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paleoanthropology, genetics and evolution

forensics

  • The DNA portrait artist

    Fri, 2013-05-31 13:44 -- John Hawks

    Twitter gets results! A group of geneticists (honestly, including me) were kvetching on Twitter about this NPR story: "Litterbugs Beware: Turning Found DNA Into Portraits". The story profiles an artist, Heather Dewey-Hagborg, whose chosen project blends the idea of genetics with identity:

    Yet it might seem Dewey-Hagborg would be more comfortable in a studio than a laboratory. She's an artist; a doctoral student in Information Art at Rensselaer Polytechnic Institute in Troy, N.Y. For her most recent project, though, much of the creative process takes place in front of a centrifuge, wearing latex gloves, deep in the map of the human genome.

    In short, Dewey-Hagborg extracts DNA from these samples of trash and turns that information from code into life-sized 3-D facial portraits resembling the person who left the sample behind. She can code for eye color, eye and nose width, skin tone, hair color and more.

    Now, for those of us who are actually working in human genetics, the premise of this story is obviously science fiction. There is no way to create accurate "life-sized 3-D facial portraits" of people based on their DNA. There is some information about skin, hair and eye pigmentation, but even that is not sufficient to generate a portrait of these traits for an individual with forensic accuracy.

    Forbes reporter Matthew Herper caught wind of the Twitter convo and began investigating the story. He interviewed Dewey-Hagborg by e-mail and got her response to the criticism that her portraits are not rooted in scientific accuracy. I think her responses stand for themselves: "Artist Creates Portraits From People's DNA. Scientists Say 'That's Impossible'". It's a conceptual art project, as she writes, "The point of the work is to create a provocation".

    Well, it is provocative. My concern is that it plays on people's fears of genetics in ways that reinforce widespread misconceptions about the power and process of science.

    Herper concludes:

    But though our genetic privacy may not be safe, our faces probably are. Dewey-Hagborg’s portraits may rarely resemble the people whose DNA she’s using to generate them. The whole thing — most disturbingly the fact that she’s been contacted by law enforcement officials — shows how ill-prepared we are for dealing not only with what biotech may do in the future, but for what biotech can do now. She needs to work at making her message clearer.

    It would be more illustrative to use a series of photographs of people who have the same genotypes as the person who left a cigarette butt, to show the range of different facial shapes and features instead of pretending we can focus on a single one. After all, we already know the effects of stereotyping upon witness reports from crime scenes. Adding a new category of genetic stereotyping based on a very limited degree of gene-phenotype associations can only push things further into the realm of misinformation.

  • Alfred, possibly not under a car park

    Fri, 2013-03-29 21:08 -- John Hawks

    So after they found the bones of Richard III under a parking lot, now everybody is apparently going crazy to dig up bones under parking lots, churchyards, unmarked graves, wherever.

    Now we hear that churches and institutions that have bones under their parking lots are digging them up to prevent forensic anthropologists from doing it first: 'Alfred the Great' bones exhumed from unmarked grave".

    His body was first buried near Winchester Cathedral, moved at least once there, then moved again to Hyde Abbey in a great procession in 1110. As in Leicester, that church was destroyed in the dissolution of the monasteries, and his remains too were assumed to lie under a modern car park which had previously been the site of a prison. In 1999 there was great excitement when archaeologists found the foundations of abbey buildings, and then human bone – but it proved to be that of an elderly woman who had suffered from painful arthritis.

    Here, they have a body from an unmarked grave in a cemetery that they believe to be Alfred's. They've dug it up as a prophylactic against digging it up. Or something.

    Does England have any parking lots without bodies under them? Can the ghosts of medieval monarchs turn your Lancia into another Christine? Is there any chance that these bones won't be subjected to forensic study leading to another TV show?

    By the way, the most interesting use of genetics here would be to get a whole genome and make an estimate of the proportion of ancestry of common Britons that come from the royal family 1000 years ago...

  • The Mayflower criminal registry

    Fri, 2012-01-13 22:25 -- John Hawks

    Of some interest with respect to DNA databases and privacy concerns: "DNA links 1991 killing to Colonial-era family".

    The DNA sample was taken in the death of 16-year-old Sarah Yarborough, who was killed on her high school campus in Federal Way, Washington, in December 1991. The King County Sheriff's Office has circulated two composite sketches of a possible suspect -- a man in his 20s at the time with shoulder-length blonde or light brown hair -- but had been unable to put a name to the sketch.

    In December, though, the department sent the DNA profile to California-based forensic consultant Colleen Fitzpatrick. Fitzpatrick compared the profile to others in genealogy databases and found the closest match was to the family of Robert Fuller, who settled in Salem, Massachusetts, in 1630 and had relatives who came over before him on the Mayflower.

    This is a Y chromosome match based on the genealogical research of people who may be completely unknown to the "suspect". Fitzpatrick offers that a Y-chromosome match may be expected to share a surname, which is probative in the forensic situation. Obviously there are many possible scenarios in which such information will not lead to discovery of a suspect: the chance of non-acknowledged paternity events across 200 years is very high. I don't view the result as strongly actionable, but I do think it raises important questions about the future of genealogy databases.

    We are near the time when whole-genome sequencing will make this kind of identification much more likely because unique genetic matches to 3rd and 4th degree relatives will be plausible. Finding a handful of rare mutations shared between a crime scene sample and an individual in a whole-gneome database would be a strong indication of a relationship. It's possible that the databases for whole genomes will grow faster than the technology will allow reliable whole-genome sequencing from a crime scene sample. So in this case, the issues with database use may be primary.

    It would be an interesting exercise to estimate the fraction of unknown samples from crime scene Y chromosome and mtDNA that could be matched to a 10th-degree relative in the Genographic (or any other large) dataset.

  • Body donation is a weighty matter

    Thu, 2012-01-12 16:42 -- John Hawks

    Barbara King gives a shout-out to the Forensic Anthropology Center at the University of Tennessee ("Cremation, burial, or Body Farm?").

    Twenty-two years ago, Dr. William M. Bass founded the Body Farm, or, as it's properly known, the University of Tennessee's Forensic Anthropology Center (UTFAC). Today it's a leader in a field populated by programs it inspired, as a newspaper article last week informed me.

    Last week a science news story went around that medical schools don't want to accept obese body donations ("Nobody wants a chubby corpse"). The embalming makes them too heavy for the dissection tables, the story went, and medical students are supposed to learn "normal" anatomy, not "abnormal" obese people.

    What America are these anatomy programs living in?

    At any rate, my first thought was that forensic anthropology programs would be happy to get a broad representation of donated remains. Many of the qualities that have been developed to distinguish sex and age from the skeleton depend on samples donated 80 years ago or more. Today's weightier population differs -- bone size, robusticity, and age-related changes all vary with body mass. Doing good forensics on today's population takes a more updated sample, of the sort that continues to be built beneath the Tennessee football stadium.

  • Oetzi's curse

    Mon, 2011-02-21 16:08 -- John Hawks

    I did not know there was an iceman mummy curse:

    But Oetzi's notoriety has also been linked to a supposed curse surrounding the mummy, after several people -- authors, researchers, even mountain guides -- who came in contact with it died over the years.

    One of the couple who discovered Oetzi was found dead after a mountain hike in 2004. A forensic expert, who had closely examined the find, meanwhile died in a car accident in 1992 on his way to a lecture about Oetzi.

    Well, sounds more like coincidence...so far! But maybe there's a movie script here.

    (via Dienekes)

    Tags: 
  • Neandertal band of brothers

    Tue, 2010-12-21 11:48 -- John Hawks

    Carles Lalueza-Fox and colleagues [1] have a new analysis of the mitochondrial DNA from El Sidrón, Spain. The site has a minimum number of 12 Neandertal specimens, dating to 49,000 years ago. The authors recovered mtDNA from all of the skeletal individuals, and additionally tested for the presence of Y chromosome to diagnose sex.

    They found that all the adult males in the sample are close maternal relatives -- that is, they all share a single mtDNA haplotype. In contrast, the adult females and juveniles have a range of different haplotypes. Using some conclusions about the archaeological context (discussed below), they interpret the 12 individuals as part (possibly all) of a kin-structured group. They note that the relationships are then consistent with a patrilocal residence pattern: The men in the group are linked by kinship, the women have come from other kin networks, possibly transferred from other groups.

    In the last paragraph of the paper, the authors suggest a further conclusion about life history:

    Based on the ages of the El Sidrón group members and their mtDNA lineages, we speculate that juvenile 2 is the offspring (or close matrilineal relative) of female adult 5 and that juvenile 1 and the infant are the offspring of female adult 4. If correct, the latter relationship would indicate an interbirth interval of around 3 y for Neandertals. This period fits with the average 3-4-y interbirth interval reported for several modern hunter-gatherer groups (19).

    That conclusion would be based on a single birth interval. It depends on the assumption that these juveniles are in fact siblings, which further depends on the proposed site deposition scenario. So although it is consistent with the data, I think it is very weak evidence. Still, it's a lot more evidence that I expected to have anytime soon. Moreover, it seems to me that the birth interval is testable with reference to dental development. A 3-4 year birth interval implies weaning in or before the fourth year of life, which ought to be reflected in enamel formation.

    Awesome! We can now test hypotheses about Neandertal social organization directly from DNA evidence. The authors' hypothesis about patrilocality is consistent with the mtDNA, and I think it is likely to be the correct one.

    Still, we have many reasons to be cautious about the interpretation. For one thing, Neandertals are already known to be relatively low in mtDNA variation, with very little regional population structure in the mtDNA. In such a population, it wouldn't be surprising to find individuals sharing the same mtDNA haplotype, even if they were not close kin. It might seem surprising that the individuals sharing the mtDNA haplotype are all men, but with a sample of only 12 individuals, that coincidence isn't really all that unlikely. The limited mtDNA variation would then be a sign of inbreeding at a regional level, not necessarily the kin structure of a particular group at a particular time.

    Placing those individuals together as part of the same group is a forensic challenge. For most bones at archaeological sites, we would assume that the individuals lived at different times, possibly hundreds or thousands of years apart. The interpretation that they represent a single group requires several assumptions about the deposition of the remains, which amount to a detailed and surprising scenario. Lalueza-Fox and colleagues describe the El Sidrón skeletal assemblage as a result of systematic cannibalism:

    The excavations to date have yielded > 1,800 hominin skeletal fragments and ∼400 Mousterian stone tools made in situ (3), but faunal remains are very scarce. The Neandertal bones are in a secondary position, and the original deposit, worn out by erosion, is thought to have been placed either on the surface or in an upper karst level (2). The present assemblage occurred shortly after the death of the individuals by the collapse of an upper gallery into the Ossuary Gallery triggered by a natural event, probably a violent storm that also dragged down pebbles and clay (Fig. S1). Given that (i) ≈18% of the lithic industry can be refitted, and (ii) the widespread spatial distribution of these refitted artifacts, it may be surmised that they result from a single and brief cultural activity. This likelihood lends even more support to the synchrony of the whole assemblage (2, 3), dating to around 49,000 y ago (4). Some evidence, such as skeletal parts still in anatomical articulation, indicates little site disturbance since formation. Ex hypothesis, the fact that all types of skeletal remains show evidence of anthropic activities associated to cannibalism (2) could indicate that the assemblage corresponds to a Neandertal group processed by other Neandertals on the surface. Although it is impossible to be sure that the individuals represent a contemporaneous group, alternative explanations, such as recurrent accumulation over time of cannibalized individuals that were closely related through the female line, seem less plausible.

    If this interpretation is correct, it would be the most stunning example of intergroup violence known from the Pleistocene. Imagine the circumstance in which a group of hunter-gatherers would kill and butcher 12 individuals in one paroxysm of aggression. Certainly it was not mere survival, it was warfare.

    Is it true? The problem is the "violent storm". How do we know that the existing assemblage is a good representation of the original deposition site? The high number of refits does imply that we're not looking at a random sample of an originally much larger assemblage, but it's hard to be more definitive. If we have the remains of 12 individuals, how many may have been involved in the act?

    Naturally, if the remains had actually accumulated over a longer time, the conclusions about patrilocality would be unwarranted. In that case we would be back to a more general question of regional or local inbreeding among Neandertals, interesting from the point of view of population structure, but with less concrete information about social organization.

    The forensic case provides a window into behavior that is potentially much broader. Krapina is another site with hundreds of skeletal fragments representing an even larger number of individuals, which may also represent one or more instances of cannibalism. In that case, the debate about cannibalism (versus secondary reburial of defleshed bones) has flared off and on for years. It is just very difficult to attain a reasonable certainty about such behaviors from the archaeological and skeletal evidence at hand.

    I will be interested to read more about the context at El Sidrón as the research continues. The issues of kinship can be easily settled with nuclear DNA sequencing, and should in fact lead to some extremely interesting science, if that can be accomplished. The authors list some of the barriers to such sequencing, given a relatively low DNA yield in many of the specimens, but the field has rapidly progressed. Meanwhile, the archaeological interpretation of the site may allow us to revisit some other Neandertal assemblages, looking for other signs of aggression, violence, and social organization.


    References

    Synopsis: 
    Analysis of mtDNA from El Sidron cave shows relationships among the males, presumed to be an ancient group.
  • Amelia news

    Thu, 2010-12-16 07:30 -- John Hawks

    More news about Amelia Earhart:

    The suspected finger is being tested for human DNA. It may turn out to be from a turtle – which have similar bones in their flippers.

    But the other discoveries lend credence to the theory that Earhart died on the atoll after going missing en route to Howland Island in July 1937 at the age of 41 – she was declared legally dead 18 months later.

    They include part of a mirror from a woman's compact, a zip from a Pennsylvania factory and travel-sized bottles made in New Jersey as well as a pocket knife listed on her aircraft's inventory, all manufactured in the 1930s.

    I met the TIGHAR head, Ric Gillespie, one year when they were announcing the results of a previous expedition to Nikumaroru. I hope they're on to something, because I think Earhart is one of the really compelling historical forensic cases. We always used to use it as an exam question. But then, I'm from Kansas, so I have an attachment. At any rate, if they're right it's sort of depressing:

    "A crash at sea, that's nice and clean and a quick ending. Ending up as a castaway on a waterless atoll, and struggling to survive for a time and failing and ultimately being eaten by crabs is not nearly as pretty.

    Well they've found an assortment of stuff that's hard to explain without Amelia Earhart -- it's what a forensic historian would call tantalizing. That may be what there is to find. Still, there are many unknowns -- it may only take one person with trade goods on the island within the right decade.

  • Charlemagne the tall

    Fri, 2010-09-24 10:10 -- John Hawks

    I found an interesting, short paper doing a bit of forensic investigation on Charlemagne [1]:

    Charlemagne (ca. 747–814 CE; Fig. 1) – or Carolus Magnus meaning “Charles the Big” as well as “Charles the Great” – is one of the most important historical personalities. Being son of “Pippin the Short” (714–768 CE), his physique is only known from historical descriptions, which may be biased by his political greatness reflected in his title of Pater Europae. His friend and courtier Einhard (ca. 770–840 CE) described him as a large and strong person, being lofty but not disproportionally tall, and measuring exactly seven times the length of his own foot (Einhard, 1880). Charlemagne's earthly remains are inaccessible since he was canonised in 1165 CE and as sacrosanct his bones are sealed in the sarcophagus at the Aachen cathedral in Germany. However, the left tibia (Fig. 1) exhibited in the cathedral's treasury was made available for our study by Church authorities.

    They found he would have stood around 184 cm, putting him in the 99th percentile for height in his day. That's only around the 75th percentile for height now in the same area -- a reminder of how much stature has increased in post-industrial Europe.


    References

    1. Rühli FJ, Blümich B, Henneberg M. Charlemagne was very tall, but not robust. Economics & Human Biology [Internet]. 2010;8:289–290. Available from: http://dx.doi.org/10.1016/j.ehb.2009.12.005
  • DNA arrest database

    Fri, 2010-05-21 09:28 -- John Hawks

    In yesterday's DNA news, the U.S. House of Representatives wants to pay for an expansion of federal DNA databases to include all arrestees:

    By a 357 to 32 vote, the House approved legislation that will pay state governments to require DNA samples, which could mean drawing blood with a needle, from adults "arrested for" certain serious crimes.

    The linked article has a slant towards civil liberties; it was the one I found that discussed the unusual procedure of the vote.

    House Speaker Nancy Pelosi and the Democratic leadership scheduled Tuesday's debate on the bill--called the Katie Sepich Enhanced DNA Collection Act of 2010--using a procedure known as the "suspension calendar" intended to be reserved for non-controversial legislation.

    "Suspension of the rules is supposed to be for praising the winner of the NCAA championship or renaming Post Offices," Harper says. "Things like collecting Americans' DNA are supposed to be fully debated in Congress."

    I take that as a sign of how little debate there is among the political class about this issue.

    I don't have strong feelings about DNA sampling at arrest. The potential for abuse comes from how easy it is to arrest someone. If the feds are paying the bills, that takes away an important impetus for local oversight. Still, there's little doubt that some unsolved cases will be resolved by an expanded database. Probably more would be impacted if more funding were provided for backlogs in profiling of crime scene samples.

    Oh well, how bad can it be? After all, university freshmen now are being asked for samples with enrollment!

    Maybe if Congresspeople would provide samples to get the ball rolling, I'd feel better. We can reassure them that their profiles will be protected by giving them unique bar codes.

    More: "Privacy, politicians and genetic testing."

  • The Neandertal fraction

    Tue, 2010-05-11 11:43 -- John Hawks

    I've gotten the same question a few times, and have seen it elsewhere, so I thought it would be worth a short post to explain it. And for those readers who've also been asked this question, I thought that being able to provide a simple explanation might be a great help.

    How can we say that today's non-Africans derive 1-4% of their genomes from Neandertals, when we are 99.86% genetically similar to Neandertals? Or 98% similar to chimpanzees? I mean, how do we have 4% to work with to make this estimate at all?

    Let me explain with another example.

    You are approximately 99.9% similar to any other random human today. You're just a bit closer to your relatives, because you got some of your DNA directly from them, or you both share DNA from an immediate ancestor.

    Your great-grandmother on average gave you 1/8 of her genes, making up on average 12.5% of your genome.

    You are more than 99.9% similar to your grandmother, on average, yet she contributed only 12.5% of your genome.

    In other words, these percentages are different things -- the fraction of your total ancestry you can trace to her, versus the fraction of base pairs you actually have identical to hers. Your genome is much more identical to hers than can be explained solely by your descent from her -- this is because you share other ancestors in common with her, and because mutations don't happen very often.

    Or, think about it the opposite way. Suppose that the 12.5 percent of your genome you inherited from your great-grandmother meant that you were only 12.5 percent genetically similar to her. Where did you get the rest of your genes from? A turnip? No, you got them from other people, all of whom are roughly 99.9 percent like your great-grandmother. You're 12.5 percent more like your great-grandmother than you are like randomly chosen people in the population.

    For the Neandertals, we have to separate these two kinds of similarity, sorting out the genes that we must have inherited from them, from the ones that we share because we share a more distant ancestry.

    Now, suppose we don't know that this woman was your great-grandmother, that it's only a hypothesis. It's kind of thing a forensic anthropologist might want to figure out, if your great-grandmother was Anastasia. We can answer the question in this way: Test the hypothesis that she's unrelated to you, by examining whether you are equally genetically similar to her as you are to the average, randomly chosen individual from your population.

    This is a statistical test. In fact some of the people in the population share more genetic similarity with you than others, and our statistic has to account for that variation. We can put whatever level of statistical confidence on it we like. If your putative great-grandmother shares substantially more with you than all but some very small fraction of people, we may conclude that she is your relative.

    We might do substantially better -- if the variation in the population doesn't work against us, we might even conclude that she is in fact a third-degree relative who contributed between 10 and 14 percent of your genome. Or even better.

    Our conclusion has to depend on the structure of the population. If randomly chosen people tend to look like you, for some reason of population structure, we'll have to model that population structure directly. This is, of course, what was done in the case of the Neandertal genome -- a specific population model was significantly favored by the data, and alternatives that did not include population mixture were demonstrated to be so unlikely as to be essentially impossible.

    And as I pointed out the other day, if Neandertals had not donated any genes to later populations, then the most recent common ancestors of human and Neandertal genes would all be earlier than the divergence of those populations, more than 250,000 years ago. It is the observation of chromosomal segments that are identical or very near some living human chromosomes that shows that, for some genes in some living people, the Neandertals are not different enough. We have to have some of their genes.

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.