john hawks weblog

paleoanthropology, genetics and evolution

out-of-Africa

  • Lost in Arabia

    Thu, 2010-09-23 19:38 -- John Hawks

    The BBC is reporting on a talk by archaeologist Michael Petraglia, at the British Science Festival:

    But Dr Michael Petraglia, of Oxford University, and colleagues say stone artefacts found in the Arabian Peninsula and India point to an exodus starting about 70,000 to 80,000 years ago - and perhaps even earlier.

    ...

    "I believe that multiple populations came out of Africa in the period between 120,000 and 70,000 years ago," he said. "Our evidence is stone tools that we can date."

    Most of the tools are from far inland - hundreds of kilometres from the coasts. This means it was more likely humans migrated by land than in boats, he said.

    I think the Neandertal genome has pretty much killed the "southern route" theory that had modern humans beachcombing their way across the Bab-al-Mandab.

    Right now we're investigating the genetics, I'll hopefully be able to share some details soon.

    Tags: 
    Late Pleistocene
    West Asia
    Arabia
    out-of-Africa

  • Mailbag: mtDNA "out of whack"

    Fri, 2010-08-20 10:13 -- John Hawks

    Re: "Time to revise the mtDNA timescale?":

    You said "The timescale of mtDNA divergence is already out of whack with the rest of the genome."

    What's the time scale for the rest of the genome? It seems to me it should be expected to be at least twice as much as that for mtDNA since at least half the instances of mtDNA - those in males - dead end each generation. With perfect mixing and replacement, 50% of the mtDNA instances pass from one generation to the next, while 75% of the autosomal instances do. Imperfect mixing and replacement would make both numbers lower, but the mtDNA number would still remain much lower than the autosomal number, so the coalescence time should still be expected to be much lower.

    Thanks for noticing that, it's leading to something but I haven't yet described the problem. My apologies for being less than clear.

    What you're describing (you probably already know) is commonly described as the "four-times rule" -- the uniparental inheritance and single copy number give mtDNA one fourth the effective size, on expectation, as an autosomal locus.

    That's in a constant-sized population. Which of course we haven't been. For around the past 100,000 years, African populations were big enough that genetic drift didn't decrease their genetic diversity markedly. The mtDNA coalesces around 100,000 years before that, compared to more than 700,000 years for the typical autosomal locus -- it's 7 times instead of four. That discrepancy is probably not significant given the huge intrinsic variance of the coalescent. But I don't think it's been seriously investigated.

    The real problem is that the out-of-Africa timescale for mtDNA is now very short -- less than 65,000 years -- while the nuclear timescale looks long -- maybe up to 140,000 years. Maybe these can also be reconciled; it's not yet clear. But it's a problem.

    Tags: 
    out-of-Africa
    mtDNA migrations
    population genetics
    mtDNA

  • Population models and testing human origins

    Sat, 2010-04-24 12:11 -- John Hawks

    Earlier in the week, I pointed to a news story about upcoming research that substantiates some amount of gene flow among Pleistocene groups, persisting into living populations ("Multiregional evolution lives!"). That scenario made a bit of a splash in the news, but the result is not unprecedented.

    Last year around this time, I noted a study by Wall, Lohmueller and Plagnol that came to a similar result -- estimating that around 5 percent of the gene pool of today's people outside Africa derived from ancestral non-Africans. That followed on earlier work by Plagnol and Wall from 2006 with essentially the same result.

    Looking back at the blog, this has been a recurring topic since the beginning. For example, back in 2005 when I was still doing a meetings update, I posted about several conference presentations on the topic ("Genetics and multiregional evolution, meetings 2005"). At that time the new results were from Alan Rogers, Jody Hey, and Mike Hammer's lab, all suggesting that ancestral diversity either suggested some ancestral population structure outside Africa, or at least didn't reject it. A key finding was published by Garrigan and colleagues (2005), who found a pseudogene on the X chromosome with an unusually deep gene tree in East Asia ("Modern human origins: X marks the spot?").

    But there's a lot of literature out there that contradicts this line of research. Some of it is still being published. A case in point is the paper released in PLoS ONE this week by Guillaume Laval and colleagues (2010). The key part of the abstract:

    Our results support a model in which modern humans left Africa through a single major dispersal event occurring ~60,000 years ago, corresponding to a drastic reduction of ~5 times the effective population size of the ancestral African population of ~13,800 individuals. Subsequently, the ancestors of modern Europeans and East Asians diverged much later, ~22,500 years ago, from the population of ancestral migrants. This late diversification of Eurasians after the African exodus points to the occurrence of a long maturation phase in which the ancestral Eurasian population was not yet diversified.

    That seems to directly contradict all the research suggesting some component of intermixture among pre-modern populations outside Africa. So what's the deal?

    I have a good idea what's going on now with these apparent contradictions, thanks to a recent paper by Alan Templeton (2010). I'll discuss that paper in detail later this week, as I'm covering these issues now in my graduate seminar.

    In the meantime, I want to give a little thought to the new paper by Laval and colleagues. Following through their simulation methods may give us some ideas about how we can resolve the discrepancies among these tests of human population history. I also want to explore some of the ways that paleontology and paleogenomics may help to inform our tests about these issues.

    Here's a nice paragraph from the results section of the paper that outlines many of the simulation methods. I'd like to have seen some issues laid out more clearly, as some of the parameter combinations are hidden in the supplements and not clearly explained there. It means that as I discuss these, I may not quite have understood everything correctly.

    First, we determined the evolutionary scenario that took place in the ancestral lineage that culminated in the emergence of modern humans (for a complete list of parameter symbols used along the manuscript, see Tables 2 and S4). We tested different evolutionary models [2], [5], [19], [22], [51]–[56] that allow different levels of introgression of archaic hominids to modern human populations. We assumed an early diffusion of archaic hominids (Homo erectus) out of Africa ~1.25 and ~2.25 million years ago [57], various ancestral migration rate intensities (m0, ancestral migration rate is the proportion of migrants before the Out-of-Africa exodus) and an African exodus of modern humans between ~40,000–100,000 years ago [38]. By tuning the replacement rate δ, we then simulated scenarios that consider different levels of replacement of archaic hominids by modern humans (i.e. different levels of introgression of archaic material into the modern gene pool), including the most extreme cases of complete (δ = 1) and no replacement (δ = 0) as well as several scenarios with varying intermediate levels of replacement (Figures 3A and S2, Table S4). The summary statistics were calculated by merging all population samples (except for global FST) in order to minimize the effects of recent demographic events related to the continental populations. We thus considered in all models a constant size for the three modern human populations. The model with residual ancestral migration rate (m0~10−10) and full replacement (δ = 1) clearly better fitted our data than any other model (Figure 3A, highest ψ1, the ψ1 of this model is significantly higher after correction for multiple testing when compared with the other ψ1 values, P

    For a long time, I've been bothered in the back of my mind about the outcomes of these analyses based on simulations and "approximate Bayesian computation" (ABC). I learned a long time ago never to argue statistics with a Bayesian. It's not that the approach is infallible, it's just that if someone is clever enough to use Bayesian statistics, it's going to turn into a long argument.

    By my count the model has 18 parameters, and we could reshuffle them in lots of ways. Can it really be that no combination of the parameters provides a better fit than zero admixture? Intuitively, it seems wrong -- because it would mean that one combination of the other 17 parameters gave a near-perfect fit to the data. Perfect fits don't happen, not with genetic data as messy as in humans.

    The conceptual scheme of the paper is an island model with migration, growth, and replacement as possibilities, between the three populations -- Africa, Europe and East Asia. Since any of the parameters could in concept vary from zero to infinity, each specific model ought to be a proper subset of the general island model, and they ought to grade continuously into each other. In other words, an out-of-Africa replacement is just one extreme of the general multiregional/admixture/introgression model.

    That has some predictable consequences. A nonzero migration rate before a complete replacement ought to behave very much like a structured population within Africa before a replacement. An analysis that prefers the second really shouldn't be distinguishable from the first. Likewise, a very small population outside Africa before a slight replacement should look very much like a larger population with a more complete replacement. These options aren't identical, but they ought to grade continuously into each other.

    But in the paper, the authors bounded the parameters in ways that make these different specific models discontinuous. For example, consider the parameter that defines the time of the initial population spread out of Africa:

    We assumed an early diffusion of archaic hominids (Homo erectus) out of Africa ~1.25 and ~2.25 million years ago

    If the time of founding of these populations could vary down toward the time of possible replacement (in the last 100,000 years), the continuity and replacement models would grade continuously. This would be the logical connection implied by the island model, but by limiting the range of times, the authors have generated an artificial difference between the models.

    In principle, we could have a good reason for separating the models in this way. For example, we know that Europe and Asia were occupied by hominids before 1.25 million years ago, and we might specifically be interested in those people.

    But in reality, we know that a 1.25-million-year old split between European and African populations is in conflict with paleogenomics. The Neandertal genome shows that we shared a small common ancestral population with Neandertal ancestors at most around 300,000 years ago, and possibly much more recently. If the human-Neandertal ancestral population was dispersed across Eurasia and Africa at that time, it must have had relatively high gene flow, enough so to behave as a single population with a small effective size.

    So this is a possible problem. None of the "admixture" models included in the paper have a feature which the paleogenomic evidence says is necessary. My point is that the authors have generated a "rugged landscape" of models by eliminating the continuity between them. It may not be surprising that one choice of parameters fits the data much more strongly than alternatives, because the intermediates have not been examined.

    There are other parameters for which uncertainty might be substantially reduced by using other evidence. For example, the authors consider a range of migration rates varying over three orders of magnitude between recent (modern) populations on different continents. The actual value of this rate has a large effect on the appearance of admixture, because it determines the likelihood that ancestral African variation has recently dispersed out of Africa into Eurasia. But we can probably obtain a good estimate of this rate of recent gene flow from other data, since we have large datasets of genome-wide SNP and microsatellite polymorphisms from these regions. These data could also provide a better test of the proposed Europe-Asia "split". Why are these aspects important? Because recent events will disturb or cover up the evidence for earlier dispersals and interactions. If we can constrain the recent events using other evidence, we can increase our power to test hypotheses about earlier events.

    Although many possible intermediate models are excluded in the study, the authors in the end find an overlap in results between two apparently very different parameter combinations:

    Among the 24 models tested, the model assuming a complete replacement rate of archaic hominids (δ = 1) and a residual ancestral migration (m0~10−10) exhibited the significantly highest ψ1 except when compared with the model assuming an almost complete replacement rate of archaic hominids (δ≥0.99).

    That result might seem paradoxical. At face value, it means that ancestral humans outside Africa did contribute genes to living populations, but only by means of very rare gene flow from Eurasia back into Africa before a subsequent replacement. In other words, the first modern humans in Africa would have been descendants of Africans and of Eurasian people. It's not surprising that the outcome is close to a model with very slight survival of Eurasian populations.

    As we think of ways to improve these tests, I think we need to introduce independent tests of each parameter. This won't always be possible, and there will be cases where changing one parameter will impose a trade-off with one or more others. But that's the nature of these models -- each parameter is a dial, and twisting one of them may be corrected by turning others. The important point is that we can already falsify many of the conceivable possibilities. Until we have a model in which paleontology, archaeology, paleogenomics and the genetics of living people all form a single consistent picture, our work isn't done.

    (see also, Gene Expression)

    References:

    Garrigan D, Kingan SB. 2006. Archaic human admixture: A view from the genome. Curr Anthropol 48:895-902. doi:10.1086/523014

    Garrigan, D., Mobasher, Z., Severson, T., Wilder, J. A., Hammer, M. F. 2005. Evidence for archaic Asian ancestry on the human X chromosome. Mol. Biol. Evol. 22:189-192. doi:10.1093/molbev/msi013

    Hawks J, Cochran G. 2006. Dynamics of adaptive introgression from archaic to modern humans. PaleoAnthropology 2006:101-115. Open access

    Hawks J, Cochran G, Harpending HC, Lahn BT. 2007. A genetic legacy from archaic Homo. Trends Genet doi:10.1016/j.tig.2007.10.003

    Laval G, Patin E, Barreiro LB, Quintana-Murci L (2010) Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions. PLoS ONE 5(4): e10284. doi:10.1371/journal.pone.0010284

    Plagnol, V., Wall, J. D. 2006. Possible ancestral structure in human populations. PLoS Genet. 2:e105. doi:10.1371/journal.pgen.0020105

    Templeton AR. 2010. Coherent and incoherent inference in phylogeography and human evolution. Proc Nat Acad Sci USA 107:6376-6381. doi:www.pnas.org/cgi/doi/10.1073/pnas.0910647107

    Wall JD, Lohmueller KE, Plagnol V. 2009. Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol (early online) doi:10.1093/molbev/msp096

    Tags: 
    early modern
    Neandertal DNA
    multiregional
    out-of-Africa

  • Were ancient Africans divided into small, isolated bands?

    Thu, 2008-05-08 12:05 -- John Hawks

    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

    Tags: 
    mtDNA
    out-of-Africa
    Africa
    population structure
    effective population size
    demography
    migrations
    Synopsis: 
    Revisiting a paper that claims an African bottleneck, I examine the subject of population structure

  • The two "out of Africas"

    Tue, 2008-03-18 17:45 -- John Hawks

    Another of the craniometric stories going around this week (Discovery News) proposes that early Levantine modern humans (Skhul-Qafzeh) and Pleistocene Australians come from an early out-of-Africa dispersal that was later mostly replaced by true modern humans (represented by Upper Paleolithic Europeans and living people everywhere). The study is by Michael Schillaci; here's the abstract:

    This study examines the genetic affinities of various modern human groupings using a multivariate analysis of morphometric data. Phylogenetic relationships among these groupings are also explored using neighbor-joining analysis of the metric data. Results indicate that the terminal Pleistocene/early Holocene fossils from Australasia exhibit a close genetic affinity with early modern humans from the Levant. Furthermore, recent human populations and Upper Paleolithic Europeans share a most recent common ancestor not shared with either the early Australasians or the early Levantine humans. This pattern of genetic and phylogenetic relationships suggests that the early modern humans from the Levant either contributed directly to the ancestry of an early lineage of Australasians, or that they share a recent common ancestor with them. The principal findings of the study, therefore, lend support to the notion of an early dispersal from Africa by a more ancient lineage of modern human prior to 50 ka, perhaps as early as OIS 5 times (76-100 ka).

    But the Skhul-Qafzeh sample and the Pleistocene Australia + Wadjak sample used in the paper (a subset of all the actual specimens) are all males, and the Upper Paleolithic Europeans and recent skeletal samples are (as you might expect) half female.

    Seems like a problem....

    References:

    Schillaci MA. 2008. Human cranial diversity and evidence for an ancient lineage of modern humans. J Hum Evol (in press) doi:10.1016/j.jhevol.2007.10.010

    Tags: 
    out-of-Africa
    Neandertals
    Qafzeh
    Skhul

  • D'Errico on Neandertal language

    Sat, 2008-03-15 11:56 -- John Hawks

    Edmund Blair Bolles is reporting from the Evolang conference in Barcelona. Unfortunately I had to cancel my presentation there, but it has been great to read these summaries of some of the papers. I wanted to point readers to his account of Francesco D'Errico's talk:

    Neanderthals had language comparable to that of Homo sapiens, Bordeaux-based archaeologist Francisco D’Errico told participants in the Evolang conference in Barcelona this morning (Saturday, March 15, 2008). This claim totally discards the older Big Bang theory that said language arose only very recently (40 to 75 thousand years ago), and also challenges the Out-of-Africa theory that proposes Homo sapiens emerged in Africa about 200 thousand years ago and spread over the rest of the world, carrying language and culture with the, beginning about 60 thousand years ago. A new history will have to be written.

    If you have been reading here, you have seen many of the new perspectives D'Errico is talking about, but together they make a very compelling package. Consider:

    1. We now know that australopithecines had ape-like vocal tracts, complete with pharyngeal air sacs.

    2. We now know that Middle Pleistocene humans (Atapuerca) had humanlike hyoids, unlike australopithecines, so modern human vocal tract anatomy was plausibly a derived feature of Homo, including Neandertals.

    3. We have good evidence of pigment use from MSA Africa and Mousterian Europe. The Neandertals in particular appear to have been coloring skin with manganese crayons.

    4. Decorative/ornamental artifacts were manufactured both by MSA Africans and Neandertals.

    5. Neandertals shared the modern human-derived FoxP2 variant.

    I have some notes on D'Errico's work (with Maria Soressi) on Neandertal pigment use that I'll post later. Given the confluence of the recent evidence from genetics, archaeology, and anatomy, I do not see how anyone can maintain the hypothesis that Neandertals (and presumably, other Late Pleistocene humans) did not have language.

    Now, that is not to say that they (or any Late Pleistocene humans) were identical in their linguistic adaptations to living or recent people. I still think that communication is the most likely focus of evolutionary change in the Late Pleistocene -- but a change based within a pre-existing community of language users, not a newly-sprung linguistic skill. In fact, I think the next constructive step should be to characterize the variation in linguistic adaptations in recent people, who are surely not identical to each other. That verges on the subject of my presentation, which -- if you attend the AAPA meetings this spring, you will still get a chance to hear. That is, if you stick around until Saturday!

    Tags: 
    Middle Pleistocene
    Neandertals
    out-of-Africa
    MSA
    Atapuerca
    Late Pleistocene

  • Serial founder effects, again

    Wed, 2008-02-20 22:59 -- John Hawks

    A flush of papers this week (two today in Nature, one tomorrow in Science) describe new analyses of SNPs across the genome. Two of the papers sample SNPs in global samples numbering more than 500 individuals.

    This Reuters story by Maggie Fox is typical of the press coverage:

    Gene studies confirm 'out of Africa' theories

    WASHINGTON - Two big genetic studies confirm theories that modern humans evolved in Africa and then migrated through Europe and Asia to reach the Pacific and Americas.

    ...

    The studies, published in the journal Nature on Wednesday, paint a picture of a population of humans migrating off the African continent, and then shrinking at some point because of unknown adversity.

    Later populations grew and spread from this smaller genetic pool of founder ancestors -- a phenomenon known as a bottleneck.

    These studies have very, very exciting potential. Here in my lab, we will be immediately using the data from these papers to test hypotheses about recent human evolution.

    But it is beyond me to understand why anyone thinks that the "serial founder effect" story is news!

    For one thing, the idea is based on 12-year-old research demonstrating that human diversity declines for some genetic loci with distance from Africa. This observation was replicated for genome-wide STR loci in a well-publicized paper three years ago. This paper clearly demonstrated how a model involving a chain of bottlenecks could result in a cline of diversity -- one population leaving Africa, a small group from this population moving to Jordan, another small group moving from Jordan to Mesopotamia, another small group from Mesopotamia to the Zagros, etc.

    In other words, there's nothing new here. It's no surprise that genome-wide SNPs and copy-number variants (CNVs) should replicate the pattern already shown for genome-wide STRs.

    What's worse, all these papers from the Stanford school of genetic orthodoxy fail to even test the hypothesis! I pointed out this problem three years ago:

    The data that the paper attempts to explain are (1) the correlation of genetic distance and geographic distance among human populations, and (2) the decrease in genetic diversity in populations farther from Africa. We may ask, what other hypotheses would explain the same data? And what kind of evidence could test these hypotheses, instead of just asserting that they "match" the pattern of evidence.

    One scenario that matches the evidence is multiregional evolution with a recent African dispersal of some adaptive genes. This is the hypothesis presented by Eswaran (2002). The idea is that human populations interacted for a long time in Africa and Eurasia, and that during the Late Pleistocene, adaptive changes within Africa allowed those populations to spread alleles into existing populations in Eurasia. The strength of the "founder effect" in this scenario depends on the genetic structure and selective advantage of the new African adaptive complex. Ramachandran et al (2005) actually cite Eswaran (2002) as an example of a serial founder effect. So the idea that there was widespread genetic movement out of Africa does not necessarily imply an out-of-Africa population replacement. The data do not require a replacement, and some -- even many -- of the genetic variants outside of Africa may have nothing to do with recent genetic movement out of Africa.

    A second hypothesis is presented by Templeton (2002), who proposed that several founder effects happened at different times in the Pleistocene, each carrying one or more genetic variants out of Africa. The pattern of genetic variation appears to indicate that some genes left Africa during the Lower or Middle Pleistocene, while others dispersed later, during the Late Pleistocene. For Templeton (2002), this pattern indicates multiple dispersals, none of which was sufficient to wipe out the genetic contribution of earlier dispersals. This scenario also would lead to a pattern of correlation of genetic and geographic distance (because most genes have been affected by isolation-by-distance for a long time), while the recurrent dispersals would explain the decline in genetic variation outside of Africa.

    A third hypothesis is that population size was simply greater within Africa than within Eurasia. The smaller population size (along with isolation-by-distance) would explain the difference in genetic variation; the correlation of genetic and geographic distance would be explained by isolation-by-distance. We may consider a fourth hypothesis also: that natural selection has tended to create slightly more genetic uniformity within Eurasia and slightly more genetic diversification in Africa. Such a scenario might be justified on ecological grounds: African populations cover a wider range of ecologies and have historically had a greater exposure to zoonotic disease, for example.

    Except for the serial founder effect with population replacement, none of the other hypotheses are mutually exclusive. In other words, some genes might have been influenced by natural selection, most might have been somewhat influenced by differences in population size, but the largest effect might have been recurrent population dispersals.

    Reading over the whole post, I think it did a good job of laying out the situation with serial founder effects in 2005, and there is little reason to change it now. Still nobody has tested the model! Again, this is a case of science by consistency -- the results of simulations generate the same kind of correlations as the observed data, so the authors claim support for their hypothesis.

    But the necessary test should be carried out by dating haplotypes, finding the ages of "founder mutations" and eliminating the possibility of introgression from ancestral Eurasian populations. One of the key points in my earlier post is that the model proposed by Eswaran (2002) would generate exactly the distribution expected for serial founder effects -- despite the fact that it describes a wave of genetic change within an already-established pan-Old-World population.

    This study doesn't support an out-of-Africa migration; it merely assumes it. Now, I'm one who thinks that there was an important trend of strong gene flow out of Africa in the Late Pleistocene. But data showing a correlation between diversity and distance from Africa just cannot show the critically important facts about the timing and magnitude of such gene flow.

    Somebody will eventually straighten all this out. What I wonder is why it never seems to be the reviewers!

    References:

    Jakobsson M and 23 others. 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998-1003. doi:10.1038/nature06742

    Eswaran V, Harpending H, Rogers AR. 2005. Genomics refutes an exclusively African origin of humans. J Hum Evol 49:1-154.

    Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. 2005. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Nat Acad Sci USA 102:15942-15947.

    Templeton AR. 1998. Human races: a genetic and evolutionary perspective. Am Anthropol 100:632-650.

    Templeton AR. 2002. Out of Africa again and again. Nature 416:45-51.

    Tags: 
    genomics
    multiregional
    Middle Pleistocene
    introgression
    Late Pleistocene
    out-of-Africa

  • French Connection to China Syndrome, dentally

    Tue, 2007-08-07 13:28 -- John Hawks

    I've read through the new paper by Martinón-Torres et al., on Eurasian continuity in the Middle Pleistocene. They've put out an interesting hypothesis, with some support from previous work, but ultimately I think their methods are too weak to test it.

    The press coverage of the paper so far (e.g., this AP article) has been a little confusing, because it misses this point: this paper is not about modern human origins, it's about much earlier evolutionary relationships. National Geographic News resorts to the always-safe:

    The finding suggests that the hominid family tree could be much more complex than previously thought.

    Ah, so that's what it means! More complex than previously thought! Why isn't there ever a story that makes things simpler than previously thought? I mean, isn't it a sign of a failed science if you have to add complexity to your hypothesis every time you make a new observation? It's like Ptolemaic paleoanthropology!

    Anyway, enough of that rant. Let's look at what the paper really says, which is much more interesting than the press! Here's the abstract:

    A common assumption in the evolutionary scenario of the first Eurasian hominin populations is that they all had an African origin. This assumption also seems to apply for the Early and Middle Pleistocene populations, whose presence in Europe has been largely explained by a discontinuous flow of African emigrant waves. Only recently, some voices have speculated about the possibility of Asia being a center of speciation. However, no hard evidence has been presented to support this hypothesis. We present evidence from the most complete and up-to-date analysis of the hominin permanent dentition from Africa and Eurasia. The results show important morphological differences between the hominins found in both continents during the Pleistocene, suggesting that their evolutionary courses were relatively independent. We propose that the genetic impact of Asia in the colonization of Europe during the Early and Middle Pleistocene was stronger than that of Africa.

    OK, so this is about the initial colonization of Europe and the subsequent evolutionary trends in Europe, Asia, and Africa. The observation is that European teeth show a continued similarity to Asians during the Middle Pleistocene, and there is no evidence that European teeth evolved in the direction of Africans during that time period.

    Why is that interesting? Two reasons:

    1. The hypothesis directly conflicts with the idea that Middle Pleistocene Europeans were linked to Africans. A large number of anthropologists have been pushing the European-African link, under the old hypothesis that these ancient people belonged to a species that was distinct from East Asians. The European-African clade in this hypothesis is often called Homo heidelbergensis; the Asian clade remains Homo erectus.

    2. The hypothesis also seems to conflict with genetic data, which suggest that the relationship of European and African hominids is more recent than the early Middle Pleistocene. In particular, the genetic divergence time between human and Neandertal genomes appears to date to more recently than 700,000 years ago (Green et al. 2006, Noonan et al. 2006), which means that the population divergence must be still more recent. Also, Alan Templeton's papers (e.g., 2002, 2006) claim evidence for migrations from Africa into Europe and Asia during the Middle Pleistocene. Those claims are consistent with the Neandertal genome data, as far as we know it, and they suggest gene flow from Africa into Eurasia.

    So, the authors ought to deal with these issues. They do so in their discussion, which in this short paper is one long paragraph. I'm quoting it here in full to comment on the details:

    If the population of the Eurasian continent during the Early and
    Middle Pleistocene was mainly the result of several out-of-Africa incursions, we should have found African influences in the morphology of the Eurasian populations. However, the continuity of the "Eurasian dental pattern" from the Early Pleistocene until the appearance of the Upper Pleistocene Neanderthals suggests that the evolutionary courses of the Eurasian and the African continents were relatively independent for a long period and that the impact of Asia in the colonization of Europe was stronger than that of Africa.

    That is the conclusion of the analysis, in brief. The strength of the conclusion depends on the power of the analytical methods to detect gene flow based on morphological similarities. More on that below.

    This finding does not necessarily imply that there was not genetic flow between continents, but emphasizes that this interchange could have been both ways (25, 26).

    This seems a little misleading. They have no particular evidence of gene flow from Eurasia to Africa (that would be the "both ways"). Nor do they have evidence in their analysis of gene flow from Africa to Eurasia, after the initial colonization. So they don't have any evidence for gene flow at all. So the finding doesn't emphasize anything about gene flow, other than that the teeth don't show obvious evidence for it.

    Around 1 Ma, hominins appear to have dispersed into temperate latitudes as far north as 40 - 45° N (27-29), not only from Africa, but also within Eurasia (29 - 31). These populations were probably descendants of an ancient out-of-Africa exodus, rather than a later one at the end of the Early Pleistocene (30).

    This is an important assertion. Other workers have emphasized the similarities of some African fossils to East Asian fossils (mainly from Java, plus Gongwangling in China) in the late Early Pleistocene. That has always been the case with OH 9, and it influenced the description of the Daka and Buia crania as well. The question is how early Asian populations became morphologically distinctive. Here, the authors argue that it was very early, without substantial signs for later interaction, which in the context of the cranial comparisons is now an extreme claim.

    In addition, a recent study on the European Lower Pleistocene hominin populations has revealed a possible Eurasian origin for these groups (32).

    This refers to the description of the ATD6-96 mandible, which contains an earlier assertion about Asian-European connections. I return to this below.

    Furthermore, it has been pointed out that during the Middle Pleistocene there was hardly any faunal exchange bet ween East Africa and the Levant (33) and that the desert between the Sahara and Arabia was an important barrier at that time (26), therefore contributing to the isolation of both continents.

    This is an important argument in support of their hypothesis. If movement between Africa and Eurasia was difficult during this time span, that reinforces their claim, and makes it less plausible that there were large-scale dispersals out of Africa during the Middle Pleistocene. That leaves us with a mention of a major exception to their proposed pattern: the evolution of humans in the Late Pleistocene:

    With the exception of the SAP [i.e., H. sapiens] out-of Africa dispersion based mainly on genetic data (2), the history of human populations in Eurasia may not have been the result of a few high-impact replacement waves of dispersals from Africa, but a much more complex puzzle of dispersals and contacts among populations within and outside continents. In the light of these results, we propose that Asia has played an important role in the colonization of Europe, and that future studies on this issue are obliged to pay serious attention to the "unknown" continent (Martinón-Torres et al. 2007:3).

    The citation of the ATD6-96 mandible leads us to a passage from that earlier paper (Carbonell et al. 2005), which also describes the hypothesis that the founding population of Europe was Asian. Remember that this research group calls the Gran Dolina sample, Homo antecessor, and they initially had written that this species probably colonized Europe from Africa in the late Lower Pleistocene. Here's the relevant paragraph from the cited paper (Carbonell et al. 2005):

    The differences in dimensions and robustness between the TD6 mandibles and the East and North African mandibles cast doubt on the African origin of H. antecessor. In contrast, our comparative analysis suggests looking toward the Asian continent. In this respect, it is relevant to mention some data that remained unpublished in 1997, when the new species was named (10), and that are relevant to this discussion. The partial cranium Nanjing I, recovered in 1993-1994 from the Hulu Cave (Tangshan Hill, eastern central China), shows clear modern midfacial traits similar to those observed in the specimen ATD6-69 (19). Wang and Tobias (20) also found similarities between Nanjing I and the Zhoukoudian hominins. Geochronological dates, combined with ecological and paleoclimatic evidence, indicate that the Nanjing skull is ~600 thousand years old (21). Furthermore, the Locality 1 levels at Zhoukoudian, which yielded most hominin specimens, are now considered at least 800 thousand years old (22). Thus, these Chinese hominins may be contemporaneous with or slightly younger than the TD6 hominins. If the Gran Dolina and Chinese populations are phylogenetically related, they should share a common ancestor that also had a modern midfacial pattern and a gracile mandible. In the cranium, this hypothetical common ancestor would have had a low and flat temporal squama, and an unfused styloid process. These traits would have been retained in the Asian hominins but lost in the TD6 hominins, who exhibit a fused styloid process, a convex temporal squama, and probably a significant increase in cranial capacity (19). The Ceprano calvaria (Italy), which has been tentatively assigned to H. antecessor (23), exhibits a convex temporal squama and a cranial capacity of about 1,057 ml (24). Interestingly, TD6 and Zhoukoudian are the only hominins that have a zygomaxillary tubercle before the Upper Pleistocene (19).

    So that provides cranial and mandibular evidence of an Asia-Europe connection, supporting the dental evidence provided in the current paper. Still, that evidence is from the initial founding of Europe in the Early Pleistocene and doesn't necessarily apply to the trends during the Middle Pleistocene.

    After working through the data supplements for the paper, I think that the analysis is much weaker in statistical power than it could be. In their analysis, they disregard much of the variation within these ancient samples and focus on the differences between samples according to their scoring methods. This may reveal the broad relationships among samples -- if we disregard the possibility of selected parallelisms -- but it does not say anything about the possibility of gene flow among the samples.

    Indeed, the result of their analysis (a dendrogram, or branching tree) is quite incapable of showing genetic exchanges at all. It can only show branching events, which means that the result will show either an exclusive relationship between Europeans and Asians, or an exclusive relationship between Europeans and Africans, but never a mixed relationship.

    The only result in the paper that indicates a European-Asian relationship is from their cladistic analysis of a subset of the data. And it isn't especially strong evidence, since the Middle Pleistocene Africans are limited to the relatively early sites of Rabat and Tighenif (Ternifine). Granted, the later sample is also small in number, but this isn't really a test of relationships; it's more of a suggestion.

    The phenogram inexplicably omits Middle and Lower Pleistocene Africans entirely, and considers only australopithecines and habilines as the African sample.

    So, at the moment I consider this to be a very interesting hypothesis in search of a good test. There is no test of gene flow here, just an assertion. Yet, the cranial comparisons give the assertion some plausibility -- and remember, another idea out there is the hypothesis that early Homo originated in Asia and migrated to Africa later.

    I think that these topics together constitute the important problem in early human relationships right now, so I'll be writing some more about them. There are many additional interesting facts to consider...

    References:

    Martinón-Torres M, Bermúdez de Castro JM, Gómez-Robles A, Arsuaga JL, Carbonell E, Lordkipanidze D, Manzi, G, Margvelashvili A. 2007. Dental evidence on the hominin dispersals during the Pleistocene. Proc Nat Acad Sci USA (early) doi:10.1073/pnas.0706152104

    Stringer C. 2002. Modern human origins: progress and prospects. Phil Trans Roy Soc Lond B 357:563-579. doi:10.1098/rstb.2001.1057

    Rightmire GP. 1998. Human evolution in the Middle Pleistocene: the role of Homo heidelbergensis. Evol Anthropol 6:218-227. doi:10.1002/(SICI)1520-6505(1998)6:63.0.CO;2-6

    Carbonell E and 19 others. 2005. An Early Pleistocene hominin mandible from Atapuerca-TD6, Spain. Proc Nat Acad Sci USA 102:5674-5678. doi:10.1073/pnas.0501841102

    Bruner E, Manzi G. 2005. CT-based description and phyletic evaluation of the archaic human calvarium from Ceprano, Italy. Anat Rec A 285A:643-657. doi:10.1002/ar.a.20205

    Tags: 
    Middle Pleistocene
    Late Pleistocene
    Atapuerca
    out-of-Africa
    Homo erectus
    Early Pleistocene
    Neandertals
    Zhoukoudian

  • Snapshots of the science

    Sun, 2007-03-11 22:07 -- John Hawks

    The new Human Origins hall at the American Museum is the occasion for a big Newsweek story, with the tagline, "The New Science of Human Evolution". Author Sharon Begley isn't stingy with the prose:

    Whether or not you believe the hand of God was guiding these changes, the discoveries are overturning longstanding ideas about how we became human.

    Not that fossils are passé. New discoveries are pruning and reshaping humankind's family tree as radically as bonsai. The neat traditional model in which one species gave rise to another like Biblical "begats" has been replaced by a profusion of branches, representing species that lived at the same time as our direct ancestors but whose lines died out. It's like discovering that your great-great-grandfather was not an only child as you'd thought, but had a number of siblings who, for unknown reasons, left no descendants. New research also shows that "progress" and "human evolution" are only occasional partners. More than once in human prehistory, evolution created a modern trait such as a face without jutting, apelike brows and jaws, only to let it go extinct, before trying again a few million years later. Our species' travels through time proceeded in fits and starts, with long periods when "nothing much happened," punctuated by bursts of dizzying change, says paleontologist Ian Tattersall, co-curator of the American Museum's new hall.

    It's a little sad to see the article organized around a 15-year-old storyline. No More Unilineal Evolution! Hey, if it's a "new science", why do we keep hearing from the same old people?

    Still, there are some brain evolution subplots, and a few genes mentioned. Aside from the flowery analogies, Begley is a good writer and can capture the essence of most of these stories in a few lines. As an exercise, let's try to take those few lines and change one crucial word to find the weakness of each hypothesis. For each quote, I'll strike out a word in the article and add the correct word in brackets.

    You dirty louse

    For example, let's start where the article does, with the "body lice = no fur" story:

    That fork in the louse's family tree, [Mark Stoneking] and colleagues at Germany's Max Planck Institute for Evolutionary Anthropology concluded, occurred no more than 114,000 years ago. Since new kinds of creatures tend to appear when [correct word: after] a new habitat does, that's when human ancestors must have lost their body hair for good - and made up for it with clothing that, besides keeping them warm, provided a home for the newly evolved louse.

    You see how easy that is? Yes, new species adapt to new niches, but there is no reason to think this happens immediately. For that matter, there is no reason to think that hominids lost their fur instantaneously.

    And hey, if the theme of the article is that human evolution has lots of extinct branches, then why doesn't that apply to louse evolution? We just saw last week how complex the louse phylogeny has been in hominoids. Who says that the current body louse was the first to fill that niche?

    Oh, savanna, don't you cry for me!

    Here's a short one:

    The apes that stayed in the forests hardly changed; they are the ancestors of today's chimps. Those that ventured into the newly formed habitat of dry grasslands [correct phrase: open woodlands] had taken the first steps toward becoming human.

    None of the earliest hominid sites are open savanna. All of them come from sites that preserve other woodland creatures.

    By the way, my favorite quote in the whole thing comes here:

    Instead, evolution played Mr. Potato Head, putting different combinations of features on ancient hominids then letting them vanish until a later species evolved them.

    I just love that analogy! Forget "mosaic evolution". I'm calling it "Mr. Potato Head evolution" from now on.

    My what small teeth you have

    This part is a little confused:

    And it helps explain why Lucy's kind were the way they were. Afarensis women and men stood three to five feet tall and weighed 60 to 100 pounds. They had small [correct: big] teeth good for fruits and nuts, but not meat. (The available prey was [correct: competing predators were] enough to make one a confirmed vegetarian: hyenas the size of bears, saber-toothed cats and other mega-reptiles and raptors.) That suggests that early humans were more often prey than predators, says anthropologist Robert Sussman of Washington University, coauthor of the 2005 book "Man the Hunted." The evidence is as stark as the many [correct: two] fossil skulls containing holes made by big cats and [correct: one containing] talon marks from raptors.

    Well, that's taphonomy for you. There is plenty of evidence for predation on ancient hominid bones, and a National Geographic News article from 2002 details work showing the contribution of felids. But only two skulls have holes that may have come from ancient cats (those would be SK 54 from Swartkrans and D2280 from Dmanisi). Only Taung has evidence of raptor damage.

    Splitting straws on habiline brains

    Dmanisi has left people pretty confused about what explains hominid dispersal from Africa. Some are groping for other hypotheses. Just check out this paragraph:

    Erectus shows that brain size is too crude a measure of a species' talents. At Dmanisi, the brains range from 600 to 770 cubic centimeters, comparable to the more primitive habilis. But while erectus did not distinguish themselves in brain size, brain structure is more telling [correct: nor does its brain structure provide any clues]. They were [correct: They were not] the first of our ancestors to have an asymmetric brain, as modern humans do; Australopithecus species do not [correct: did]. Asymmetry is a mark of increasing specialization and therefore complex cognitive ability [correct: of questionable value, since apes and australopithecines have asymmetries to varying extents]. Erectus used it to, among other things, discover and tame fire [add: apparently much later]. What they did not use it for is technology. Tools found with the Dmanisi fossils include cutting flakes, rock "cores" from which flakes were made and a chopper, all primitive even for their time [correct: like those made in Africa]. "The old idea that you needed a master's degree in stone tools to leave Africa is crazy," says Bernard Wood.

    Wow, how confusing. The Dmanisi crania had H. habilis-sized brains. They're like KNM-ER 1470. So brain size isn't the key characteristic that allowed hominids to disperse from Africa. Nor is body size, since the Dmanisi hominids were relatively small. That's a genuinely interesting problem.

    But asymmetry doesn't solve it. KNM-ER 1470, either Homo habilis or Homo rudolfensis depending on your taste in hominids, has a well-defined Broca's area on the left hemisphere, which I would say is the main informative aspect of asymmetry in fossil endocasts. Chimpanzee brains are asymmetrical in some respects, so "asymmetry" itself is an irrelevant criterion without some specific anatomical feature in mind. The thing that people used to think might be important was petalial asymmetry -- one hemisphere of the cortex shifted forward compared to the other. Early Homo endocranial surfaces show fairly strong petalial asymmetries, including KNM-ER 2598 and KNM-WT 15000. But some Australopithecus endocasts share a similar pattern of asymmetry with later hominids (Holloway and De La Costelareymondie 1982). We don't know how to interpret petalial asymmetry in functional terms, by the way. There appears to be some correlation with handedness, but it's not clear that hand preferences and petalial asymmetries evolved at the same time or for the same reason.

    Somebody could write a really interesting story just out of the material in this one paragraph. Just not this story!

    Out of Africa

    The bottleneck scenario always seems like a hard one for journalists to get right. This article is no better than usual:

    Peter Underhill, a molecular anthropologist at Stanford University, tracked 160 such changes in the Y's of 1,062 men from 21 populations across the world. Applying the molecular-clock technique, he concludes that the most recent common ancestor of all men [correct: all Y chromosomes] alive today lived 89,000 years ago in Africa. The first modern humans-and therefore, unlike the earlier wave of Homo erectus into Asia a million years ago, the ancestors of everyone today-departed Africa about 66,000 years ago.

    These pilgrims were strikingly few. From the amount of variation in Y chromosomes today, population geneticists infer how many individuals were in this "founder" population. The best estimate: 2,000 men. Assuming an equal number of women, only 4,000 brave souls ventured forth from Africa [correct: were isolated from other humans for thousands of years inside Africa]. We are their descendants.

    Hard to get straight: genetic drift takes a long time to fix a gene. We don't necessarily know the number of founders of the out-of-Africa population; what we do know is how many individuals the ancient African population must have had under the hypothesis of genetic drift.

    Other genes might well have more recent common ancestors, who would also have been more recent common ancestors of all men. This is especially true if any genes were under selection.

    People who see my meetings talk will appreciate the irony of that last sentence...

    References:

    Holloway RL, De La Costelareymondie MC. 1982. Brain endocast asymmetry in pongids and hominids: some preliminary findings on the paleontology of cerebral dominance. Am J Phys Anthropol 58:101-110. doi:10.1002/ajpa.1330580111

    Tags: 
    Homo erectus
    Dmanisi
    Swartkrans
    Homo rudolfensis
    Homo habilis
    out-of-Africa
    A. afarensis
    paleonews

  • Shellfish use by Neandertals

    Sun, 2006-09-10 00:08 -- John Hawks

    I got the Neanderthals on the Edge volume by interlibrary loan to follow up the Barton shellfish consumption reference. Here is the relevant passage from the discussion of that chapter:

    Until recently any discussion of shellfish exploitation by Neanderthals or other archaic humans would have been restricted to just a few exceptional examples. However, following publication of work on the Italian Mousterian by Mary Stiner and others, there are now a growing number of instances where evidence has been documented for deliberate harvesting of marine shellfish resources by Neanderthals. These include cave sites and rockshelters in the Ligurian Riviera (Costa dei Balzi Rossi, Riparo Mochi, Barma Grande), further south in Latium (Grotta dei Moscerini) and in the southern Italian province of Puglia (Grotta dell'Alto, Grotta del Cavallo, Grotta Uluzzo C, Grotta Mario Bernadini, Grotta dei Giganti) (Stiner 1994, fig 6.9). Further afield in Africa similar occurrences have been reported from Middle Stone Age deposits at Blombos Cave in the southern Cape (Henshilwood and Sealy 1997) and at the Haua Fteah in Cyrenaica (Klein and Scott 1986). To these can now be added the localities of Vanguard and Gorham's Caves and the Devil's Tower, Gibraltar. The Gibraltar examples indicate that mussels and otehr shellfish probably contributed regularly to the Neanderthal diet. Furthermore they show that selective use was made of the larger shells collected from estuarine habitats and these small packages of food were carried up to four kilometres to the caves to be prepared and consumed. Much larger accumulations of shellfish in association with the Mousterian deposits are also known from unpublished sites north of Gibraltar near Torrelmolinos, in teh Spanish Costa del Sol (Miguel Cortés Sánchez pers. comm.).

    The presence of thin in situ ashy hearth horizons in Vanguard Cave has helped establish that the use of the site by Neanderthals was generally episodic with individual occupation events usually being short-lived. Ephemeral use of this cave is exemplified by the upper hearth and midden which probably represented a single episode of use of no more than a few hours duration. Further down the sequence more intensive evidence of occupation is indicated by accumulations of butchered bones of ibex and red deer but here too the data are consistent with short-term occupational use. In both the upper and middle section of this cave it was noticeable that te hearths were positioned in proximity of hte soutehrn cave wall. Similar juxtapositions have been noted at other Mousterian sites (e.g. Tor Faraj, south Jordan; Henry 1998), but unlike Tor Faraj there is no suggestion of multiple individually spaced hearths. Indeed it is noreworthy that the single hearth in the middle section of Vanguard was re-used at least three times. This may reflect the generally lower density of human groups occupying the site at one time. The position of the hearths near the cave wall and the extensive ash spread in the upper part of the cave may also have been partly connected with sleeping or resting activities. For example in ethnographic contexts, it has been noted that ashy spreads between the hearth and the rock wall may coincide with places where bedding was laid down (Parkington and Mills 1991) (Barton 2000:218-219).

    McBrearty and Brooks (2000:511-512) give a long list of MSA and associated sites with shellfish remains (taken broadly to include land snails and tortoises). This is a very long passage, and so I won't quote it, except for the conclusion:

    Evidence from coastal Italy (Stiner, 1993, 1994; Stiner et al. 1999) and Gibraltar (Barton et al., 1999) shows that Neanderthals did sometimes eat marine shellfish, but the impressive escargotière at Mumba [Rock Shelter, Tanzania] and the numbers of coastal African sites containing quantities of shellfish seem to indicate a more regular intensive use of small scale resources in the MSA (McBrearty and Brooks 2000:512).

    This is certainly one of those where I wouldn't want to have to be the graduate student to test that assertion -- after all, how many coastal Neandertal sites are there? And the occurrence of a unique site where land snails were intensively exploited doesn't seem like the best evidence. Notice how Barton described the relatively nonintensive occupation of the Gibraltar Mousterian caves. It would take some pretty sophisticated sampling to work out whether Neandertals and MSA Africans were significantly different in use of these resources.

    Common sense suggests they wouldn't be, at least not without some reason. After all, the other protein-rich foods they had available were vastly more dangerous and risky to acquire. Finding shellfish at coastal sites would seem more like filling an obvious archaeological blind spot than saying something distinctive about resource collection abilities.

    But then, the use of shellfish in particular figures into the "coastal dispersal" hypothesis for out-of-Africa. The idea that archaic humans were incapable of exploiting coastal resources is inconsistent with the data. But Paul Mellars (2006) presents a curious alternative view:

    The second major factor in stone tool technology lies in the specific functions for which the tools were required. If, as most of the current models suggest, the initial colonization of southeastern Asia and Australasia followed a primarily coastal route (12, 18, 20, 21, 61), then the technologies would be likely to adapt primarily to the exploitation of coastal resources, such as fish, shellfish, and marine mammals (together with tropical plant foods) with perhaps only a minor component of hunting larger land mammals, of the kind that clearly formed a major part of the human economy in both Africa and the whole of western Asia and Europe (21, 59). This would presumably have involved much less emphasis on various forms of hunting equipment (such as spears, meat-processing tools, etc.), as well as equipment involved in the manufacture of elaborate skin clothing, or the construction of tents and other living structures, that were essential to survival in much colder, more northerly environments (59, 62).

    In other words, Mellars proposes that southeast Asia and Australasia lost stone tool complexity that would have been present in their African ancestors, because they didn't eat many large land mammals.

    This takes shellfish-dependence full circle -- hunters that once took African big game found instead that they could live the easy life following the coast and eating marine resources. Well, maybe -- it still seems like a lot of arm-waving based on distributions that may not be different from each other in any real way.

    References:

    Barton N. 2000. Mousterian hearths and shellfish: late Neanderthal activities on Gibraltar. In Stringer CB, Barton RNE, Finlayson JC, eds., Neanderthals on the Edge: Papers from a conference marking the 150th anniversary of the Forbes' Quarry discovery, Gibraltar. Oxbow Books, Oxford. pp. 211-220.

    McBrearty S, Brooks AS. 2000. The revolution that wasn't: a new interpretation of the origin of modern human behavior. J Hum Evol 39:453-563.

    Mellars P. 2006. Going East: new genetic and archaeological perspectives on the modern human colonization of Eurasia. Science 313:796-800. DOI link

    Tags: 
    MSA
    Neandertals
    out-of-Africa
    shellfish
    diet
    foraging
    aquatic resources
    Synopsis: 
    I thumb through some references about Neandertal and MSA use of aquatic resources.

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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.

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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.