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  Anthropology, Genetic Diversity, and Ethics 
 
 
A workshop at the Center for Twentieth Century Studies 
University of Wisconsin-Milwaukee  
 
 
 
Frederika Kaestle*
[Participant Information]

First, I'd like to express my thanks to everybody who organized this and did so much work to do this, and to everybody who's here, because we don't get anywhere unless we do this.  So I'm going to talk maybe a little bit differently than some of the other speakers who spoke before me, because I want to talk a little bit about the data behind what I do, just to get sort of a background to start with.  So -- could somebody flip the switch there, turn the thing on?  Thanks.  Okay, that's me.  When you're dealing with ancient DNA, it's a little bit of a special situation, because although when an individual is alive, their body repairs DNA, [and] the damage caused by oxidation and hydrolysis and radiation and chemicals, once that individual is dead, those processes don't continue, and so DNA degrades over time.  It gets broken, the molecules get changed, and essentially, over enough time, DNA disintegrates.  And this leads to special problems, and it causes most of us to work with a special kind of DNA called mitochondrial DNA.  This is a bad slide of a cell, and most of our DNA, billions of bases, is found in the nucleus of the cell.  We only have two copies, one from Mom, one from Dad, but about 16,000 bases of our DNA are found in organelles called mitochondria.  They're what helps the cell produce energy, and there's 700 or 800 of them per cell, so there are many more copies of mitochondrial DNA in a cell than nuclear DNA.  And that means that if you're working with ancient DNA, you're much more likely to find intact mitochondrial DNA, a few copies of it, than intact nuclear DNA.  So that really limits a lot what you can do with ancient DNA.  All of the procedures and protocols that we work with with modern DNA are not available to us.  mitochondrial DNA also has other advantages.  It has a very high rate of mutation.  This means two individuals or two groups are going to have many more differences in the mitochondrial DNA than they are in the nuclear DNA.  And this means mitochondrial DNA is appropriate mostly for questions of recent evolutionary history, questions within a species' history.  So that again limits what we can do with ancient DNA.  In addition, it's only maternally inherited.  That means a mother passes on her mitochondrial DNA to all of her children; the father passes on none of his.  And her daughters will pass it on, but her sons will not.  This makes mitochondrial DNA a little easier to model and understand, but it also means that it generally traces what's going on with women.  What's going on with men may be different. 

Okay.  DNA, of course, is made of polypeptide chains held together in a double helix, with four bases, A, G, C, and T.  It's the order of those bases that hold the information of the DNA.  And with ancient DNA, what we do is we amplify the DNA.  We target a specific area of the DNA, and we amplify copies of it.  Because even though mitochondrial DNA has many more copies than nuclear, it's still very little DNA.  And so we use essentially the same process that we use in our own bodies to copy DNA, only we take it out into the lab, and from one copy we can make two, from two copies we can make four, from four eight, and it only takes a few minutes to do each copying.  So, from a few copies you can, in a few hours, end up with millions or even billions of copies of a very small fragment of the DNA.  When we have this copy we can analyze the mitochondrial DNA in a couple of ways.  A coarse level of resolution is what's called RFLP, or restriction fragment length polymorphism.  And this is when you take enzymes that recognize a very specific set of DNA bases.  For example, here, Alu I recognizes AGCT.  So if it goes along the DNA chain, which is a double chain, and sees AGCT, it will cut the DNA in half right there.  And we have surveyed many different populations, many different individuals, the whole mitochondrial genome, for where the most common cut sites are, which means that we can look at those specific sites and see if an individual's DNA cuts there or doesn't cut there.  And the presence of a cut site that, in the majority of humans, isn't there, or the absence of a cut site that in the majority of humans is there, means there was a mutation in this small region of DNA, so that it doesn't get recognized anymore.  And when we look at the pattern of these cuts, it turns out that mitochondrial DNAs can be classed into groups that share certain cuts.  For example, this mitochondrial genome is a circular genome, rather than one big long chain.  There are four sites here that are sites that are commonly found among Asian and Native American individuals.  And -- here they are again -- these divide these individuals up into groups who share mitochondrial DNA, that's inherited from the maternal lineage, that is more closely related to each other, because they share these mutations, and they can trace their ancestry back to a common maternal ancestor.  That's true of this -- these are called haplogroups -- of D, and then these two haplogroups can trace themselves back to an even earlier maternal ancestor, and that's true for the whole human species.  You go back far enough, and we trace ourselves all back to one female human ancestor. 

The other way we can look at mitochondrial DNA is to look at the actual sequence of a fragment of DNA.  We tend to look... this is again that circular region, and it's got all of the genes -- there are 37 genes on mitochondrial DNA -- labeled, and then there's a region of DNA that doesn't code for a gene.  It's usually called the D-loop or the control region, there's a couple of names for it.  And it's even more variable than the rest of the DNA in mitochondrial DNA, and that makes it useful for identifying differences between individuals.  Most individuals that are not closely maternally related are going to have differences here.  And it turns out that some of these differences can be correlated with these haplogroups that we defined with the restriction enzymes, these RFLPs.  For example, these are individuals from the Pacific.  This isn't in very good focus.  And you can see, these are the bases that vary in these individuals in a D loop, and there are some obvious patterns here -- depending on the focus.  There's a bunch of individuals who share these ACTs, and in fact they also share some markers out here, and those also correlate with other restriction sites that make them a haplogroup, which is very originally named Haplogroup 2.  But in addition to that, these individuals have other mutations that make them different from each other.  And sometimes they can be found in subgroups that are geographically located; sometimes they don't seem to be. 

So, using these two tools with mitochondrial DNA, we can help answer questions that are of interest to many fields: anthropology, archaeology, linguistics, history, conservation biology, evolutionary genetics, forensic sciences -- I'm doing the promise part of my talk right now [laughter] -- and some of the examples that I'm familiar with as an anthropologist involve looking at kinship among ancient individuals, and this can help us understand social structure, marriage patterns, burial customs, in these ancient groups.  In addition, you can look at nonhuman ancient DNA and usually identify the genus and sometimes the species of ancient animals found at the site.  This helps us understand ancient dietary patterns, hunting patterns, the ecology at the time the site was inhabited, and also when and how animals and plants were domesticated in different areas.  We can also detect the DNA of ancient diseases.  One common example is what was the distribution of tuberculosis in prehistory, and that has implications for its treatment today. 

Also, we're just now beginning to be able to look at nuclear DNA, and this is important for a couple of reasons.  It allows us to genetically sex individuals; this is important when you have very fragmentary remains, or remains of young individuals who can't be sexed just by looking at the anatomy.  And this allows us to get at, again, social structure, status, there's forensic science applications, and also patterns, differential patterns by gender of disease, diet, material possessions, and that sort of thing. 

And then, of course, there's the question that a lot of us here are concerned with, and that is identifying prehistoric groups and their relationships to modern groups.  With large sample sizes, the frequencies of these haplogroups and D-loop mutations can be used to characterize populations.  Because populations inherit these markers from their ancestors, although social boundaries are permeable to genes, they're not completely permeable.  So you do have different frequencies of these markers in different groups.  And so groups that are closely related are likely to have very similar frequencies, and groups that don't have, groups that have very, very different frequencies, are not likely to be closely related.  An example of how we can use this -- oops, I'm missing a slide.  Well, okay, here you go, mapping the past.  An example of how we can use this is in the Pacific, there's a marker in the mitochondrial DNA called the nine base pair deletion, and its frequency is, obviously, it varies quite a bit.  It's very frequent out in the Polynesian islands, very infrequent in Australia, New Guinea and some other groups, and by examining, looking for the presence or absence of this marker in ancient individuals in these islands, this can help us understand how these islands were peopled, from where they were peopled, how they interacted with each other after they were peopled, how these genetic groups correlate with linguistic groups, that sort of thing. 

So those are the types of questions I'm interested in.  They may not be the types of questions you're interested in, and that's part of a later issue we're going to discuss.  That was the promise of ancient DNA.  Now, for the problems!  There are some obvious methodological problems working with ancient DNA, and the major one is contamination.  Because of the technology that allows us to access this ancient DNA, we also have to worry about getting contamination from modern sources.  This may be the archaeologist who excavated the remains, the museum curator who moved them from one drawer to another, the technician who packaged the tubes in which you're storing the DNA, the person in the laboratory who sneezed on his or her gloves and then handled them, other ancient individuals who you have amplified and then spilled on the lab bench, their DNA.  So it's essential when you're working with ancient DNA to have very stringent contamination controls, to decontaminate the surfaces of the samples before you look at them, and of course to monitor for any evidence of contamination. 

Then sample size, as I mentioned earlier, is a huge issue here, especially when you're dealing with defining groups.  To understand prehistoric behavior, to get an accurate picture of the ancestor-descendant relationships, requires that we look at the range of behavior and relationships in a group, and get an accurate estimate of these frequencies.  You cannot do this unless you have a large sample size.  A sample size of one doesn't get you a frequency of anything.  A frequency of 100% in a sample size of one doesn't tell you what else was present in that group of people at the time that this individual lived.  So sample size from ancient groups is often limited, because you don't find very many ancient individuals.  In addition, sample size from modern groups is an issue, because you can't connect an ancient group with a modern group unless you can compare them to that data in a modern group.  And this slide depicts -- is backwards! -- and depicts that frequency of that nine base pair deletion.  It's okay, I don't need it forwards, I can tell you what it says.  The frequency of that deletion that I talked about in Polynesia?  Well, it's present across Asia and the Americas, and we've got the frequency in South American groups, Central, North, Siberian, Southeast Asian, Oceanic groups.  And as you can see, it does vary quite a bit from group to group.  But if we could actually read the names down there, of these groups, you would notice a whole heck of a lot of groups aren't there.  We don't have any idea what the frequencies in these groups are.  The other thing, if you could read this, you would notice, is, for example, you've got some groups that don't seem to have the deletion at all.  But if you could read the sample sizes, they would be 10, 12 individuals from a whole population.  Well, if the frequency of that deletion is 10% 6%, only sampling 10 individuals from that population is likely not to catch that.  So, again, sample size is a big issue. 

And then data analysis is another big issue.  There's a long history of looking at modern genetic variation and there are many methods developed to do this.  But it's unclear how they can be profitably and successfully applied to samples that span not only space, that are from different geographic areas, but as sampled across time, because ancient groups, when you sample them, often you get one individual from each generation, or one individual perhaps every hundred years.  So we're only just beginning the empiric -- how we can do this using empirical data, simulation data, and extensions of modern theory. 

So that's usually where a review of ancient DNA in the literature would stop.  But obviously, we haven't gone far enough, because there's a qualitatively different set of questions.  Because when we deal with human ancestors, there are living peoples with widely different social, political, religious and legal beliefs and interests.  Although we may be advancing the pursuit of knowledge (or may not be), we are certainly going to be affecting the lives of the modern members of our species when we study these ancient individuals.  So our results, especially in today's climate of genetic essentialism, are often going to be interpreted to have serious social meaning and policy implications, and we need to know what those are before we decide to undertake a study.  An obvious example of this is the Kennewick Man remains, which were discovered a few years ago off the Columbia, on the banks of the Columbia River, and they are the remains of about a 9,000 year-old individual.  And today's contemporary attitudes towards the importance of genetic study, and all the media attention lately on "really cool" ancient DNA stuff, like Neanderthal DNA, has seemed to lead to a bias toward science in the covering of this story.  It's even been covered in science fiction magazines.  There was an article in this October/November 1998 Asimov Science Fiction, where we got a "Science Fact" article about Kennewick.  And in your reader, there was a New Yorker article written about the Kennewick case.  A bunch of scientists have filed suit to protect the remains against repatriation, on the insistence that it must be studied, whereas the federal government insists that under NAGPRA law, it should be repatriated and reburied, or not, depending on what Native Americans decide.  In this 11-page article, the author, Douglas Preston, directly quoted 13 scientists: anthropologists, archaeologists, geneticists, geologists; and he directly quoted, or even mentioned, one Native American, and didn't seem to have interviewed anybody at the Army Corps of Engineers, the federal agency responsible for this decision. 

So, obviously, we're dealing with a situation where the attitudes towards ancient study differ from different groups, and the Western attitude favoring scientific study seems to be the one that's the popular attitude in popular science, popular literature and media.  So we know now, or we're starting to know now, that we can't just take this attitude.  Science is not performed in a vacuum, and so these attitudes have begun to be challenged.  Because they have implications -- discrimination, racism -- our results may contradict deeply held beliefs, and of course may affect legal claims. 

Now, this is true of modern genetic variation studies too.  Ancient DNA has a separate or related set of problems, because you can't consult the ancient individual, obviously, which means you're left really with two choices: consult no one, which, we seem to be arriving at the conclusion, is not generally an acceptable attitude; or consult the modern descendants or some modern group who has an interest in this ancient individual.  But that's easier said than done.  Usually, or in many cases, we're not sure who that modern descendant is.  In fact, in a lot of cases, the study is undertaken to help find that out. 

So, what evidence do we use to decide who to ask?  And if that evidence is contradictory, what do we go with?  With Native Americans, that particular issue seems to be settled with NAGPRA, except of course for various interpretations of NAGPRA.  But it's obviously not settled with most other groups.  What if, when you're doing your study, your preliminary evidence suggests that you've asked the wrong group?  For example, in Kennewick, the Kennewick Man case, had the Native Americans given permission for study, and the genetic evidence suggested that this particular individual didn't fall into the general variation found among Native Americans, and instead fell within the variation found within some other group?  Should we stop that study right then and go to that other group and ask them, "Should we continue?"  What if they say no?  Should we stop?  If they say yes, and it turns out we were wrong with our preliminary conclusions, what do we do? 

These are all questions that are of interest to those of us who study ancient DNA, and also those of us who are descended from these individuals, and I'm hoping that we're going to get somewhere on this today, and Dennis is going to talk a little bit about his efforts to figure this sort of thing out.  Thanks. 

*This talk has been edited for web publishing by the author.

 
 
 
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