john hawks weblog

paleoanthropology, genetics and evolution

phylogenetics

  • When anthropological and geological facts collide

    Mon, 2011-11-28 01:56 -- John Hawks

    This passage is the first paragraph of the introduction to Franz Weidenreich's monograph, The Skull of Sinanthropus pekinensis [1].

    In my earlier contributions to the study of Early Man I pointed out repeatedly the danger of confusing anthropological facts with geological facts. In determining the character of a given fossil form and its special place in the line of human evolution, only its morphological features should be made the basis of decision; neither the location of the site where it was recovered nor the geological nature of the layer in which it was imbedded [sic] are important. Discrepancies cannot be smoothed out by bringing morphological facts and opposing geological data into closer harmony with artful interpretations or by touching-up reconstructions. It is a generally accepted conception that Man has developed in the course of time by gradual transformation from an ape-like type to the type he presents today. Viewed from this fundamental standpoint, it is logical to assume that the more a form resembles the supposed ancestor the more ancient it will be, or that the more ancient it is the more "primitive" it should be.

    I am concerned with this passage today because of a re-emerging mismatch of evidence from the morphology of Middle Pleistocene humans and the genetics of Neandertals. Some paleoanthropologists have asserted that Europeans of the Middle Pleistocene were the exclusive ancestors of Neandertals. I have in the past written that Middle Pleistocene Europeans were among the ancestors of Neandertals, with sustained gene flow from other populations including Africa [2]. The Sima de los Huesos people, maybe 600,000 years old, resembled the (much) later Neandertals in several aspects of their anatomy, as did other Middle Pleistocene Europeans.

    The genetic differences between living people and the ancient Neandertal genomes appear consistent with the emergence of distinct African and Neandertal populations only within the last 400,000 years or less [3], [4].

    Such a recent date seems a poor match for the morphological evidence of Neandertal ancestry in Europe. I can think of several ways to make these morphological and genetic comparisons concordant with each other, all of which balance some shift in one body of inference against the other. As long as we can't pin down the human mutation rate within a factor of two ("What is the human mutation rate?"), there's a lot of room to make different population models consistent with the genetic data.

    This is, in today's language, Weidenreich's point. Morphological data must be interpreted in accordance with evolutionary principles, and if it doesn't fit a temporal scheme, it doesn't fit. Likewise, genetic similarities must be explained in their own evolutionary framework. These two sources of evidence must in the end be consistent with a single history. We will find that consistency not by shoehorning the evidence together, but by interpreting each with the strongest possible skepticism concerning assumptions and models.

    Weidenreich's introduction illustrates two cases. The simpler, from our point of view today, was Piltdown. Many establishment anthropologists, particularly in Britain, had maintained that Piltdown was a morphologically advanced ancestor of modern humans, which had lived early in the geological record of human evolution. Weidenreich had been an early and prominent critic of this idea, because he was convinced that the specimen simply did not fit together with its supposed geological context.

    I cannot believe, even making very liberal allowances for these uncertainties, that such incongruity between morphology and chronology as is found in the case of Piltdown can be completely brought into accord. The only hope of solution in this case would lie in assuming that the human bones were not contemporaneous with the layer in whih they were found but were deposited there later. Otherwise, modern man must be much more ancient than we ever imagined, or else Western European man did not pass through evolutionary stages as did the hymans of other regions of the earth.

    We now know, of course, that Weidenreich was entirely correct. The apparent geological facts were false, and the "advanced" characters of the specimen were simple reflections of the fact that the skull is a modern human skull.

    The other problem Weidenreich discussed in some detail was the phylogenetic position of the Steinheim skull. Like Piltdown, this specimen had been placed in a Presapiens context by other workers. Steinheim lacks most of the derived characteristics of later Neandertal specimens. Weidenreich, along with many of his contemporaries, accepted its lack of Neandertal features as evidence for affinity with modern humans. In Weidenreich's view, this similarity with modern humans was "anachronistic". Even so, the case did not challenge an evolutionary interpretation, only the assumption that features could evolve from "primitive" to "modern" along a single line. If we admit that Neandertal features were not in all cases "primitive", even if they may resemble superficially the characteristics of some apes, we can accommodate specimens like Steinheim within a population model where both moderns and Neandertals may have derived (and in some cases, secondarily derived) characters that appeared afterward.

    This scenario requires us to straighten out the analysis of the characters themselves, a process for which larger fossil samples are essential. It was to that end that Weidenreich supposed the Sinanthropus sample to be of such great utility. The subtext of the introduction was to illuminate the kinds of evolutionary problems that could be further illuminated by a full description of fossil variation. Finding variation in fossil humans did not repudiate the concept that modern humans had evolved in stages from primitive ancestors, but helps to clarify cases where the evolution has not been a simple linear progression. In many cases, features that are superficially "primitive" may actually have been secondarily derived in recent humans compared to earlier hominins.

    Along similar lines, I ran across this old post: "Dobzhansky on Weidenreich's species concept", in which Dobzhansky predicts:

    Some modern populations may carry genes that were present in the Neanderthaloids, and other moderns may not carry such genes.


    References

    Synopsis: 
    Weidenreich's introduction to the Sinanthropus cranial monograph illuminates some issues I'm facing with ancient genomes.
  • Questioning phylogenetic inferences about language

    Sat, 2011-11-26 21:59 -- John Hawks

    Bruce Bower of Science News enters an article covering the last year of application of phylogenetic methods to questions of language evolution: "Darwin's Tongues".

    He gives a description of work by Quentin Atkinson and Russell Gray and colleagues, which have attempted to place the origination of modern human languages (in Africa, naturally), and separately have challenged the Chomskian assertion that human languages are constrained by deep structure. A number of linguists challenge these conclusions, and Bower describes the debates ably.

    Others suspect Atkinson’s analytical approach could be fruitful if informed by more sophisticated assumptions about how languages change. “I think many linguists would praise Atkinson’s contribution if it weren’t for the fact that his conclusions are so outlandish and contrary to linguistic intuition,” says linguist Michael Cysouw of Ludwig Maximilians University Munich in Germany.

    I think criticism of these approaches is in the "throw everything and see what sticks" phase. I've seen it before, in the modern human origins arena. In this phase, many of the criticisms lack force -- they emerge from skepticism about the conclusions, not necessarily an understanding of the method. That means the method has not yet been described in ways sufficient for linguists to understand its limitations, nor has it been applied in contexts where the answer is already well known from other approaches. Personally, I think the phylogenetic methods being applied to linguistic corpus data are statistically very useful and powerful, but that doesn't mean the alternative hypotheses have been differentiated cleanly from each other.

  • Quote: Higher-level taxa

    Sat, 2010-04-03 11:17 -- John Hawks

    I ran across this passage in a book chapter by D. Tab Rasmussen, covering early catarrhine evolution. I think it captures an important point about the fossil record:

    Ironically, debates about higher level taxonomy often increase as the density of the fossil record improves. Higher-level taxa were initially defined and diagnosed as such because the species that happened to survive to the present often clump into distinct groups, each easily defined by a substantial assemblage of shared specialized traits and well separated from its nearest relatives. But the gaps between extant forms are only an illusion generated by extinctions, and the fossil record fills in the gaps. One by one, supposedly diagnostic traits are peeled away from the assemblage so that the recognition of a higher taxon comes to rely on fewer and fewer traits, thus becoming less and less reliable. The cranium of Aegyptopithecus showed, for example, that the tubular ectotympanic is not a diagnostic catarrhine trait, and Catopithecus demonstrated that mandibular fusion is not a diagnostic anthropoid trait. Our assessment of Catopithecus as an anthropoid or as a catarrhine now depends on a controversial fraction of the characters that were initially used to define these clades. As the fossil record improves paleontologists must inevitably place less value on assemblages of shared derived features found within living clades and rely more on evolutionary patterns that are discernible in the stratigraphic and geographic contexts of the morphological finds.

    References:

    Rasmussen DT. 2002. Early catarrhines. Pp. 203-220 in Hartwig WC, ed, The Primate Fossil Record. Cambridge University Press, Cambridge UK.

  • Domesticated yeast face ancient amber-yeast competitors

    Tue, 2008-09-23 22:27 -- John Hawks

    So, they've resurrected 45-million-year-old yeast from amber, and are using it to brew beer under the "Fossil Fuels" label:

    The beer has received good reviews at the Russian River Beer Festival and from other reviewers. The Oakland Tribune beer critic, William Brand, says the beer has "a weird spiciness at the finish," and The Washington Post said the beer was "smooth and spicy."

    Part of that taste comes from the yeast's unique metabolism. "The ancient yeast is restricted to a narrow band of carbohydrates, unlike more modern yeasts, which can consume just about any kind of sugar," said Cano.

    I have this incredible compulsion to taste the stuff. Actually, I really like the entire idea of the taste qualities of these micro-adapted yeast strains -- which go into everything from San Francisco sourdough bread to the wild yeasts living on grape skins in Bordeaux.

    But last week I went to a talk by Alan Moses, who's been working in "population genomics" -- essentially, comparative population genetics taken across the genome. The major model organisms for this work so far have been yeast -- the domesticated Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. There were a lot of interesting things coming out of that work (not only about yeast, but also about people and mice).

    One of the easiest analyses was a simple overlay of phylogeny on geography for the two yeast species, described in a preprint by Moses' collaborators on Nature Precedings. The wild S. paradoxus has a very clear population structure, with genetically distinct populations in Europe, America, East Asia, and Hawaii. These populations are easily pulled out of a STRUCTURE analysis, so there are a large set of distinctive alleles that characterize them.

    In contrast, the domesticated S. cerevisiae has been extensively crossed, hybridized, and managed by humans. This has led to a population structure that does not clearly distinguish strains by their geographic locations -- and in fact, strains are not easily distinguished by their use (wine versus sake, for instance). The geographic structure has largely been smudged out of existence by human intervention and recombination between strains. Moreover, some changes of adaptive importance, such as nonsense or missense mutations in the galactase pathway, have been repeated more than once in these human-managed strains. That's a very clear contrast, and other aspects of the genomic variation bear the marks of selection.

    To me, there is a practical import to these analyses. If the domesticated strains have tuned in countless ways to operate in our food, what are the chances that genuine "wild" strains of yeast have actually persisted for years and years in the face of this boundary-crossing contact between yeasts? We say that these are original wild yeasts, because a lump of starter has been replenished and renewed for years and years, or because the natural yeasts enter from the grape skins, or some other story. But that starter is not in a hermetically sealed chamber, and people don't put on bunny suits to work on it. Our gregarious domestic yeast strains have gotten in there, and they've probably replaced the original yeast strains many times over.

    So, if we take yeast out of 45-million-year-old amber, what are the chances it's going to last long in culture? Maybe it will do surprisingly well. But this is a case where genetic barcoding might be in order.

    References:

    Carter D, Liti, G, Moses A and 22 others. Population genomics of domestic and wild yeasts. Preprint. Available at Nature Precedings

Subscribe to phylogenetics

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.