesting to know what the diversity is for on the Y chromosome in chimpanzees.
[00:18:12] RORI: Totally. And tried and true to be like, well, what about the comparative angle?
[00:18:16] ANNE: Yes.
[00:18:17] RORI: Let's think about this.
[00:18:18] ANNE: So he was like, yeah, that sounds kind of interesting.
And this is where the networking of your advisors is super helpful because he. Another person in Alan Wilson's lab was my camera. Mm-hmm. Who was definitely one of the active people in the Y chromosome human terrain. Yeah. And so I reached out to him and we started brainstorming and kind of one of my first ideas was to look at these repeats.
[00:18:39] RORI: Yeah.
[00:18:40] ANNE: And yeah, so I wrote an NIH postdoc proposal and that got funded,
[00:18:46] EMILIA: was my camera at University of Arizona.
[00:18:48] ANNE: Yeah. In ecology and evolutionary biology. And so that's, I ended up being there for two years.
[00:18:54] EMILIA: Where would you get the samples from?
[00:18:55] ANNE: Mostly from zoos and primate centers. Okay. You get permission, of course.
This was before shotgun sequencing. Yeah. Was really, um, doable. Mm-hmm. As well. Mm-hmm. So, yeah, so it was, uh, a bit more laborious. I think my grad students could probably do my dissertation in one sequencing run.
[00:19:13] RORI: It's humbling. Thank you. Technology.
[00:19:16] ANNE: I spent my time writing my dissertation in the computer room and doing the analyses in the computer room because it wasn't till really the end of my graduate school career that people actually could afford a laptop.
[00:19:28] RORI: Wow. Yeah. Okay, so you were doing this chimpanzee y chromosome variation work with my camera and finishing up your postdoc. The way we're talking about the story now, it feels like accomplishment built on accomplishment. Was there ever a moment where, you know, you ran into a really hard time or you doubted the path that you were taking?
[00:19:48] ANNE: Well, when I was finishing my dissertation, I hit a period of about four months where everything was contaminated, right? Mm. And it was just disheartening. Disheartening. Mm-hmm.
[00:19:59] EMILIA: Maybe we should explain what contamination is,
[00:20:01] ANNE: right. So when I would test the reagents to make sure that they didn't have any human DNA I would.
Get human DNA Uhhuh from Modern Source and I couldn't identify the source. So that was disheartening. Luckily did have a supportive community and it did have supportive mentors.
So yeah, I did finally manage to get it all clean and move forward.
[00:20:21] RORI: You started thinking about faculty positions, I imagine. Did you know, were you like, yes, it's really clear to me.I wanna get a faculty position, or was it Yeah.
[00:20:29] ANNE: By then? Yes. By then, yeah. By then, yeah. Uhhuh. Yeah.
[00:20:32] RORI: Why did you want that? What was it about a faculty position that was appealing?
[00:20:34] ANNE: Because I wanted to ask my own questions. Some people find interdisciplinary work uncomfortable because you're not clearly in one field or another.
And I actually find it a bit freeing because people don't, people don't really know what you're supposed to be doing, free you from expectations, but
[00:20:49] EMILIA: sometimes they make you feel like you don't belong. Right. Because they say You're not this. You're not that.
[00:20:54] ANNE: Yeah. And there were definitely people who told me that, and I'm really good at it. Just being stubborn and deciding that I'm not going to listen to them, you know? And I thought, well, if this doesn't work, I'll get a job somewhere. Yeah. And actually the first year on the job market, I didn't think I was gonna get a job. There were four jobs and I, um,
[00:21:15] RORI: There were four jobs. You're like there.That's the number of jobs that exist in bi fields, biological anthropology in my
[00:21:21] ANNE: Who is looking for a kind of a geneticist?
[00:21:23] RORI: Okay. That's a very small number.
[00:21:25] ANNE: Yeah, and one of 'em I didn't apply to, and I won't say where because I didn't think I was interested in living in that place.
[00:21:32] RORI: Okay. I mean, it's real.
[00:21:34] ANNE: Yeah. And then I interviewed at two and I was the second choice at one, but the first choice declined and I got the job at the University of New Mexico.
[00:21:45] EMILIA: So you remained in the southwest?
[00:21:47] ANNE: Yeah. Weirdly, the other. The place I interviewed was Penn, actually in Philadelphia. You know when there's four options, you pretty much with academia, you kinda have to apply everywhere. Right.
[00:21:58] EMILIA: And how long did you stay there?
[00:22:00] ANNE: I was there for I think three and a half years. And then I was at Cold Spring Harbor and Bill Kimball called, actually s Deer, came up to me and said, oh, we hear you're moving to a SU. And I said, really? I did not know this. And Bill Kimball, who was the. The Director of the Institute of Human Origins had been, I guess, trying to call, and he's like, and we've decided that we wanna hire an anthropological geneticist.
And I was like, great. And then he was like, and we've decided we want to hire you. I was like, oh. So I was the targeted hire actually. Okay. I've been at a SU since then for 22 years.
[00:22:39] RORI: Wow. Yeah. So did you like to go through the job application process? I mean, they invited you, you gave a seminar.
[00:22:45] ANNE: So I gave a seminar talked about the chimpanzee work, actually, Uhhuh, why wouldn't they work and yeah, ended up accepting the offer and moving.
[00:22:52] RORI: You said that you were excited about the faculty job 'cause you had got to ask your own questions, even very difficult questions that would be hard to answer. Did you get to do that right away.
[00:23:02] ANNE: Yeah. I was continuing to work on the chimpanzee y chromosome variation from the postdoc. I was kind of finishing that up. And I also at the University of New Mexico, started collaborating with Jane Bisra bio archeologist.
[00:23:17] RORI: Mm-hmm.
[00:23:17] ANNE: Jane and I have been collaborators ever since. She had a longstanding interest in tuberculosis, and when I was a graduate student, the Norris Farms community actually had a number of cases of tuberculosis. What it looked like. Classic chronic tb,
[00:23:32] RORI: which you knew from the bones or from,
[00:23:33] ANNE: yeah. It causes bony changes. If you get TB and you get really sick and you die quickly, your bones look beautiful. But if you have TB for years and years and it's chronic, it can disseminate into your bones and particularly affect the vertebra in the spine.
[00:23:48] RORI: Mm-hmm.
[00:23:49] ANNE: Which can start to kind of collapse. And so I had actually tried in Cervantes lab to amplify the ancient tb, which didn't work.
[00:23:59] EMILIA: Oh, so you were trying to do pathogens back then as well? Yeah, ancient pathogens.
[00:24:02] ANNE: Yeah. I tried that. I also tried to, Avante had this piece of skin from an Italian mummy that had smallpox.
[00:24:10] RORI: Hmm.
[00:24:11] ANNE: And so I actually also tried to recover smallpox from an individual, which was. Also very tricky 'cause there wasn't any sample that you could use as a control to design the primers.
[00:24:21] RORI: Oh.
[00:24:21] ANNE: Cause smallpox was only in C, D, C and in Russia. Yeah. Uhhuh. So that was challenging. That didn't work either actually. You know, in retrospect. It's good that it didn't work in a sense because there wasn't the comparative data from modern samples. You know, all of the clinical work at the time was, does this person have TB or not? Mm-hmm. It wasn't what is the relationship among strains? So there wasn't any comparative data that didn't happen till later,
[00:24:47] RORI: But then you were thinking about, Hey, could we revisit this?
[00:24:49] ANNE: Yeah. So a lot more data had started to accumulate from modern strains and Jane was like, Hey, do you think we could. See, I was like, oh, I can try. And it was pretty difficult. It wasn't until the next gen sequencing methods and the capture methods were developed that we really were able to push that forward in, in the way that I really wanted to, you know, be able to do the kind of analysis that we wanted.
[00:25:13] RORI: Mm-hmm.
[00:25:13] ANNE: And I started collaborating with Johannes Raza and Kirsty Boss. And that's when we ended up with the Peruvian paper, the Peruvian Ancient tb. But before we started that project, actually, I was just working with some Peruvian collaborators to look at genetic diversity in Peru. And human populations human human populations.
[00:25:31] EMILIA: The TB paper, correct me if I'm wrong, we didn't know that TB was present in the Americas, right?
[00:25:38] ANNE: So the archeological data made it clear that there was something that. Seemed to be tb, but we didn't know what kind, what species, and where it had come from. We hypothesized that people had brought it over across the bearing Strait.
We had this beautiful hypothesis, made a lot of sense. It was completely wrong, which is more interesting. Actually. It turned out that the. Pre-contact people had basically acquired TB from seals, probably from hunting and eating seals butchering.
[00:26:07] RORI: Mm-hmm.
[00:26:08] ANNE: And eating seal meat. That was undercooked. That is the root of infection.
So that was a huge surprise that the pre-contact TB in the Americas is mycobacterium pen ape. And we still don't know how TB originally got into humans. But all the animal strains now are nested within the human strains, so we gave it back to animals. Oh.
[00:26:28] RORI: Oh, interesting. Can I return to something, you know, you were talking about collaborating with some Peruvian colleagues and thinking about how genetic diversity will improve. Mm-hmm. And I'm just thinking in the span of your career, kind of the. Standard scientific thoughts about our culture around informed consent for genetic studies at all, and thinking about how we think about using or getting consent for using ancient DNA. How we do studies in collaboration if we're studying a population that's far from where we are to study in collaboration with researchers has really changed in my understanding.
But I would be so curious to hear from you, like. In your time on the ground, what have you noticed change?
[00:27:08] ANNE: You know, early on there was informed consent. There's the whole history of how informed consent develops after the Nuremberg trials and after the discussions about human rights. Mm-hmm. And other incidents as a graduate student. There were discussions about that. There were also discussions about. Nagpra. Mm-hmm. Because that certainly was in the process of being formulated and implemented. Mm-hmm. So we had many discussions about that. And I think there's also, um, a tradition of many anthropologists who often. Spend years working with communities and getting to know communities of them. Realizing that to do ethnography, to do whatever science you're doing well, you need to collaborate with and listen to the people that you're working with. And I think that definitely influenced me.
[00:28:00] RORI: I guess now when we think of people coming from a population genetics perspective, they don't come up with this idea.
[00:28:06] ANNE: Right? 'cause you don't have to consult about fruit flies. No. Right? Yeah. You know, humans are tricky. I think, 'cause I came up through anthropology.
[00:28:14] RORI: You grew up in quotes. You grew up with like the idea that yeah, in order to do rigorous science, you need to be,
[00:28:20] EMILIA: you need to engage with the community.
[00:28:22] ANNE: Also, it helped that I grew up in a small town, um, Uhhuh, you know, and you kind of realize how people are connected to each other and that there's a lot of small town politics about everything. And that's true wherever you are in the world. Mm-hmm. Mm-hmm. And you know, I was still interested, obviously, in the Americas, and I realized that South America was understudied and I reached out to people in Peru who were kind of interested in some of the same questions.
[00:28:50] RORI: Mm-hmm.
[00:28:51] ANNE: And so I worked with Veronica Rubin De and Ragga.
[00:28:56] RORI: Mm-hmm.
[00:28:56] ANNE: And two universities in Peru over the course of five, six years. This was also a time when Peru was politically becoming more stable. 'cause there was a time with the shining path that you kind of couldn't work in Peru for safety reasons and so that had changed.
[00:29:14] RORI: You've also done some really interesting work in forensic genetics, which is fairly. Niche field. I would say first, how did you get started in that?
[00:29:23] ANNE: In 2016, Donald J. Trump was elected president and I, I'm like,
[00:29:30] RORI: Why are you telling us this?
[00:29:32] ANNE: I realized that perhaps it might be wise to diversify my grant funding portfolio, Uhhuh Uhhuh, and I also realized that because of the methods we were using in the lab, they were very applicable to really challenging forensic samples, but a lot of that next generation's technology hadn't been applied to forensics.
[00:29:52] RORI: Mm-hmm. Right.
[00:29:53] ANNE: So the forensics field is very much focused on short tandem repeats, because that's what's used to type. Crime scene samples and potential perpetrators, we're kind of in that But it's a rut that doesn't work when you have severely degraded samples.
[00:30:11] RORI: Yeah. Right. So you're talking about human remains? Like human remains highly degraded,
[00:30:15] ANNE: found, you know, skeletonized often, or from burn context. Mm-hmm. Burning. Mm-hmm. It is really not great for DNA. So we decided that we could test various samples that hadn't worked for standard analyses. Mm-hmm. We could also experimentally burn individuals. This is from the Forensic Anthropology Center, the Body Farm. So these are people who specifically consented. To, yeah. Uh, this, and there was specifically a question, you know, can we burn your body, potentially? Mm-hmm. So it was part of a questionnaire that they filled out before they died and they donated their body to science and so we were currently analyzing data actually from 10 individuals who agreed. Mm-hmm. And. Finding out very interesting things about the preservation of DNA and a lot of contaminants that are produced during the burning process. Mm-hmm. And kind of trying to figure out ways to reduce those contaminants that inhibit PCR, that inhibit.
You know, making DNA libraries that inhibit sequencing. We started a series of projects that were just beginning to publish at this point,
[00:31:25] RORI: and it's primarily looking at how to extract DNA of high enough quality from Yeah, burned human remains.
[00:31:33] ANNE: Yeah. And so we're also trying to be mindful of what's useful to the forensic community.
They operate under specific constraints related to. The fact that they have to testify in court.
[00:31:43] RORI: I guess I kind of pictured the technologies that you're kind of helping develop would be most useful for identifying victims in disasters.
[00:31:51] ANNE: Yes.
[00:31:51] RORI: And so probably less often presented in court.
[00:31:55] ANNE: Yes. No, but you always have to be mindful.
[00:31:57] RORI: That's, I mean, it is, you're talking a forensic, forensic community. Thinking about it, right?
[00:32:01] ANNE: Yeah. Is is this gonna be admissible in court?
[00:32:03] RORI: Yes. Thanks for getting into that a little bit. 'cause I don't know many other people who are in the forensics world and in the academic world it's a treat to be able to talk about.
[00:32:11] EMILIA: It's really impressive to see how you've done very distinct projects. I feel inspired by the previous work. Do you get bored with the other stuff?
[00:32:20] ANNE: No. I, if you look, I kind of circle back continually. To different things. Some of it's definitely driven by the interests of my students. You know, sometimes I have students who come and they're like, Hey, I really love the work you're doing on TB or forensics.
I wanna be part of that project and I wanna take it in some direction. And I'm like, awesome. And I did that, so I can't fault 'em. You know, for example, PJ Perry was the one who. Got me involved in thinking about amylase. Yeah. And he was really interested in copy number variation and amylase is one of those. So that ended up being a super fun project. And you know, Maria Vez Colon, who's now an assistant professor at the University of Minnesota, she. Was from Puerto Rico and had worked on archeological sites in Puerto Rico as an undergraduate and was interested in mitochondrial DNA and was interested in expanding that, and so she showed up in my lab and started working on that.
[00:33:17] RORI: That's so cool. It's cool to be able to follow some of your students' interests.
[00:33:20] EMILIA: So we have a segment called Revise and Resubmit where we ask you about something that you would change or revise and resubmit about the past.
[00:33:30] ANNE: What would I do differently? I've been really fortunate. I did learn how to code and do analysis and bash Right?
[00:33:37] RORI: That's right. When did you learn to code
[00:33:38] ANNE: as a grad student? 'cause you're sticking the floppy dis in and
[00:33:41] RORI: Oh yeah. You're in the computer room. Talking about trying to get that thing to work.
[00:33:45] ANNE: By the time I was a postdoc, the real bioinformatics that is involved in analyzing shotgun data and shotgun sequencing data and the next gen data was really kind of as I was beginning as an assistant professor, which is a really hard time actually to stop and learn Pearl, and I didn't learn Pearl and I kind of wish I had. The problem is when you're an assistant professor, you're just so swamped.
[00:34:11] RORI: Totally. Right. You're like learning. Everything.
[00:34:13] ANNE: But I think in the future me, if I could go back and talk to you, I'd be like, Hey, you know, I know you spent that one summer in Spanish school the next summer. I should have sent myself to bioinformatics school for six weeks.
[00:34:25] RORI: yeah. Uhhuh.
[00:34:26] EMILIA: Well, Dr. Ann Stone, thank you so much for coming. It was a pleasure to have the opportunity to chat with you.
[00:34:32] ANNE: It was a pleasure to be here. Thank you for having me.
[00:34:34] RORI: Thank you so much. And I mean, you did host us here at ASU for a day. That was a total blast. We can't wait for the next time we get to cross paths.
[00:34:45] EMILIA: Thanks for listening to this episode. If you like what you heard, please share it with someone.
[00:34:49] RORI: This episode was produced and edited by Maribel Quezada Smith Sound Engineering by Keegan Stromberg. Special thanks to Dr. Anne Stone. The hosts of Science-Wise are Emilia Huerta-Sanchez and Rori Rohlfs.
.
[00:00:06] EMILIA: who are not only very experienced, but also really inspiring scientists.
[00:00:11] RORI: I'm Rori Rohlfs, an associate professor in data Science at the University of Oregon.
[00:00:14] EMILIA: And I'm Emilia-Huerta Sanchez, an associate professor at Brown. Our guest today is Dr. Anne Stone. A Regents professor and associate director of the Center for Evolution and Medicine at Arizona State University. Both Rory and I first became acquainted with Dr. Anne Stone's work when we read her papers as graduate students and postdocs at journal clubs. We later had the privilege of attending her lectures at conferences organized by one of our scientific societies, the Society for Molecular Biology and Evolution.
Dr. Ann Stone received her PhD in anthropology at Penn State, followed by a postdoc at University of Arizona, and she went on to University of New Mexico to start her first faculty position and later moving to Arizona State University where she is now. Dr. Stone's work has contributed to our understanding of how humans.
And infectious diseases have evolved over time. Her work is highly recognized in the field, and she has received many awards and honors. For example, she has been a Fulbright fellow, a Catholic scholar, and she received a Guggenheim Foundation Fellowship In 2011, in 2016, she was selected as a member of the National Academy of Sciences, which is one of the biggest honors for a scientist. Her lab is constantly making new biological discoveries that continue to inspire my own work and others in the field. It is my absolute pleasure to have her here today as one of our guests,
[00:01:48] RORI: Dr. Ann Stone, welcome to Science-Wise. Thank you so much for sitting with us, courtesy of our amazing producer, Marita Smith here in person in Phoenix. Your AM ACE paper is something that I presented at Journal Club back when I was a PhD student, and I was like, this is the coolest thing I have ever read. I was so amped about it.
[00:02:09] ANNE: Thank you so much.
[00:02:10] RORI: Well, maybe we'll start by talking about your life a long time ago. Like your kid hood. Can you tell us about your family?
[00:02:17] ANNE: Sure. I grew up in Tennessee, in South Carolina. Oh. And I was a grad school baby, actually. Okay. My dad ended up being a professor at the University of Tennessee, Martin.
[00:02:25] It was a small school actually, while he was still finishing his PhD in chemistry. And you know, Martin Tennessee was a small town and we lived on the edge of a big forest, and so we ran all over the place
[00:02:38] RORI: having like you played in the forest a lot.
[00:02:40] ANNE: Oh yeah, I had a really nice childhood. I was always a big reader involved in scouts, involved in a lot of various art projects.
[00:02:48] My mom was an artisan, a craftsperson.
[00:02:51] RORI: What kind of crafts did she do?
[00:02:52] ANNE: She did kind of a traditional cone craft. Oh. Making wreaths and candle rings and ornaments and things like that. So we went to a lot of craft fairs when I was a kid. Okay. So it was a good kid hood.
[00:03:04] RORI: And then your dad, he was a university professor.
[00:03:08] ANNE: So he finished his dissertation and when I was five years old, he did a postdoc at the University of Zurich in Switzerland.
[00:03:15] RORI: Oh wow.
[00:03:16] ANNE: And so I actually went to kindergarten in Switzerland, which was a great experience.
[00:03:20] EMILIA: Do you have memories of that?
[00:03:21] ANNE: I definitely have memories of that. Some of them are quite funny because now when I go back to Zurich, I recognize things that I realized were very important to a 6-year-old.
[00:03:31] RORI: What was, what mattered to you then?
[00:03:33] ANNE: You know, you'll turn a corner in the old. Part of the city and see a really cool fountain or playground and I'll be like, oh yeah, I remember that. Or the chocolate shop.
[00:03:44] RORI: Yeah. Playgrounds and chocolate shops.
[00:03:45] ANNE: Right. And then I just sort of chuckle 'cause I'm like, oh right. 6-year-old me.
[00:03:49] EMILIA: So how long did you stay there?
[00:03:51] ANNE: A year. Just a year.
[00:03:52] EMILIA: Did you learn some German?
[00:03:53] ANNE: Yeah, actually I became fluent in Swiss German.
[00:03:56] EMILIA: Oh
[00:03:56] ANNE: Wow. I've unfortunately forgotten a lot of, but it turned out to be helpful in grad school when I did a Fulbright in Germany. So some of it kind of came back
[00:04:06] RORI: and you grew up with like understanding how kind of the academy works, how.
[00:04:11] Academic life is, did you picture yourself in that life when you were young?
[00:04:14] ANNE: I think I sort of did.
[00:04:15] RORI: Okay.
[00:04:15] ANNE: Actually, I was a big mystery reader and I loved trying to figure things out and you know, I think that sort of drew me to research. Well, for a while I wanted to be an astronomer. I actually started to make my own telescope lens.
[00:04:29] RORI: Whoa. That's hardcore.
[00:04:31] ANNE: Yeah.
[00:04:32] EMILIA: How old were you?
[00:04:32] ANNE: Was probably when I was in about fifth or sixth grade. Wow. You know, so I got it as a Christmas present, one of those kits where you uhhuh, polish. And then I sort of slid toward biology more and became interested in that. My mom actually had a master's degree in Botany.
[00:04:47] RORI: Oh wow.
[00:04:48] ANNE: So I also grew up. Helping her collect nuts and cones and all these things.
[00:04:53] RORI: When you say cone crafts, you're talking about like, you're like taking pine cones and making beautiful things outta pine cones.
[00:04:58] ANNE: Right.
[00:04:58] RORI: But your mom did this with a botanist perspective.
[00:05:01] ANNE: Yeah. So she had taken a course in Western North Carolina where my grandparents lived.
At one of the community colleges that's actually really well known for its craft and had gotten into it and I think saw it as a way that she could stay home with us, but also, you know, in a small town, kind of the options were perhaps a little more limited, but she could basically work from home. These were the days before Etsy.
So, um, instead we do sort of craft fairs on the weekends and later. In life. She actually was part of the Highland Guild of Craftspeople in Western North Carolina.
[00:05:40] RORI: Mm-hmm.
[00:05:41] ANNE: So I actually learned a lot of botany on the side
[00:05:45] RORI: because you would go with her to collect these,
[00:05:46] ANNE: would go with her to collect uhhuh.
I think sometimes she would pay us like 5 cents a. Cup full or something. Wow. Okay. So there were some incentives there.
[00:05:55] RORI: Uhhuh Uhhuh motivation.
[00:05:57] EMILIA: So when you became interested in biology, was that like in middle school or in high school? I
[00:06:01] ANNE: I think it was toward high school that I kind of got interested in biology.
[00:06:04] EMILIA: And was it your decision or did somebody influence you?
[00:06:08] ANNE: By then? We had moved to South Carolina. Mm-hmm. Uh, because my dad
did a two year stint at NSF and then he joined Clemson.
[00:06:15] EMILIA: So after Zurich, he came back to, he went back to Tennessee. Okay.
[00:06:19] ANNE: And we were there for several years. And then middle school was in Maryland and then high school in South Carolina.
I would say that I became interested in biology maybe despite my bi high school biology teacher. Okay.
[00:06:32] EMILIA: What was that like? He was the soccer coach. Oh. And he was mostly interested in soccer.
[00:06:38] RORI: I see. Okay.
[00:06:39] ANNE: And it was also South Carolina in the eighties, and we completely skipped the evolution chapter,
[00:06:44] EMILIA: which is the best part.
[00:06:45] ANNE: Right. So of course, if people are gonna say, oh, we're not gonna read something, I'm like, well, I'm gonna read that. Oh, right. It's like the whole band book thing. Yeah. You know, Uhhuh. Is this band,
[00:06:55] RORI: Why is this band right?
[00:06:57] ANNE: Of course I read it and uh, I became interested in that and I think like most biology majors, at some point I was like, well, maybe I could be a doctor, but, and I went to college at the University of Virginia and while there I ended up majoring in biology and I double majored.
Actually, I had a. Interdisciplinary major in archeology as well, because I took a human Origins class and thought that was really interesting.
[00:07:20] RORI: Mm-hmm.
[00:07:20] ANNE: They didn't actually have biological anthropology, so Oh, okay. I kind of ended up cobbling together classes that interested me, that turned out to be sort of bi biological anthropology.
[00:07:31] EMILIA: Did you write an undergraduate thesis?
[00:07:33] ANNE: I did not write an official thesis. I did end up doing an independent research project with Paul Adler, who was a. Fruit fly geneticists. And so I spent a whole year with fruit flies and miraculously did find the ISO that we were looking for. And yeah, so I did that for a year. And then I also participated in some archeology projects.
[00:07:57] EMILIA: Did you do any field work?
[00:07:58] ANNE: Yeah, I actually went to Copan, Honduras. Oh, so part of the requirements for archeology. My major was to do some field work. And so a lot of people were like going to Monticello and excavating, you know, Jefferson's Rose Garden or something.
[00:08:12] RORI: Mm-hmm.
[00:08:13] ANNE: And I was more interested in something more further. So I looked at opportunities in Europe, I think I looked at one in Israel and then a couple in the Americas. I actually worked a couple summers at the Grand Canyon.
[00:08:26] EMILIA: Doing what?
[00:08:27] ANNE: Working in a gift shop at the Grand Canyon. Exactly. I applied to a bunch of different national parks and that's the one, and I think I got slotted into the gift shop because I knew some German, so I could talk to tourists badly.
[00:08:42] RORI: That's your little foot in the door. Okay. But then you went to Hon Toura for this field work.
[00:08:46] ANNE: Yep.
[00:08:47] RORI: What was that experience like?
[00:08:48] ANNE: So we were actually in, at the large side of Copan. I mean, there were excavations that were happening all around, but I ended up inside a tunnel that was going into one of the temples.
I actually spent most of my time mapping a profile, so drawing, okay. The excavated wall and making sure all the features were in. This was before all the fancy radar. And everything. So it was a little more old school, you know? So obviously we took a lot of pictures, but there are some things that maybe aren't as obvious in pictures, and so we would draw and annotate.
[00:09:25] EMILIA: Like now there's a lot of collaborations between archeologists and geneticists, for instance. How was it back then?
[00:09:32] ANNE: There was none. And so when I decided to go to grad school, I kind of wanted to marry my two interests of biology and archeology. And my very first year in grad school at Penn State, you know, you're in your first semester in grad school and you're like, oh, I have to write this research paper.
What am I gonna write it on? And my roommate, who's a biology graduate student said, oh, this really cool paper just came out. I just saw it. And she actually said, take a look at this. And it was the hagberg that got all 89 DNA from bone. And so. I thought, wow, that's really interesting. And so I wrote my term paper on getting DNA from ancient remains, and there were not very many papers mm-hmm.
On that at all. And I kind of ended up at the right place at the right time, I would say, because that first year of grad school is when Penn State searched for a geneticist for the. The Anthropology department then hired Mark Stone King.
[00:10:30] RORI: Mm-hmm. Oh, and so, so after you were there, he was hired?
[00:10:32] ANNE: Yeah, so he started my second year of grad school.
[00:10:36] EMILIA: Okay. Penn State was also already really strong in like population genetics.
[00:10:40] ANNE: Yeah. And when Mark showed up, I remember pretty much maybe his first week there, I sort of poked my head around the corner of his office and introduced myself and said, you know, I'm interested in ancient DNA. Yeah. So I sort of had the right background.
[00:10:56] EMILIA: How did you choose Penn State?
[00:10:58] ANNE: Actually, the archeologists that were my mentors at the University of Virginia were like, well read these articles and read the journal, the American Journal of Physical Anthropology.
[00:11:08] RORI: Mm-hmm.
[00:11:09] ANNE: And you know, you start getting ideas and I thought, well, maybe I want to. To be involved in Osteology, I wasn't quite sure.
And so George Milner and, well, Ken Weiss and some other folks, it was just a really strong biological anthropology group within the anthropology department at Penn State. So I kind of knew that I could develop my interests there. And then it just so happened that Mark was hired.
[00:11:35] RORI: So some careful planning and some luck.
[00:11:38] ANNE: Mostly luck.
[00:11:40] RORI: And then once Mark came on the scene. Did you like to develop a formal mentoring relationship with him or a collaboration relationship?
[00:11:49] ANNE: I basically joined the lab, me and, okay. Me and another couple students just sort of decided that we wanted to do anthropological genetics.
[00:11:58] EMILIA: How did it work back then?
You know, like now it's like people ask, do you have funding?
[00:12:03] ANNE: No, it was less. Formal. It just sort of happened organically, I would say. And I ended up kind of doing my own project, right. He would support me in the summers. He usually found funds fortunate for me. He had been at Berkeley and was a graduate student of Alan Wilson's.
[00:12:19] RORI: Mm-hmm.
[00:12:20] ANNE: And he was in the Wilson Lab when he was a postdoc.
[00:12:24] EMILIA: Oh, that's how they met? Yeah.
[00:12:26] RORI: Oh, interesting.
[00:12:26] ANNE: And he was like, oh, okay. I know a little bit about ancient DNA. So then basically it was a discussion of, all right, well, what do you wanna work on within that? And we decided to apply for permission to see if we could test ancient DNA, and it happened to be a site where there was good preservation. However, these were the old days of PCR and Sanger sequencing. Pretty labor intensive. Yeah. And I had to set up my own sort of. Ancient DNA lab. I actually went to the first international ancient DNA meeting in Nottingham, England.
[00:13:05] EMILIA: What were the topics back then? What can you get DNA out of? What meaningful information could you get? Right? And so there were a lot of people trying new methods, trying to make sure that. The results were real, mostly looking at mitochondrial DNA because of the higher copy number, it was really difficult to get any nuclear DNA results.
[00:13:27] RORI: Mm-hmm.
[00:13:28] ANNE: And so by the time of the, the, the first ancient DNA meeting people were, you know, trying to test other bones. So most of the human work was looking at mitochondrial DNA, the folks working on ancient. Human DNA were very much focused on mitochondrial DNA.
[00:13:43] RORI: Yeah, it was both what's available,
[00:13:44] ANNE: So I was interested in the people of the Americas.
How many waves of migration, when did people come over? Mm-hmm. The other thing I was actually really interested in was the spatial patterning of burials at the site and the relationships between individuals.
[00:14:00] RORI: Hmm.
[00:14:01] ANNE: So over the course of my dissertation, I extracted DNA from 150 some odd individuals.
[00:14:07] RORI: Wow.
[00:14:08] ANNE: And I managed to get mitochondrial DNA out of 108.
[00:14:11] EMILIA: Oh, that's pretty good.
[00:14:12] ANNE: But we didn't have the data to, to really look further. I did also develop a method to identify sex, which is easy to do, easy. Ish to do physiologically with adults.
[00:14:24] RORI: Mm-hmm.
[00:14:25] ANNE: But it's very difficult with children. Mm-hmm. Unfortunately, children's bones are also much less dense, and I was trying to only sample ribs, which are not a great source of DNA generally.
[00:14:35] EMILIA: Was it easy to get samples or
[00:14:37] ANNE: It wasn't easy, I would say. I mean, this was really just as NAGPRA was beginning. Right. The whole Native American grave Repatriation act. Mm-hmm. And discussions about the ethics surrounding excavation, skeletal analysis, and ultimately DNA and other types of analyses.
[00:14:54] EMILIA: All this work that you were doing that was part of your PhD thesis?
[00:14:57] ANNE: Right.
[00:14:58] EMILIA: Okay.
[00:14:58] ANNE: So at that first international ancient DNA meeting, I actually met Savante Pabo for the first time. And so I got up the nerve to ask if I could. Try to apply for a Fulbright Fellowship to be in his lab for a year and ended up doing that and getting it. His first position was at the Ludwig Maxil University, which turns out to be probably the most expensive city to in Germany.
[00:15:24] EMILIA: So all of these projects were developed mostly by you, or how was. Mark helping you develop these projects?
[00:15:31] ANNE: He was cheering me on, but he was also definitely helping me think through the different parts. I think what was great was that George Milner and Mark Stone King were my co-chairs. Mm-hmm. And so George was the archeologist and Mark was the geneticist, and I was sort of the person in the middle knowing some of both. And so we would brainstorm ideas of questions to ask.
[00:15:52] EMILIA: That's a really interesting interdisciplinary training.
[00:15:55] ANNE: Yeah.
[00:15:55] EMILIA: And so how was your year as a Fulbright student?
[00:15:58] ANNE: It was great.I spent six weeks in keel learning some German before being in Munich for the year. I took samples to the lab there, got to meet a great group of people, and yeah, it was an exciting lab. There were a lot of things happening. I shared an office with Oliva Hunt who was working on the Iceman. While I was there, I actually got to go see the ice span and we took samples and uh, my other office mate was Mathias K Kinks, who was involved in a lot of the cave Bear kind of work.
So it was a really great experience.
[00:16:31] EMILIA: So when you went to Leipsic, what year were you?
[00:16:33] ANNE: I had just finished my Master's, so I was in the third year.
[00:16:37] EMILIA: Back at Penn State, you had two PhD advisors, and now here you are by yourself in this new institute.
[00:16:43] ANNE: Yep.
[00:16:43] EMILIA: How long did it take you to adapt or to make progress?
[00:16:47] ANNE: I would say I was pretty driven, so I pretty quickly got to work.
You know, there was a good community of grad students. I think I was really fortunate in mentors, you know, and I could always send an email to George or Mark, and they were very supportive.
[00:17:01] RORI: And then as you finished up your PhD, how did you think about your next steps?
[00:17:05] ANNE: So right as I was finishing my PhD, I got involved in the first Neanderthal paper.
[00:17:09] RORI: Okay.
[00:17:09] ANNE: And I think a lot of people thought, oh, you know, she's done this ancient DNA and she's done the Neanderthal stuff. Surely she's going to keep doing ancient DNA, which was something that I planned to do. But I also realized that if I was gonna be a tenure track professor, ancient DNA is really terrible for actually getting things to work, right?
[00:17:29] And as a tenure track professor, you need to produce results.
[00:17:33] RORI: You gotta have your, you gotta papers, a couple of papers a year, all the things, all the things.
[00:17:37] EMILIA: You were thinking about all these things. Yes. As a PhD student. Yeah,
[00:17:41] ANNE: and I also realized that as a postdoc, this was kind of my opportunity to learn something new and some of this is actually because of Mark when you're trying to finish up your PhD and you're kind of in that really intense PhD dissertation brain stage where you're just super focused. He actually pulled me aside about six months before I finished. And said, okay, this week you're not gonna work on your dissertation.
It's what is your postdoc going to be this week? Oh, oh. So I thought, well, it'd be really interesting to know what the diversity is for on the Y chromosome in chimpanzees.
[00:18:12] RORI: Totally. And tried and true to be like, well, what about the comparative angle?
[00:18:16] ANNE: Yes.
[00:18:17] RORI: Let's think about this.
[00:18:18] ANNE: So he was like, yeah, that sounds kind of interesting.
And this is where the networking of your advisors is super helpful because he. Another person in Alan Wilson's lab was my camera. Mm-hmm. Who was definitely one of the active people in the Y chromosome human terrain. Yeah. And so I reached out to him and we started brainstorming and kind of one of my first ideas was to look at these repeats.
[00:18:39] RORI: Yeah.
[00:18:40] ANNE: And yeah, so I wrote an NIH postdoc proposal and that got funded,
[00:18:46] EMILIA: was my camera at University of Arizona.
[00:18:48] ANNE: Yeah. In ecology and evolutionary biology. And so that's, I ended up being there for two years.
[00:18:54] EMILIA: Where would you get the samples from?
[00:18:55] ANNE: Mostly from zoos and primate centers. Okay. You get permission, of course.
This was before shotgun sequencing. Yeah. Was really, um, doable. Mm-hmm. As well. Mm-hmm. So, yeah, so it was, uh, a bit more laborious. I think my grad students could probably do my dissertation in one sequencing run.
[00:19:13] RORI: It's humbling. Thank you. Technology.
[00:19:16] ANNE: I spent my time writing my dissertation in the computer room and doing the analyses in the computer room because it wasn't till really the end of my graduate school career that people actually could afford a laptop.
[00:19:28] RORI: Wow. Yeah. Okay, so you were doing this chimpanzee y chromosome variation work with my camera and finishing up your postdoc. The way we're talking about the story now, it feels like accomplishment built on accomplishment. Was there ever a moment where, you know, you ran into a really hard time or you doubted the path that you were taking?
[00:19:48] ANNE: Well, when I was finishing my dissertation, I hit a period of about four months where everything was contaminated, right? Mm. And it was just disheartening. Disheartening. Mm-hmm.
[00:19:59] EMILIA: Maybe we should explain what contamination is,
[00:20:01] ANNE: right. So when I would test the reagents to make sure that they didn't have any human DNA I would.
Get human DNA Uhhuh from Modern Source and I couldn't identify the source. So that was disheartening. Luckily did have a supportive community and it did have supportive mentors.
So yeah, I did finally manage to get it all clean and move forward.
[00:20:21] RORI: You started thinking about faculty positions, I imagine. Did you know, were you like, yes, it's really clear to me.I wanna get a faculty position, or was it Yeah.
[00:20:29] ANNE: By then? Yes. By then, yeah. By then, yeah. Uhhuh. Yeah.
[00:20:32] RORI: Why did you want that? What was it about a faculty position that was appealing?
[00:20:34] ANNE: Because I wanted to ask my own questions. Some people find interdisciplinary work uncomfortable because you're not clearly in one field or another.
And I actually find it a bit freeing because people don't, people don't really know what you're supposed to be doing, free you from expectations, but
[00:20:49] EMILIA: sometimes they make you feel like you don't belong. Right. Because they say You're not this. You're not that.
[00:20:54] ANNE: Yeah. And there were definitely people who told me that, and I'm really good at it. Just being stubborn and deciding that I'm not going to listen to them, you know? And I thought, well, if this doesn't work, I'll get a job somewhere. Yeah. And actually the first year on the job market, I didn't think I was gonna get a job. There were four jobs and I, um,
[00:21:15] RORI: There were four jobs. You're like there.That's the number of jobs that exist in bi fields, biological anthropology in my
[00:21:21] ANNE: Who is looking for a kind of a geneticist?
[00:21:23] RORI: Okay. That's a very small number.
[00:21:25] ANNE: Yeah, and one of 'em I didn't apply to, and I won't say where because I didn't think I was interested in living in that place.
[00:21:32] RORI: Okay. I mean, it's real.
[00:21:34] ANNE: Yeah. And then I interviewed at two and I was the second choice at one, but the first choice declined and I got the job at the University of New Mexico.
[00:21:45] EMILIA: So you remained in the southwest?
[00:21:47] ANNE: Yeah. Weirdly, the other. The place I interviewed was Penn, actually in Philadelphia. You know when there's four options, you pretty much with academia, you kinda have to apply everywhere. Right.
[00:21:58] EMILIA: And how long did you stay there?
[00:22:00] ANNE: I was there for I think three and a half years. And then I was at Cold Spring Harbor and Bill Kimball called, actually s Deer, came up to me and said, oh, we hear you're moving to a SU. And I said, really? I did not know this. And Bill Kimball, who was the. The Director of the Institute of Human Origins had been, I guess, trying to call, and he's like, and we've decided that we wanna hire an anthropological geneticist.
And I was like, great. And then he was like, and we've decided we want to hire you. I was like, oh. So I was the targeted hire actually. Okay. I've been at a SU since then for 22 years.
[00:22:39] RORI: Wow. Yeah. So did you like to go through the job application process? I mean, they invited you, you gave a seminar.
[00:22:45] ANNE: So I gave a seminar talked about the chimpanzee work, actually, Uhhuh, why wouldn't they work and yeah, ended up accepting the offer and moving.
[00:22:52] RORI: You said that you were excited about the faculty job 'cause you had got to ask your own questions, even very difficult questions that would be hard to answer. Did you get to do that right away.
[00:23:02] ANNE: Yeah. I was continuing to work on the chimpanzee y chromosome variation from the postdoc. I was kind of finishing that up. And I also at the University of New Mexico, started collaborating with Jane Bisra bio archeologist.
[00:23:17] RORI: Mm-hmm.
[00:23:17] ANNE: Jane and I have been collaborators ever since. She had a longstanding interest in tuberculosis, and when I was a graduate student, the Norris Farms community actually had a number of cases of tuberculosis. What it looked like. Classic chronic tb,
[00:23:32] RORI: which you knew from the bones or from,
[00:23:33] ANNE: yeah. It causes bony changes. If you get TB and you get really sick and you die quickly, your bones look beautiful. But if you have TB for years and years and it's chronic, it can disseminate into your bones and particularly affect the vertebra in the spine.
[00:23:48] RORI: Mm-hmm.
[00:23:49] ANNE: Which can start to kind of collapse. And so I had actually tried in Cervantes lab to amplify the ancient tb, which didn't work.
[00:23:59] EMILIA: Oh, so you were trying to do pathogens back then as well? Yeah, ancient pathogens.
[00:24:02] ANNE: Yeah. I tried that. I also tried to, Avante had this piece of skin from an Italian mummy that had smallpox.
[00:24:10] RORI: Hmm.
[00:24:11] ANNE: And so I actually also tried to recover smallpox from an individual, which was. Also very tricky 'cause there wasn't any sample that you could use as a control to design the primers.
[00:24:21] RORI: Oh.
[00:24:21] ANNE: Cause smallpox was only in C, D, C and in Russia. Yeah. Uhhuh. So that was challenging. That didn't work either actually. You know, in retrospect. It's good that it didn't work in a sense because there wasn't the comparative data from modern samples. You know, all of the clinical work at the time was, does this person have TB or not? Mm-hmm. It wasn't what is the relationship among strains? So there wasn't any comparative data that didn't happen till later,
[00:24:47] RORI: But then you were thinking about, Hey, could we revisit this?
[00:24:49] ANNE: Yeah. So a lot more data had started to accumulate from modern strains and Jane was like, Hey, do you think we could. See, I was like, oh, I can try. And it was pretty difficult. It wasn't until the next gen sequencing methods and the capture methods were developed that we really were able to push that forward in, in the way that I really wanted to, you know, be able to do the kind of analysis that we wanted.
[00:25:13] RORI: Mm-hmm.
[00:25:13] ANNE: And I started collaborating with Johannes Raza and Kirsty Boss. And that's when we ended up with the Peruvian paper, the Peruvian Ancient tb. But before we started that project, actually, I was just working with some Peruvian collaborators to look at genetic diversity in Peru. And human populations human human populations.
[00:25:31] EMILIA: The TB paper, correct me if I'm wrong, we didn't know that TB was present in the Americas, right?
[00:25:38] ANNE: So the archeological data made it clear that there was something that. Seemed to be tb, but we didn't know what kind, what species, and where it had come from. We hypothesized that people had brought it over across the bearing Strait.
We had this beautiful hypothesis, made a lot of sense. It was completely wrong, which is more interesting. Actually. It turned out that the. Pre-contact people had basically acquired TB from seals, probably from hunting and eating seals butchering.
[00:26:07] RORI: Mm-hmm.
[00:26:08] ANNE: And eating seal meat. That was undercooked. That is the root of infection.
So that was a huge surprise that the pre-contact TB in the Americas is mycobacterium pen ape. And we still don't know how TB originally got into humans. But all the animal strains now are nested within the human strains, so we gave it back to animals. Oh.
[00:26:28] RORI: Oh, interesting. Can I return to something, you know, you were talking about collaborating with some Peruvian colleagues and thinking about how genetic diversity will improve. Mm-hmm. And I'm just thinking in the span of your career, kind of the. Standard scientific thoughts about our culture around informed consent for genetic studies at all, and thinking about how we think about using or getting consent for using ancient DNA. How we do studies in collaboration if we're studying a population that's far from where we are to study in collaboration with researchers has really changed in my understanding.
But I would be so curious to hear from you, like. In your time on the ground, what have you noticed change?
[00:27:08] ANNE: You know, early on there was informed consent. There's the whole history of how informed consent develops after the Nuremberg trials and after the discussions about human rights. Mm-hmm. And other incidents as a graduate student. There were discussions about that. There were also discussions about. Nagpra. Mm-hmm. Because that certainly was in the process of being formulated and implemented. Mm-hmm. So we had many discussions about that. And I think there's also, um, a tradition of many anthropologists who often. Spend years working with communities and getting to know communities of them. Realizing that to do ethnography, to do whatever science you're doing well, you need to collaborate with and listen to the people that you're working with. And I think that definitely influenced me.
[00:28:00] RORI: I guess now when we think of people coming from a population genetics perspective, they don't come up with this idea.
[00:28:06] ANNE: Right? 'cause you don't have to consult about fruit flies. No. Right? Yeah. You know, humans are tricky. I think, 'cause I came up through anthropology.
[00:28:14] RORI: You grew up in quotes. You grew up with like the idea that yeah, in order to do rigorous science, you need to be,
[00:28:20] EMILIA: you need to engage with the community.
[00:28:22] ANNE: Also, it helped that I grew up in a small town, um, Uhhuh, you know, and you kind of realize how people are connected to each other and that there's a lot of small town politics about everything. And that's true wherever you are in the world. Mm-hmm. Mm-hmm. And you know, I was still interested, obviously, in the Americas, and I realized that South America was understudied and I reached out to people in Peru who were kind of interested in some of the same questions.
[00:28:50] RORI: Mm-hmm.
[00:28:51] ANNE: And so I worked with Veronica Rubin De and Ragga.
[00:28:56] RORI: Mm-hmm.
[00:28:56] ANNE: And two universities in Peru over the course of five, six years. This was also a time when Peru was politically becoming more stable. 'cause there was a time with the shining path that you kind of couldn't work in Peru for safety reasons and so that had changed.
[00:29:14] RORI: You've also done some really interesting work in forensic genetics, which is fairly. Niche field. I would say first, how did you get started in that?
[00:29:23] ANNE: In 2016, Donald J. Trump was elected president and I, I'm like,
[00:29:30] RORI: Why are you telling us this?
[00:29:32] ANNE: I realized that perhaps it might be wise to diversify my grant funding portfolio, Uhhuh Uhhuh, and I also realized that because of the methods we were using in the lab, they were very applicable to really challenging forensic samples, but a lot of that next generation's technology hadn't been applied to forensics.
[00:29:52] RORI: Mm-hmm. Right.
[00:29:53] ANNE: So the forensics field is very much focused on short tandem repeats, because that's what's used to type. Crime scene samples and potential perpetrators, we're kind of in that But it's a rut that doesn't work when you have severely degraded samples.
[00:30:11] RORI: Yeah. Right. So you're talking about human remains? Like human remains highly degraded,
[00:30:15] ANNE: found, you know, skeletonized often, or from burn context. Mm-hmm. Burning. Mm-hmm. It is really not great for DNA. So we decided that we could test various samples that hadn't worked for standard analyses. Mm-hmm. We could also experimentally burn individuals. This is from the Forensic Anthropology Center, the Body Farm. So these are people who specifically consented. To, yeah. Uh, this, and there was specifically a question, you know, can we burn your body, potentially? Mm-hmm. So it was part of a questionnaire that they filled out before they died and they donated their body to science and so we were currently analyzing data actually from 10 individuals who agreed. Mm-hmm. And. Finding out very interesting things about the preservation of DNA and a lot of contaminants that are produced during the burning process. Mm-hmm. And kind of trying to figure out ways to reduce those contaminants that inhibit PCR, that inhibit.
You know, making DNA libraries that inhibit sequencing. We started a series of projects that were just beginning to publish at this point,
[00:31:25] RORI: and it's primarily looking at how to extract DNA of high enough quality from Yeah, burned human remains.
[00:31:33] ANNE: Yeah. And so we're also trying to be mindful of what's useful to the forensic community.
They operate under specific constraints related to. The fact that they have to testify in court.
[00:31:43] RORI: I guess I kind of pictured the technologies that you're kind of helping develop would be most useful for identifying victims in disasters.
[00:31:51] ANNE: Yes.
[00:31:51] RORI: And so probably less often presented in court.
[00:31:55] ANNE: Yes. No, but you always have to be mindful.
[00:31:57] RORI: That's, I mean, it is, you're talking a forensic, forensic community. Thinking about it, right?
[00:32:01] ANNE: Yeah. Is is this gonna be admissible in court?
[00:32:03] RORI: Yes. Thanks for getting into that a little bit. 'cause I don't know many other people who are in the forensics world and in the academic world it's a treat to be able to talk about.
[00:32:11] EMILIA: It's really impressive to see how you've done very distinct projects. I feel inspired by the previous work. Do you get bored with the other stuff?
[00:32:20] ANNE: No. I, if you look, I kind of circle back continually. To different things. Some of it's definitely driven by the interests of my students. You know, sometimes I have students who come and they're like, Hey, I really love the work you're doing on TB or forensics.
I wanna be part of that project and I wanna take it in some direction. And I'm like, awesome. And I did that, so I can't fault 'em. You know, for example, PJ Perry was the one who. Got me involved in thinking about amylase. Yeah. And he was really interested in copy number variation and amylase is one of those. So that ended up being a super fun project. And you know, Maria Vez Colon, who's now an assistant professor at the University of Minnesota, she. Was from Puerto Rico and had worked on archeological sites in Puerto Rico as an undergraduate and was interested in mitochondrial DNA and was interested in expanding that, and so she showed up in my lab and started working on that.
[00:33:17] RORI: That's so cool. It's cool to be able to follow some of your students' interests.
[00:33:20] EMILIA: So we have a segment called Revise and Resubmit where we ask you about something that you would change or revise and resubmit about the past.
[00:33:30] ANNE: What would I do differently? I've been really fortunate. I did learn how to code and do analysis and bash Right?
[00:33:37] RORI: That's right. When did you learn to code
[00:33:38] ANNE: as a grad student? 'cause you're sticking the floppy dis in and
[00:33:41] RORI: Oh yeah. You're in the computer room. Talking about trying to get that thing to work.
[00:33:45] ANNE: By the time I was a postdoc, the real bioinformatics that is involved in analyzing shotgun data and shotgun sequencing data and the next gen data was really kind of as I was beginning as an assistant professor, which is a really hard time actually to stop and learn Pearl, and I didn't learn Pearl and I kind of wish I had. The problem is when you're an assistant professor, you're just so swamped.
[00:34:11] RORI: Totally. Right. You're like learning. Everything.
[00:34:13] ANNE: But I think in the future me, if I could go back and talk to you, I'd be like, Hey, you know, I know you spent that one summer in Spanish school the next summer. I should have sent myself to bioinformatics school for six weeks.
[00:34:25] RORI: yeah. Uhhuh.
[00:34:26] EMILIA: Well, Dr. Ann Stone, thank you so much for coming. It was a pleasure to have the opportunity to chat with you.
[00:34:32] ANNE: It was a pleasure to be here. Thank you for having me.
[00:34:34] RORI: Thank you so much. And I mean, you did host us here at ASU for a day. That was a total blast. We can't wait for the next time we get to cross paths.
[00:34:45] EMILIA: Thanks for listening to this episode. If you like what you heard, please share it with someone.
[00:34:49] RORI: This episode was produced and edited by Maribel Quezada Smith Sound Engineering by Keegan Stromberg. Special thanks to Dr. Anne Stone. The hosts of Science-Wise are Emilia Huerta-Sanchez and Rori Rohlfs.
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