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
The Multiregional Stipulation Society
This morning a good friend wrote me to ask about the "multiregional stipulation of random mating and constant population size." What an odd thing for anyone to say, I thought. No anthropologist that I know of thinks that humans mated randomly in the past, or that the population size has been constant. But, as usual, I felt a sinking feeling: if somebody was sending along this weird sentence, it sure must have been published somewhere. And Science comes out on Friday....
Then I found the source for the quote. It was written by Vincent Macaulay and colleagues in this week's Science. The issue includes a letter from Henry Harpending and Vinayak Eswaran (2005), regarding two papers that appeared earlier this year on mtDNA migration through southern Asia. The authors of each of those two papers have a response along with the letter, and Macaulay et al. (2005b) is one of these responses.
Reading these letters is what set off my thoughts about pork barrel paleoanthropology, which became long enough I split them off into a separate post. But the letters certainly provide a good illustration: one asks a very simple question; the others respond in ways that somehow miss the key issues.
Harpending and Eswaran (2005) raise a very simple point: the data aren't all consistent with the preferred explanation; some account must be found that will explain all the data; the papers ignored this central issue in their interpretations.
I think their letter is pretty subtle, and certainly more so than what I wrote about the papers after they came out, where I pointed out some of the data they ignored. And I noted the complete lack of confidence intervals on their estimates. Heck, rereading what I wrote about these papers reminds me just how many problems they had, especially Macaulay et al. (2005). That paper tried to construct an overarching theory -- based only on mtDNA -- about how humans sailed along the coast of the Indian Ocean to settle Southeast Asia, ignored any piece of information that might contradict the story, and suggested that the archaeological evidence that could support their story must have been buried beneath the waves.
Here is part of the response by Macaulay et al. (2005b) to Harpending and Eswaran's letter:
Existing autosomal data do not, in most cases, provide strong evidence for either replacement or hybridization, despite claims to the contrary. The high coalescence time of autosomal loci is not relevant, since in itself this tells us almost nothing about more recent settlement events: A small founder gene pool could well have either a deep or shallow ancestry within a replacement perspective. Given the limited amount of variation in nonrecombined stretches of the autosomes, there is typically little power to distinguish different demographic models. This is as true of the autosomal data used by Templeton (3) as it is of the data in the papers cited by Harpending and Eswaran. The authors of the most recent of these (4) are entirely open about this, but their (frequency-based) suggestion that the root of their tree lies in Asia is mistaken; there is simply insufficient branching structure to fix the geographical location of the root with any confidence. Moreover, supposedly ancient Asian-specific singlenucleotide polymorphisms such as those cited by Harpending and Eswaran are associated with age estimates of enormous uncertainty.
Bold conclusions of ancient Asian ancestry also suffer from limited sampling. Non-African mtDNAs most likely evolved in the Horn of Africa and dispersed from there, but none of the cited papers on autosomal loci include data from this region. Even if such data were available, identifying non-African founder lineages in such low-resolution systems is deeply problematic because of recent back-migration across the Red Sea (5). In cases where autosomal loci do have the necessary resolution, they suggest the replacement model (6-8). The discordant population-size estimates referred to by Harpending and Eswaran are likely more apparent than real, since these long-term values are usually obtained with the multiregional stipulation of random mating and constant population size. The analysis of overly simplistic models with methods that throw away what little information there is in most of these loci throws up straw men, such as the apparent lack of "strong signals of expansion" in some autosomal loci (9) (Macaulay et al. 2005b:1996).
This strikes me as an extraordinary amount of Rube Goldberg-like complexity. Yes, a replacement is true if:
- (a) we disregard entirely the lack of massive population expansion from nuclear genomic data [this is the part of Harpending and Eswaran's letter that there is no answer to in the response];
- (b) the evidence from autosomal data that suggests a long phylogeographic history for non-African populations mysteriously (i.e., without reference) has "little power";
- (c) "frequency-based" suggestions that the root of evolutionary trees lie in Eurasia are mistaken;
- (d) if only the Horn of Africa were sampled better;
- (e) even when you find "founder mutations" from Eurasia, they are really African because of recent back-migration across the Red Sea;
- (f) you avoid any "multiregional stipulations".
Aside from the stipulation problem, I found one other thing worthy of mention. The response cites three papers in support of the idea that nuclear and mitochondrial genetics sometimes show the same result. It apparently escaped their notice that Harpending is a coauthor of one of these papers, and edited another. He might be expected to be aware of their contents, in other words! Could it be, perhaps, that there are some newer papers that show a different pattern? Where the evidence might have more than a "little power"?
Just asking...
References:
Alonso S, Armour JAL. 2001. A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa. Proc Nat Acad Sci USA 98:864-869. Full text online
Harpending HC, Eswaran V. 2005. Tracing modern human origins. Science 309:1995-1997. Full text (subscription)
Macaulay V, et al. 2005a. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034-1036. Science Online
Macaulay V et al. 2005b. Tracing modern human origins. Science 309:1995-1997. Full text (subscription)
Thangaraj K, et al. 2005a. Reconstructing the origin of Andaman Islanders. Science 308:996. Science Online
Thangaraj K et al. 2005b. Tracing modern human origins. Science 309:1995-1997. Full text (subscription)
Tishkoff SA et al. 1996. Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins. Science 271:1380-1387. Summary
Watkins WS et al. 2001. Patterns of Ancestral Human Diversity: An Analysis of Alu-Insertion and Restriction-Site Polymorphisms. Am J Hum Genet 68:738-752.
Early European mtDNA: only mysterious if you want it to be
A paper by Wolfgang Haak and colleagues in this week's Science sequenced ancient mtDNA in 24 Neolithic European skeletons.
A review by Martin Richards (2003) lays out the genetic evidence about population dynamics in Neolithic Europe, along with the likely scenarios. I recommend the paper, it clarified matters for me. During the past thirty years, Cavalli-Sforza and others have pushed a model called "demic diffusion" for Neolithic Europe -- essentially the idea that population growth resulted in the net movement of Near Eastern genes across Europe. But there are other models for population interactions as agriculture spread and populations became more dense -- including long-distance colonizations, elite dominance by one group or another, cultural diffusion without significant genetic movement, and so on.
The main question recently has been about the strength of net movement of genes into Europe. Some have claimed that the majority of present European genes can be traced to the Near East before 6000 years ago. Others have argued that the genetic influence of West Asian populations was substantially more minor, or at least had extended over a longer time from the Upper Paleolithic to the present, instead of being concentrated in the Neolithic revolution itself.
The current paper places itself in the frame of this ongoing debate, but raises an entirely new problem! The abstract:
The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans (Haak et al. 2005:1016).
Some observations:
1. This is the latest in a long line of ancient DNA results that depends on the strangeness of the observation to argue against contamination.
The observed distinct N1a types rule out the possibility of contamination with modern samples, which can be a problem in ancient human DNA studies. It is implausible that the five types are from five different modern contaminants, because the frequency of this type today is very low anywhere in the world, at about 0.2% (23Ð25) (fig. S1). It is also unlikely that the sequence variations seen within the five N1a types are the result of random postmortem DNA damage (26, 27), because three out of six sequence types that we have identified precisely match modern sequences previously published in the literature (table S2 and supporting references); finally, two further N1a types (HAL2 and UWS5) precisely fit into predicted but previously unobserved ancestral nodes in the N1a phylogeny (Fig. 2), underlining the authenticity of the ancient DNA.
It may be that there is just nothing else to be done, but it is troublesome from the perspective of hypothesis testing. Will we ever see a paper that says "ancient DNA demonstrates perfectly ordinary sequences in prehistoric people"? OK, I guess Caramelli et al. (2003) (which reported modern mtDNA sequences in some Upper Paleolithic Italian specimens) had that theme, but I have heard many people question that result for this precise reason.
2. The pattern here is a remarkable echo of the Neandertal mtDNA problem. Here we have a common variant in Europe only 7500 years ago that today is almost gone. With the Neandertals, we have a very common variant that today, after 40,000 years, is completely gone.
You might therefore expect that some clever geneticists would claim that the Neolithic farmers contributed little or no genetic ancestry to living Europeans. And that is precisely the hypothesis discussed by Haak et al. (2005):
These simulations reject the simple hypothesis in which modern Europeans are direct descendants of these first farmers and have lost N1a mainly by genetic drift. Hence the simulations confirm that the first farmers in Central Europe had limited success in leaving a genetic mark on the female lineages of modern Europeans. This is in contrast to the success of the Neolithic farming culture itself, which subsequently spread all over Europe, as the archaeological record demonstrates. One possible explanation is that the farming culture itself spread without the people originally carrying these ideas. This includes the possibility that small pioneer groups carried farming into new areas of Europe, and that once the technique had taken root, the surrounding hunter-gatherers adopted the new culture and then outnumbered the original farmers, diluting their N1a frequency to the low modern value. Archaeological research along the Western periphery of LBK and isotope studies of some of our sampled individuals seem to support the idea that male and female hunter-gatherers were integrated into the Neolithic communities (3, 10, 29). This hypothesis implies that N1a was rare or absent in Mesolithic Europeans, which may be a reasonable assumption given the rarity of the N1a type anywhere in the world (Fig. 3). An alternative hypothesis is a subsequent postÐearly-Neolithic population replacement in Europe, eliminating most of the N1a types. Archaeological evidence for such an event is as yet scant (Haak et al. 2005:1018).
Of course, this idea depends on several unknowns. It proposes that European hunter-gatherers who were contemporary with the LBK culture had very different mtDNA types -- indeed, that they had the types that are presently common. And it proposes that the intrinsic growth rate of agriculturalists was very small, so that their genes were flooded by hunter-gatherers transitioning to agriculture.
But if their genes were so flooded at every stage of their expansion, then the N1a mtDNA sequences shouldn't be there in the first place -- they should have been left behind in the Near East. So this is a very curious event -- an expanding population saw one of its major mtDNA variants greatly contract in frequency, so much so that today it is nearly gone.
3. Let's review the facts. The mysterious N1a mtDNA type is currently rare anywhere in the world. It is carried by only 0.2 percent of Europeans. But it has a high frequency among these Neolithic Europeans -- 25 percent of the samples, which means the true population frequency was likely between 8 and 42 percent (Haak et al. 2005:1017). The paper found that this great reduction in frequency within Europe cannot have been accomplished by genetic drift.
Can someone tell me why the word "selection" doesn't appear in this paper?
References:
Balter M. 2005. Ancient DNA yields clues to the puzzle of European origins. Science 310:964-965. Full text (subscription)
Haak W et al. 2005. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310:1016-1018. Full text (subscription)
Richards M. 2003. The Neolithic invasion of Europe. Annu Rev Anthropol 32:135-162. Full text
More on the Neolithic mtDNA pool
Athena of Rites of Passage has a post critiquing the recent Neolithic aDNA paper (via Palanthsci). Her take is a bit different from mine. It makes good points as well -- focusing on the small sample size and the complexity of probable cultural interactions in the Neolithic.
Here's a good quote:
The authors argue that simulations confirm that the first farmers had limited success in leaving a genetic mark on the female lineages of modern Europeans. What are these simulations? What are their parameters? Given that their genetic data is basically flawed, this part of the argument just exacerbates whole, flawed mess. And now comes the punch line: "One possible explanation is that the farming culture itself spread without the people originally carrying these ideas." Huh? Once again... huh? They then go on to suggest "pioneer groups" who really impressed the oh-so-backward Mesolithic populations to the extent that they saw the error of their ways and they took up farming. Whooosh, we turn back the clock to ideas of farmer-missionaries.
We will always have the problem of small samples and complex interactions. All the more reason to be cautious in interpreting results.
Diffusion versus migration in North African prehistory
There is a little disagreement in the letters of this week's Science, about mtDNA evidence for migrations from West Asia into North Africa. This is in reference to a paper late last year by Olivieri and colleagues, that argued that both North African and European populations traced their ancestry ultimately to Upper Paleolithic people of the Levant.
That paper had this abstract:
Sequencing of 81 entire human mitochondrial DNAs (mtDNAs) belonging to haplogroups M1 and U6 reveals that these predominantly North African clades arose in southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago. Their arrival temporally overlaps with the event(s) that led to the peopling of Europe by modern humans and was most likely the result of the same change in climate conditions that allowed humans to enter the Levant, opening the way to the colonization of both Europe and North Africa. Thus, the early Upper Palaeolithic population(s) carrying M1 and U6 did not return to Africa along the southern coastal route of the "out of Africa" exit, but from the Mediterranean area; and the North African Dabban and European Aurignacian industries derived from a common Levantine source.
That sets out the hypothesis: a migration from the Levant some 40,000 years ago spread these haplotypes into North Africa, at around the same time as in Europe.
I took some notes on this paper at the time, because of the real paucity of any comparative information on the "Dabban" industry that is the proposed archaeological correlate of this migration. I'm not going to go into it here; let's say I was skeptical at the time, not least because geneticists have a way of assuming that industries are much more "real" or extensive than the archaeology allows. I still think that the archaeology is weak, but it is certainly possible that some significant population movement happened.
The current letter and response are interesting, not because they differ in their interpretation of the haplotype distributions (which they do) but because their arguments are almost entirely in terms of archaeological and linguistic comparisons.
Forster and Romano argue that haplotypes can't really provide evidence for early population movement, because a relatively late migration could have carried much older haplotypes along with it, or they may have entered North Africa by diffusion without any major population movement.
They argue that archaeological and linguistic evidence favor more recent migration of populations as a major mechanism for the movement of gene lineages:
Three points lead us to believe that our younger chronology for the back-migration into northern Africa still merits consideration. First, the mtDNA trees reconstructed by Olivieri and colleagues are less than conclusive because they consist of phylogeographically mixed branches, which cause uncertainty in identifying the relevant founder nodes for genetic dating. Second, in our view the fact that the North African mtDNA marker types still correspond so closely with the Afro-Asiatic language zone argues against the existence of that correlation for tens of thousands of years. Third, cave art in the Sahara shows that in Neolithic times (around 5000 B.C.), the population of the Sahara was still of sub-Saharan African ancestry (see figure), whereas "Europoid" figures documenting the arrival of west Eurasians appear later in the cave art record (3).
In response, Olivieri and colleagues claim that the recent Holocene events -- although relatively well documented, are insufficient to explain older haplotype distributions, and that archaeological evidence also supports their point of view.
The principal problem with great syntheses of languages, genes, and figurines (or pots) is that they lump together different migrational and cultural processes and especially overstretch recent events of the Holocene, thereby downplaying or swamping the genetic signals that point to much earlier events of the Pleistocene (1, 2).
Personally, I don't know which hypothesis is correct; it seems to me that mtDNA haplotypes are never going to answer this kind of question. The question is about mechanisms of genetic dispersal.
Both hypotheses more or less agree about the current distribution of haplotypes. I say "more or less" because in fact, both hypotheses are interpreting these distributions post hoc -- they're not really testing hypotheses, they're just offering archaeological arguments in support of migrations they assume the mtDNA is documenting. Remember when I mentioned the "reality" of these archaeological industries? This is what I meant.
Regardless of what we think about the archaeology, these haplotype distributions still deserve some explanation. How did a 45,000-year-old haplotype spread from its apparent origin in the Levant across North Africa? Did it get there slowly and gradually by diffusion? Or did it come all at once in a long-distance movement of a group of people -- a so-called "folk migration"?
This question, diffusion versus folk migration, is of course a very old one. It remains central to all these considerations of recent genetic variation.
A couple of weeks ago, I had the extraordinary privilege of hearing two of the real leaders in paleoanthropology having precisely this argument. How much of recent evolution has been driven by folk migration, and how much by the diffusion of genes into standing populations?
These letters are a good illustration of the question, drawn out into a particular case. We'll be hearing more about this soon, I think.
References
Forster P, Romano V. 2007. Timing of a back-migration into Africa. Science 316:50-53. doi:10.1126/science.316.5821.50
Olivieri A, and 14 others. 2007. Timing of a back-migration into Africa. Science 316:50-53. doi:10.1126/science.316.5821.50
Olivieri A, and 14 others. 2006. The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314:1767-1770. doi:10.1126/science.1135566
Did humans face extinction 70,000 years ago?
That was the headline of many of last week's stories about the paper by Behar and colleagues, drawing upon the Genographic Project African mitochondrial DNA (mtDNA) data. Here's a quote from the National Geographic Society's press release:
Previous studies have shown that while human populations had been quite small prior to the Late Stone Age, perhaps numbering fewer than 2,000 around 70,000 years ago, the expansion after this time led to the occupation of many previously uninhabited areas, including the world beyond Africa.
And here's project director Spencer Wells' quote in the same release:
Dr. Spencer Wells, National Geographic Explorer-in-Residence and Director of the Genographic Project, said: "This new study released today illustrates the extraordinary power of genetics to reveal insights into some of the key events in our species' history. Tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA."
Well, that certainly sounds dramatic. But is it true?
The paper itself does not provide any tests of the number of ancient humans indicated by the mtDNA phylogeny. The press release mentions "previous studies" that fix a small initial founding population for Africans, so I went looking through the paper to see which studies they had cited.
I found this passage, which seems relevant:
Different approaches were taken in the attempt to estimate the sub-Saharan Homo sapiens population size in different time frames.7
OK, that seems like what I want -- estimates of population size in different time frames in sub-Saharan Africa. So I looked up reference 7, and found this:
Hawks,J., Wang,E.T., Cochran,G.M., Harpending,H.C., and Moyzis,R.K. (2007). Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. USA 104, 20753-20758.
D'oh!
Now on the one hand, it is very gratifying to be recognized as an expert on the genetic demography of sub-Saharan Africa. I mean, we did work hard on that paper. But on the other hand, it seems like we might do a little better than that paper as an examination of the demographic history of sub-Saharan Africa.
And the current paper by Behar and colleagues provides exactly the right kind of information to get that more detailed demographic history. So I've put together some notes here on how we can discover whether there was a population bottleneck 70,000 years ago in Africa, using the mtDNA evidence. I'm setting aside for the moment the question of population structure -- the "isolation" story that was also made in the press release for the paper. Population structure and size are not independent of each other, and we will have to consider how they interacted in African prehistory. But the first issue should be size, because our interpretation of size is based on relatively simple aspects of genetic variation (at its simplest, the first moment), while testing hypotheses about population structure requires higher-order comparisons.
The Templeton review
The Yearbook of Physical Anthropology has a new review of the genetic evidence for modern human origins by Alan Templeton. The paper is 27 journal pages, and they are full of detail -- especially after the section describing basic coalescent theory.
I'll be going through this paper in the next few days and highlighting some of the issues it raises. In the meantime, here are some quotes from the Washington University press release:
"The 'Out of Africa' replacement theory has always been a big controversy," Templeton said. "I set up a null hypothesis and the program rejected that hypothesis using the new data with a probability level of 10 to the minus 17th. In science, you don't get any more conclusive than that. It says that the hypothesis of no interbreeding is so grossly incompatible with the data, that you can reject it."
...
The new data confirm an expansion out of Africa to 700,000 years ago that was detected in the 2002 analysis.
"Both (the 1.9 million and 700,000 year) expansions coincide with recent paleoclimatic data that indicate periods of very high rainfall in eastern Africa, making what is now the Sahara Desert a savannah," Templeton said. "That makes the timing very amenable for movements of large populations through the area."
Found via Dienekes, who seems to be one step ahead of me this week!
References:
Templeton AR. 2005. Haplotype trees and modern human origins. Yrbk Phys Anthropol 128(S41):33-59. DOI link
Zimmer on Templeton
Carl Zimmer has a post discussing Alan Templeton's work. It's a good review, covering Templeton's two essential points: history cannot be traced from any single gene locus, and evidence from multiple loci makes human evolution look like a trellis of relationships among populations, not a diverging tree originating in one population. Here's a quote:
Templeton has found that he can easily reject the idea that all our genes come from the same 200,000 year old population of African humans. Instead, he finds evidence of three separate expansions out of Africa. The first he estimates to have occurred 1.9 million years ago -- which just so happens to coincide with the earliest fossils of Homo erectus outside of Africa. Then he finds another expansion he dates to 650,000 years ago -- which just so happens to coincide with the emergence of hominids in Europe of hominids that are believed to give rise to Neanderthals. The last expansion can be traced back 130,000 years ago.
I'll have more discussion here when Templeton's new paper comes out in the Yearbook of Physical Anthropology. In the meantime, you can get a quick review by reading the post.
John Hawks Department of Anthropology
University of Wisconsin—Madison
Copyright © 2007 John Hawks