Chaw joins poop in archaeology arsenal
Well, archaeology is set to receive a once-in-a-generation influx of interest from teenagers drawn to the allure of the past. I mean, from the new Indiana Jones movie, of course.
So what do they have to go and do? Discover a real life crystal skull? Sorry, kids. If you want to be an archaeologist, it's all bodily functions from here on out.
Tom Dillehay and colleagues (2008) report in this week's Science that they have found chewed-on seaweed "cud" from Monte Verde, dated to 14,000 calendar years BP. And that paper is right next to the final publication of the Paisley Caves coprolites from Oregon, also dating to slightly before 14,000 calendar years BP.
Both papers are pretty cool -- together they emphasize that these kinds of forensic evidence are becoming increasingly important in documenting the activities (and existence) of archaeological populations. After all, a person has to poop thousands of times during his life, but he has only one skeleton.
Dillehay and colleagues interpret their seaweeds as a specialized medicinal collection, based on the presence of non-edible species and species present at different times of the year. Here's a quote from Michael Balter's news piece on the find:
Back 14,000 years ago, Monte Verde was located about 90 kilometers east of the sandy Pacific coast and 15 kilometers north of a rocky-shored inland marine bay. Algae from both environments were recovered, including inedible species that are today used as medicines in Chile and elsewhere. Moreover, the algal species found are known to flourish at different times of the year, suggesting to Dillehay's team that the Monte Verdeans were intimately familiar with coastal resources--possibly because they had originally arrived in the region via that route. Erlandson agrees: "The variety of seaweeds implies a pretty deep knowledge of coastal ecosystems and a long history of exploiting them."
Well, that's pretty impressive, even if the seaweed were chewed up. And hey, my kids are much more interested in bodily functions than they are in crystal skulls. So maybe this will bring in new archaeologists after all!
References:
Balter M. 2008. Ancient algae suggest sea route for first Americans. Science 320:729. doi:10.1126/science.320.5877.729
Dillehay TD, Ramírez C, Pino M, Collins MB, Rossen J, Pino-Navarro JD. 2008. Monte Verde: Seaweed, food, medicine, and the peopling of South America. Science 320:784-786. doi:10.1126/science.1156533
Gilbert MTP and 12 others. DNA from pre-Clovis human coprolites in Oregon, North America. Science 320:786-789. doi:10.1126/science.1154116
Death, lye thou there
Since they first walked the planet, humans have either buried or burned their dead. Now a new option is generating interest -- dissolving bodies in lye and flushing the brownish, syrupy residue down the drain.
Generally, I'm most interested in the processes that give rise to dry bones. Particularly, dry bones that don't smell bad.
"Syrupy residue," on the other hand, is not really my thing. And I guess it's not really most people's thing:
Getting the public to accept a process that strikes some as ghastly may be the biggest challenge. Psychopaths and dictators have used acid or lye to torture or erase their victims, and legislation to make alkaline hydrolysis available to the public in New York state was branded "Hannibal Lecter's bill" in a play on the movie character's sadism.
The appeal seems to be that this generates fewer emissions than cremation -- think of it as an elaborate sort of carbon sequestration. And it has to be better than pouring embalming fluid down the drain.
UPDATE(2008/05/08): Miguel Capriles writes:
[J]ust a quick comment about your post "Death, lye thou there": the reference to the "syrupy residue" made me recollect one of John Aubrey's Brief Lives when he tells about the coffin of John Colet, broken after the Great Fire of London in 1666. Aubrey tells (in modern English, as I got it on Google Books in a version published in 1982 by Boydell & Brewer):Â
"After the conflagration, his monument being broken, his coffin, which was lead, was full of a liquor which conserved the body. Mr Wyld and Ralph Greatorex tasted it and 'twas of a kind of insipid taste, something of an ironish taste. The body felt, to the probe of a stick which they thrust into a chink, like brawn. The coffin was of lead and laid in the wall about two and a half feet above the surface of the floor."
Definitively it should be a lot nicer in the English Aubrey used.
And that, my friends, is why it is cool to have a blog. Because my readers have much better imaginations than mine.
Ooooh, they tasted it?!
Were ancient Africans divided into small, isolated bands?
Last week when I wrote about the study of African mtDNA variation by Behar and colleagues, I focused on the issue of population size. To me, that must be the first parameter that we try to estimate, because the simplest relevant model of population history -- the Wright-Fisher model -- is described by that single parameter: the number of individuals. If we are going to evaluate evidence for population structure, we first must deal with the question of size.
The claim in the press release is that the African population was divided into separate populations:
Doron Behar, Rambam Medical Center, Haifa, said: "We see strong evidence of ancient population splits beginning as early as 150,000 years ago, probably giving rise to separate populations localized to Eastern and Southern Africa. It was only around 40,000 years ago that they became part of a single pan-African population, reunited after as much as 100,000 years apart."
Is it true? Certainly that describes the model tested in the paper. But is it the right model? Is there evidence to justify that model as opposed to simpler alternatives?
A real population may be structured in many ways -- by age, by caste or class, by space. If we have samples that are taken from different geographic locations, as in this study, it is natural to test hypotheses about structuring across geography. That's what Behar and colleagues did: they tested a hypothesis of panmixia, or random mating across space.
Panmixia is the simplest model -- the null hypothesis -- about population structure. If everyone mates randomly, then there is no geographic structure. The population would be a single, unstructured gene pool. The paper refutes this model, demonstrating that people did not mate randomly across the geography of Africa during a certain period of time.
But the question is: which model do we adopt once we have refuted panmixia?
I rather like isolation-by-distance as a model for human population history. Isolation-by-distance (IBD) assumes that people travel some distance before they reproduce. It's a simple model -- the distance traveled may vary among individuals, but the variance in this value is the only parameter necessary to predict the structure of the population. IBD can explain quite a lot -- why people look like their neighbors, why intermediate populations on the map tend to look intermediate in allele frequencies, and why selected alleles take some time to disperse across space. It is generally consistent with what we know about hunter-gatherer demography. People tend to stay where they are, but a fairly large fraction move to marry into neighboring groups, and a smaller fraction go beyond the neighboring groups to marry further away. So I think this is the null hypothesis once panmixia is refuted. IBD is not a hypothesis of small, isolated bands -- it is a hypothesis of a geographically dispersed population with gene flow.
The Genographic Project has done more than any other single project to extend the sampling of human populations. The paper by Behar and colleagues is a testament to that -- they are able to work with a broader and deeper sampling of mitochondrial variation in Africa than has yet been available. This is a credit both to the ambitious goals of the project and to today's genetic technology, which has made it possible to sequence more whole mitochondrial genomes on the project's budget. It is a great example of how spending money can circumvent some theoretical problems.
Still, the Project likely wanted to maximize the effectiveness of its money, so it focused on sequencing only those variants that were underrepresented or rare in previous studies. From the Methods:
Samples were chosen to include the widest possible range of Hg L(xM,N) internal variation on the basis of the previously available sequence analysis of the mtDNA control region and are, therefore, biased toward rare variants. In addition, we attempted to focus on branches (e.g., L0d, L0k), populations (e.g., Khoisan), and geographic regions (e.g., Chad) for which the current data were scant. Last, we preferred to sequence variants that the current literature suggested to be rare or anecdotal in any given geographic region (e.g., L0k in the Near East).
Ummm... wait a minute. This is definitely not what you want to do if you're going to test hypotheses of population history. They have deliberately narrowed their sample in a way that distinguishes Khoisan from other peoples, and have excluded some proportion of variants already known to be common. We can predict, based on the sampling scheme alone, that Khoisan and other people ought to be more distinct that would be expected under a random sampling of each population, and certainly more so than expected under a random sampling of the African continent. This means that if the data were to reject IBD, we would have to examine whether that was because of the population history, or instead because of the sampling scheme.
Do the data reject IBD? Well, we don't actually know from the paper. The study employs an island model, in which Khoisan and all others are assumed to represent either one panmictic population or two isolated ones. They devised a test based on permuting the number of lineages that they inferred to have existed during past time intervals. An island model with isolation of two populations predicts that each will share some gene lineages lacking in the other -- so-called "private" haplotypes. In contrast, two samples taken from a single panmictic population would each have a small proportion of "private" haplotypes, as well as some number of common haplotypes shared by both samples.
So, the study (reasonably) tests the null hypothesis that the African mtDNA samples derive from a single panmictic population going back to the mtDNA coalescent. They estimate the date of this coalescent (based on their mutation rate model) as around 200,000 years ago, so this is a test of panmixia in Africa across this time period. They use a permutation test to evaluate the likelihood that some number of closely related lineages would all be private to the Khoisan population, under the hypothesis that they are randomly drawn from the African population as a whole. The lineages they examine are the ones they infer to have been present in the Khoisan population at various time intervals in the past -- again, based on their model of mutation rate. They can disprove panmixia across times after 100,000 years and before 80,000 years. Before this time, too few coalescent lineages are inferred to have existed to obtain a significant refutation of the test of panmixia. After 40,000 years, there are obvious shared lineages between Khoisan and other samples that could only have been shared by gene flow.
I worry that there is a bias in this test. The authors applied it only to a period of time earlier than the coalescence times of recent shared lineages, but after the diversification of the ancient lineages that are not shared. In other words, there appeared to be a gap in the coalescence times of shared haplogroups. Usually, you would correct the test for multiple comparisons not only across haplogroups, but also across time periods. Given that we are considering a range of 150,000 years, across which there is evidence for gene flow both early and late in that history, what is the significance of the fact that we see few shared lineages at intermediate times? That will be less significant than the values reported in the paper, but how much less it is difficult to predict.
In the end, what do the observations in the paper mean? In the simplest interpretation, either Africans were not random-mating after 100,000 years ago or regional selection differentiated southern and other African mtDNA pools.
Did ancient Africans live in two isolated groups? I wouldn't say that: the authors didn't test that hypothesis.
Did ancient Africans live in small bands scattered across the continent? Well, all ancient humans lived in small bands. The question of whether they were scattered is a question about the population size -- and as I showed last week, the population size during this period of time was not small. So we can imagine a population structure like recent historic hunter-gatherers -- with Africa possibly having something like the population size and structure of indigenous Australians.
What's the bottom line? The results are consistent with isolation-by-distance in ancient Africans. That model, followed by a subsequent global expansion, has been around for a long time. In 1993, Henry Harpending and colleagues called it the "Weak Garden of Eden" model: a geographically structured African population that underwent an expansion and dispersal to other regions. Certainly for the mitochondrial DNA, this seems to be the model that presently best fits the data.
What remains in question is how much of the subsequent spread of mtDNA was also reflected by spread of nuclear DNA haplotypes, and how much was induced by natural selection on mtDNA haplogroups. As I continue to write about population histories, we will meet this issue again.
References:
Behar DM, 14 others, and The Genographic Consortium (consortium again? Whoa). 2008. The dawn of human matrilineal diversity. Am J Hum Genet 82:1-11. doi:10.1016/j.ajhg.2008.04.002
John Hawks Department of Anthropology
University of Wisconsin—Madison
Copyright © 2007 John Hawks