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paleoanthropology, genetics and evolution

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  • Phrenology, race and history

    Tue, 2013-02-05 22:01 -- John Hawks

    The movie Django Unchained includes a scene in which the antagonist (a rich, white, plantation owner) expounds on phrenology as a justification of slavery. James Poskett in The Guardian gives the historical context behind racist phrenology. The interesting part is the existence of anti-racist phrenology:

    [I]t wasn't just the slavers. My research revealed that some of the most vocal anti-slavery campaigners of the 19th century were also advocates of phrenology, and used it to justify their stance.

    Lucretia Mott, a particularly uncompromising American abolitionist, sent her children to phrenological lectures and spoke of the "truth of phrenology" in letters to friends. When she visited Britain she stayed with the renowned Scottish phrenologist George Combe, himself an anti-slavery campaigner. Horace Mann, another major figure in abolitionist politics, was so keen on phrenology that he subscribed to the official journal. After becoming president of Antioch College in Ohio, he even boasted in the same sentence that the professors he employed were both "anti-slavery men" and "avowed phrenologists".

    The relation between science, pseudoscience, and highbrow morality in the nineteenth century was counterintuitive. Phrenologists were steampunk witchdoctors.

  • Race and Tolkien

    Sat, 2012-12-22 12:36 -- John Hawks

    Henry Gee comments in the Guardian about the other kind of hobbits, featuring orc reproductive biology: "Hobbits and hypotheses".

    In the Silmarillion Tolkien says in one throwaway line that orcs reproduced the old-fashioned way. Boy orcs and girl orcs would get together to produce baby orcs. But this doesn't square with the evidence. Never do we see any explicitly female orcs. Sure, Middle-earth is a bit like a boys' own fantasy, so this might not be a surprise. However, Tolkien goes to great pains to mention the existence of females in every other species, even when – as in the dwarves and the ents – they are offstage.

    Elsewhere, Tolkien says that Morgoth (Sauron's boss) created orcs from captured and tortured elves, but that could hardly supply enough orcs to make a small platoon, let alone armies. There had to be a way of creating orcs from other orcs.

    In The Science of Middle-earth I offer a suggestion that is at the same time radical and yet consistent with the evidence – orcs are, in some circumstances, parthenogenetic.

    I think an anthropological explanation is more likely. Tolkien's sympathetic races concern themselves with "home and family" themes, the unsympathetic races don't. We don't really get much of a look into orc culture, or the culture of the Men of Harad, for that matter, and this blind spot is intentional; without which it would be more difficult for the reader to accept them as morally inferior races.

  • J. Barnard Davis and the variation within races

    Mon, 2012-07-02 17:58 -- John Hawks

    Once again, I'm looking through source material for a very different reason, but ran across an interesting piece of history. J. Barnard Davis was a British physician and anatomist who, as a private collector, amassed an immense collection of nearly 1800 skulls. His studies on the cranial capacity of these skulls, including comparisons of skulls of different races, were cited by Darwin in The Descent of Man (which is what brought me to Davis' work).

    He published this work on human variation in the critical period between the 1859 publication of Darwin's Origin of Species and the 1871 publication of Descent of Man. During this period, Darwin did not publish on the subject of human evolution, but was engaged in a great deal of reading and correspondence on the subject. In his stead, publications and lectures by Huxley, Wallace, and others began to apply Darwinian principles to human variation.

    I may write more about Davis, but I wanted to make a note of a passage in the introduction to the 1867 catalog of his collection, the Thesaurus Craniorum [1]. He addresses the importance of a large collection of skulls, which among other things allows an assessment of the breadth of variation within populations. One consequence of our additional sampling of human variation in the 20th century was the recognition that variation among human populations was clinal -- with characteristics forming a gradient across geographic space.

    The extent of a collection is of much moment; for, besides affording more reliable averages of measurements, a large one is far more sure to illustrate the types of each race fully, and to contain its aberrant forms. The statement made by Prof. Theodor Waitz, that only small collections of race-skulls exhibit different forms of skulls strikingly whilst rich collections fill up the apparent intervening gaps and show a continual transition from every one form to every other, is only very partially correct, and is an assertion much more characteristic of a Professor of Philosophy than a Professor of Anatomy, essentially a science of observation. Although large collections, philosophically considered, must of necessity, by containing skulls that have intermediate forms, tend to lessen distinctions, they, at the same time, serve to develope [sic] race-characters more fully, and to define the play of diversities round these race-characters with more precision.

    The citation to Waitz is to Anthropologie der Naturvölker, 1859.

    From a certain point of view, Davis was correct: An increase of sample size will increase the range of the sample, but not greatly increase the proportion of overlap between samples drawn from two populations with different means. Large samples might increase a statistical precision in the description of races. Yet, Waitz' point is also correct. Large samples destroy the typological description of races by showing that no character uniquely typifies any human race. The effect of large samples on the range is often the key evidence that populations share common biology.

    Statistics is fundamental to population biology -- so much so that population geneticists like R. A. Fisher and Sewall Wright invented many statistical concepts. Until they understand statistical concepts, people seem inevitably drawn toward essentialism. Essentialism in the history of biology led to typological concepts of species, race, characters, and developmental stages, all of which explained variation in terms of deviation from the ideal type. We now appreciate that populations transform according to statistical rules, not typological rules.

    With his immense collection of skulls, Davis showed the extensive variation within populations. He argued so forcefully for the importance of variation that he predicted that the original Neandertal skull would be soon matched within the cranial diversity of living populations. Davis maintained that the skull's elongated shape and browridges could be explained as a result of craniosynostosis, premature closure of the cranial sutures. He looked to human pathology for anatomical intermediates with the Neandertals, arguing that the variation attributable to craniosynostosis would be found to grade continuously right up to the extreme found in the Neandertal skull. In other words, he argued against typology when it came to pathology.

    He turned out to be wrong about Neandertal, it was an overreach of his assumptions about variation in development. At the same time, he believed that "race-characters" were stable and that they reflected a long history of separation of human races. He provides an interesting case of how a nineteenth-century anatomist could toss a typological salad.


    References

  • Melungeon genetic roots

    Fri, 2012-05-25 09:28 -- John Hawks

    The AP is running a story about a recent genetic study probing the ancestry of the Melungeons.

    NASHVILLE, Tenn. (AP) — For years, varied and sometimes wild claims have been made about the origins of a group of dark-skinned Appalachian residents once known derisively as the Melungeons. Some speculated they were descended from Portuguese explorers, or perhaps from Turkish slaves or Gypsies.

    Now a new DNA study in the Journal of Genetic Genealogy attempts to separate truth from oral tradition and wishful thinking. The study found the truth to be somewhat less exotic: Genetic evidence shows that the families historically called Melungeons are the offspring of sub-Saharan African men and white women of northern or central European origin.

    This is the most well-known of a fairly large number of groups of country folk in the southern U.S. with obscure genealogical origins. The story goes on to discuss speculation that their ancestry may derive from indentured servants (of both races) in 1600's Virginia. Whether or not that specific suggestion is correct, shortly after their founding, the American colonies were a remarkably fortunate place for early immigrants. Poor and largely illiterate people who made the crossing had remarkable health, survival rates and fertility by Old World standards. Written history at the level of towns is sometimes surprisingly dense for the early colonies, but was produced by the literate, following their own concerns. Genetics may recapture the dynamics of the lost history of the early colonies, if not the details.

  • The H preparation

    Tue, 2012-05-08 08:48 -- John Hawks

    Razib Khan comments on the current round of Henry Louis Gates ancestry programming: "Finding fake roots", and "Reification is alright by me! Razib notes that the criteria that tell many subjects that their ancestry is a mixture of different populations are conditioned on assumptions that don't work at all for South Asians. From the latter:

    In my post below some commenters argued that obviously implausible inferences from a thin set of reference populations are acceptable considering Henry Louis Gates Jr’s target audience. But that really wasn’t my main point. Rather, it was that he was eliding the distinction between uniparental markers, and the clusters generated by modeled based ancestry assignment algorithms, and ascribing the phylogenies of the former to the latter. It is important to note that categories like “Europeans” are only approximations. But they’re damn good approximations today! Nevertheless, note the qualification of time: they may have basically no meaning at some point in the recent past. They’re powerful when it comes to precisely partitioning modern variation, but they don’t tell us the history of that variation.

    The uniparental marker "interpretations" given to people doing genealogical work has become increasingly comical in its distance from what we now know about ancient variation. For example, I carry mtDNA haplogroup H, and here's what the Genographic Project tells me about that history in their "Atlas of the Human Journey":

    Around 15,000 to 20,000 years ago, colder temperatures and a drier global climate locked much of the world's fresh water at the polar ice caps, making living conditions near impossible for much of the northern hemisphere. Early Europeans retreated to the warmer climates of the Iberian Peninsula, Italy, and the Balkans, where they waited out the cold spell. Their population sizes were drastically reduced, and much of the genetic diversity that had previously existed in Europe was lost. Beginning about 15,000 years ago -- after the ice sheets had begun their retreat -- humans moved north again and recolonized western Europe. By far the most frequent mitochondrial lineage carried by these expanding groups was haplogroup H. Because of the population growth that quickly followed this expansion, this haplogroup now dominates the European female landscape.

    Here, a very common mtDNA haplogroup today is given its own origin myth, complete with a glacial refugium and massive expansion and dispersal. The text goes on to explain how this European haplogroup spread right out of southern Europe into central Asia, where today -- surprisingly -- it is even more variable and shows less sign of expansion. Notice how precise the story sounds, a fleshed-out history for people looking to connect their roots to European prehistoric events.

    Why do I say comical? We have ancient mtDNA from all over Europe now, from Neolithic and pre-Neolithic people, showing that haplogroup H was barely there before farming.

    I don't mean to single out Genographic for this issue, in fact the whole edifice of genealogical interpretation is built on assumptions about history that are currently known to be false. We can do much better than this, I think. But many of the same characters who failed five or six years ago keep plugging at it, persisting in describing a distorted version of human history.

    UPDATE (2012-05-08): The thing that really bugs me, is that the amount of money spent producing a season of one of these programs would be more than enough to get some of us to straighten some of these problems out. Population genetics is a lot cheaper than media. Or, to put it in a more inspiring way: any media organization that is willing to spring for a couple of postdocs along with their program can show some real science instead of making stuff up. Just saying...

  • Understanding population differentiation

    Mon, 2011-11-28 00:48 -- John Hawks
    Synopsis: 
    Devising a story problem to illustrate Fst as a measure of population differentiation

    This lab has a take-home assignment, which is worth three points when you turn it in at next week's lab section.

    The genetic differentiation among populations is very important to understanding human diversity and its historical origins. The basic measurement of population differentiation is FST. You will be designing and providing the solution to a problem involving FST.

    1. Use the "Measuring population subdivision" exercise as an example to follow.
    2. You can also refer to the "Measuring differences between populations" text.
    3. Design a story problem with three populations.
    4. Your problem should involve a single gene locus, with two alleles. Each of the three populations should have a frequency for each allele (remember, the two will add to 100%).
    5. Show how FST should be calculated in your problem, with your allele frequencies.
    6. Use 1-2 sentences to explain what aspect of population differentiation your problem helps to illustrate. For example, does it show an example with one extremely different population? With very similar populations?

    Bring your story problem back to lab next week.

    Study terms: 
  • Measuring population subdivision

    Sun, 2011-11-27 22:58 -- John Hawks
    Synopsis: 
    The statistical measurement of differentiation among populations is Fst

    The basic measure of genetic difference between two populations is the statistic, FST. In genetics, the term F generally stands for ``inbreeding'', which tends to reduce genetic variation in the population. Genetic variation can be measured by heterozygosity, and so F generally expresses a reduction in the heterozygosity in the population. FST is the reduction in heterozygosity in subpopulations compared to the total population of which they are part.

    To estimate FST, take the following steps:

    1. Find the allele frequencies for each subpopulation.
    2. Find the average allele frequencies for the total population.
    3. Calculate the heterozygosity (2pq) for each subpopulation.
    4. Calculate the average of these subpopulation heterozygosities. This is HS.
    5. Calculate the heterozygosity based on the total population allele frequencies. This is HT.
    6. Finally, calculate FST=(HT-HS)/HT.

    Don't forget that the HS term is the average across all subpopulations.

    Example: The gene SLC24A5 is a key part of the melanin expression pathway, which contributes to skin and hair pigmentation. A SNP that is strongly associated with lighter skin pigment in Europe is rs1426654. The SNP has two alleles, A and G, with G being associated with light skin, at a frequency of 100% in Utah European-Americans. The SNP varies in frequency in populations in the Americas with mixed African and American Indian ancestry. A sample in Mexico had 38% A and 62% G; in Puerto Rico the frequencies were 59% A and 41% G, and a sample of African-Americans from Charleston had 19% A with 81% G. What is the FST in this example?

  • Cranial features and race

    Sun, 2011-11-27 21:51 -- John Hawks
    Synopsis: 
    A primer on assigning forensic race to crania based on their morphology

    Individuals whose ancestry derives mostly from different parts of the world sometimes have different cranial features. Forensic anthropologists have studied these differences for many years, finding some that are especially useful for distinguishing ancestry. In American legal contexts, ancestry is usually at issue as a way of determining the racial affinity of unidentified skeletal remains. Hence, the forensic anthropologist usually tries to make a determination as to whether a skull has features that indicate African, European, Asian or Native American ancestry.

    Cranial features are not perfect indicators of ancestry: Forensic anthropologists using multiple features claim at best 85% accuracy in their assessment of racial ancestry. When we know less about the context of a skull, we will be less and less accurate.

    Here are some traits that vary between skulls with different race backgrounds. Most of them are on the face or palate.

    • Shape of the eye orbits, viewed from the front. Africans tend to a more rectangular shape, East Asians more circular, Europeans tend to have an ``aviator glasses'' shape.
    • Nasal sill: Europeans tend to have a pronounced angulation dividing the nasal floor from the anterior surface of the maxilla; Africans tend to lack a sharp angulation, Asians tend to be intermediate.
    • Nasal bridge: Africans tend to have an arching, ``Quonset hut'' shape, Europeans tend to have high nasal bones with a peaked angle, Asians tend to have low nasal bones with a slight angulation.
    • Nasal aperture: Africans tend to have wide nasal apertures, Europeans narrow.
    • Subnasal prognathism: Africans tend to have maxillae that project more anteriorly (prognathic) below the nose, Europeans tend to be less projecting.
    • Zygomatic form: Asians tend to have anteriorly projecting cheekbones. The border of the frontal process (lateral to the orbit) faces forward. In Europeans and Africans, these face more laterally and the zygomatic recedes more posteriorly.

    What to do: This station includes several casts representing skulls of different ancestries, along with one ``mystery skull''. Examine the features that vary by ancestry in this skull, comparing it with the others. Can you assess the racial origin of the mystery skull?

  • Braiding Denisovans into our ancestry

    Fri, 2011-11-04 10:39 -- John Hawks

    Dalton Luther reflects on the Denisovan admixture paper [1] that I wrote about earlier this week ("How widespread is Denisovan ancestry today?"), by referring to John Moore's work on ethnogenesis [2].

    Getting back to the original quote about Denisovan legacies, just because the Denisovans aren’t “around” anymore, doesn’t mean they’re not “around.” An ancient population is present even though in a very different form. Using the braided river metaphor, the name Denisovan refers to the contents of a particular stream that mixed back into another stream, which grew larger, amplifying its original contents.

    What seems to be the challenging concept to some geneticists is that some people today have that legacy and others don't. But it's not at all unusual for that to be true of families, kindreds, cultural traits, or even languages. So why should it be unusual for populations?


    References

    1. Skoglund P, Jakobsson M. Archaic human ancestry in East Asia. Proceedings of the National Academy of Sciences, U. S. A. 2011;108(45):18301-18306.
    2. Moore JH. Putting anthropology back together again: the ethnogenetic critique of cladistic theory. American Anthropologist. 1994;96:925–948.
  • Gould's "Unconscious Manipulation of Data"

    Wed, 2011-06-08 18:59 -- John Hawks

    OK, so I can't say it's not "brain science" because measuring skulls is as close to brain science as anthropology ever gets. But it just shouldn't be that hard to measure volume. It's a simple physical fact.

    Sure, there are complexities in measuring the volume of an object with a complicated shape and holes, like a human skull. But this is not one of the world's great mysteries. Seal the holes, fill the skull with beads or shot or something, and pour it into a graduated cylinder. Junior high stuff.

    Samuel Morton became famous in the mid 19th century as an empirical scientist for measuring the skulls of people from different parts of the world. Stephen Jay Gould claimed, first in Science in 1978 [1] and later in his book The Mismeasure of Man [2], that Samuel Morton fudged his data on skull volumes. In Gould's telling, Morton began with a strong bias toward finding that Caucasians were the superior race and made several choices in measurement and reporting statistics that tended to confirm this bias. Gould's biggest claims, in a statistical sense, were fairly obscure statistical points about the tabulation of averages and treatment of subpopulations as compared to major race groups. One claim, however, was more memorable than all the rest -- the notion that Morton used seed to measure the skulls and packed it in harder with his thumb to increase the measured volume of "White" skulls.

    Most people probably suppose Gould to have been an expert on the Morton collection, but in fact he never examined or measured the crania himself. A new paper in PLoS Biology by Jason Lewis and colleagues [3] accomplishes what no one else did in the succeeding 30 years (despite one earlier attempt): they checked Gould's facts. They find that again and again, Gould misstated the evidence or simply made stuff up.

    This is an important paper. The authors wrote in an even tone and lay out the facts in a very straightforward way. As a reader, I can't see how they managed to keep their cool. Some of Gould's mistakes are outrageous, with others it is hard for me to believe that the misstatements were not deliberate misrepresentations.

    For example, let's take the story about pushing seed into the skulls. Here is a paragraph from Lewis and colleagues, with direct quotes from Gould:

    Gould famously suggested that Morton's measurements may have been subject to bias: “Plausible scenarios are easy to construct. Morton, measuring by seed, picks up a threateningly large black skull, fills it lightly and gives it a few desultory shakes. Next, he takes a distressingly small Caucasian skull, shakes hard, and pushes mightily at the foramen magnum with his thumb. It is easily done, without conscious motivation; expectation is a powerful guide to action” [5]. While Gould offers this as only a “plausible scenario,” and did not remeasure any crania, subsequent authors have generally (and incorrectly) cited Gould as demonstrating that Morton physically mismeasured crania (e.g., [15]).

    In other words, Gould made up the whole thing. It was an utter fabulation. It is disgraceful that later authors have cited this idea as fact.

    When Lewis and colleagues examined Morton's numbers they found that there had been no bias in the direction Gould claimed. Measurements from seed had greater error than those from lead shot, in part (as Morton himself had written) because he employed an assistant for seed measurements early on, but later did these personally with shot.

    Moreover, Lewis and colleagues systematically remeasured the volumes of a sample comprising half of the skulls Morton measured, and found no systematic bias, with the few deviations in Morton's data actually in the direction opposite his supposed bias.

    With numbers like these, it is natural to wonder exactly where Gould came up with his idea that Morton's numbers were fudged. Here's how: Gould fudged his own numbers! I'm quoting here a long passage from the paper, because it is essential to understand Gould's full perfidy.

    Gould also performed his own analysis of Morton's cranial capacity data and came to the conclusion that “there are no differences to speak of among Morton's races” ([1], italics in original). For Morton's 1839 seed-based measurements, Gould claims that Morton's Native American average capacity is artificially depressed by his inappropriate use of a straight mean (taking the average of each individual specimen in the entire sample) rather than a grouped mean (first taking the average of each Native American population subsample, then calculating the mean of those means), since the former is sensitive to differences in sample sizes between “large headed” populations and “small headed” populations. In fact, the grouped mean for Morton's Native American dataset is 79.9 in3, almost identical to the straight mean of 80.2 in3 (Dataset S3). So Morton's use of a straight mean actually slightly increased his Native American average. Gould's calculation of a higher Native American average (83.8 in3) is entirely a function of Gould omitting 34 crania (of 144) as coming from populations with samples of n

    Gould's reanalysis of Morton's 1849 shot-based data resulted in a Native American mean capacity of 86 in3 rather than Morton's original 79 in3 [1]. Gould obtained his new average by again taking the group mean of Native American populations with four or more crania. But Gould also applied an additional restriction: he only included Native American crania that Morton had also previously measured with seed. This restriction is entirely arbitrary on Gould's part, as Morton's publications and analyses for his seed- and shot-based measurements are completely separate (1839 versus 1849), and Gould did not apply this restriction to the other groups he reanalyzed in Morton's shot-based data. If this restriction is lifted, Gould's Native American average would be reduced to about 83 in3, considerably below his reported 86 in3 (Dataset S3).

    Here is the most sympathetic reading I can give to these facts. Gould systematically selected data from Morton's tables that tended to inflate the measured volumes of Native American crania. He did so by averaging some group means instead of overall means (although Lewis and colleagues show that Morton himself had used group means for many comparisons, contrary to Gould's claims), by excluding some small-skulled groups entirely (claiming sample size as a criterion), and by omitting crania that had not been measured in the earlier, seed-based analysis. There is no logical reason for these choices other than selection bias -- Gould began with a conclusion about Morton's unconscious motivations, and worked to confirm that conclusion by selecting some data and omitting contrary data.

    Anyway, you can see why I find this outrageous. Gould used the well-documented work of a long-dead man to make an argument that unconscious bias is widespread in science. He posed as a concerned critic, but thereby cast doubt on the validity of the scientific enterprise. He picked volume measurement and tabulation of averages as his target, making it seem as if the simplest and most objective observations -- the Junior High-level science methods -- were themselves subject to all-encompassing cultural biases. His paper and book are very widely read and cited by people who will never examine the primary evidence. Gould owed us a responsible reading and trustworthy reporting on that evidence. In its place, he made up fictional stories, never directly examined the evidence himself, and misreported Morton's numbers.

    This stuff really ticks me off. I don't think that Gould's errors can be written off as "unconscious bias". Reading back over his 1978 article, I cannot believe that Science published it.

    The new paper is open access ("The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias"), and I think that everyone should read it. The text is easy to follow, and the authors include clear answers to common questions about Morton's work and beliefs. It is a very suitable article for assignment in classes. They note that the basic issue here (endocranial volume of different groups) is largely explained by ecogeography -- the authors mention climate explicitly, but I would add body size and life history as parameters that covary with climate. Measurement of endocranial volume was cutting edge science in 1840, but I repeat, this is simple stuff.


    References

    Synopsis: 
    A team of anthropologists finds that Stephen Jay Gould systematically misrepresented the work of Samuel George Morton.

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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.