Tree or Trellis

Over the weekend I was part of a panel at the American Anthropology Association, the topic of which was "Updating Human Evolution." I got to listen to ten presentations by scientists, each offering a look at how our understanding of our ancestry is changing with new research. While they were all interesting, I was particularly eager to hear one: Alan Templeton of Washington University. Templeton. Having just finished a book about human evolution, I knew that Templeton has been doing some groundbreaking work to figure out what our DNA has to say about our evolutionary history. I was looking forward to hearing about Templeton's latest results, and I wasn't disappointed.

The genetic study of human evolution really got off the ground in the 1980s. Allan Wilson of Berkeley and his colleagues compared the sequence of a gene in a sample of people and used their results to draw a genealogical tree. The gene came from mitochondria, energy-generating structures in our cells that also carry their own DNA. Wilson and his colleagues knew that we probably get all our mitochondria from our mothers. (Sperm apparently don't deliver their mitochondria to eggs during fertilization--only 23 chromosomes that will end up in the nucleus of the fertilized egg.) If a woman's mitochondrial DNA undergoes a mutation, she will pass that mutation down to her children, and her daughters will pass it down to their children. So finding people who share distinctive mutations allows scientists to see how closely related they are to one another. And since there was reason to think that the mutations arose at a relatively steady rate, they could even act as a molecular clock. If people shared an ancient ancestor, their mitochondria would be more different than if they shared a recent one.

The results of Wilson's study were quite striking. The tree he and his colleagues drew showed that all of the genes on the deepest branches of the tree belonged to people of African descent. Genes from Asians and Europeans were all more closely related to each other than to those from Africans. The researchers argued this meant that all living humans got their mitochondrial genes from a woman who lived in Africa less than 200,000 years ago. At a later date, one group of Africans moved out of the continent and colonized the rest of the world.

Before these results emerged, many paleoanthropologists argued that our species had evolved gradually over the past million years from Homo erectus, an ancestral hominid that lived in Africa, Europe, and Asia. Different populations evolved different traits, but enough interbreeding took place that they never became genetically isolated from one another, thus becoming a separate species. Neanderthals were thus the ancestors of living Europeans, and East Asian Homo erectus was the ancestor of Chinese and other people from that part of the world.

Many scientists saw in Wilson's tree a different story: Homo sapiens evolved much more recently in Africa, and then spread out into the other continents. Neanderthals and East Asian Homo erectus were actually separate species, and they did not leave any descendants among today's humans. If they did, the mitochondrial tree would have converged on a much older common ancestor. How they became extinct was an open question--perhaps through direct conflict or simply through competition for the food and other resources hominids needed to stay alive.

Adding more samples of mitochondrial DNA supported the basic outlines of Wilson's initial work. So did later studies of the Y chromosome. The Y chromosome acts a lot like mitochondria. Only men carry it, and they pass it down unchanged (except for mutations) to their sons. So it also serves as a good marker for genealogy. It showed much the same pattern as the mitochondria--a recent African origin and a subsequent spread to the rest of the Old World.

There's just one tricky thing about these results. All living men can trace the ancestry of their Y chromosome back to a man who lived an estimated 59,000 years ago, perhaps 100,000 years or more after "mitochondrial Eve." At the anthropology meeting, Alan Templeton explained the fundamental problem with these studies: a tree based on a single gene only tells you about the evolutionary history of that one gene. Genes may spread quickly or slowly through our species, sometimes due to natural selection and other times due to a chance-like process called genetic drift. The tree of a single gene on its own does not automatically reveal the evolutionary history of the species that carries it. People carrying the African Eve mitochondria might simply have interbred with people outside of Africa and passed their mitochondria on to later generations.

Fortunately, scientists are not limited any longer to just looking at mitochondria or the Y chromosome. Templeton has come up with a way to statistically compare the different trees of these genes, and use the comparison to test hypotheses about how our species evolved. Templeton published the first results of this method in 2002 in Nature, and at the anthropology meeting he described his newest results, in which he pushed his data set from 10 genes to 25 (the results will be published in the next issue of the Yearbook of Physical Anthropology, which should be online soon).

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.

His statistical study shows that Africans and Eurasians interbred enough to let genes flow back and forth for at least 1.5 million years (with 95% confidence). In fact, the results from a hemoglobin gene and the Y chromosome suggest a major expansion from Asia back into Africa after the latest expansion from Africa.

What's fascinating about Templeton's work (and other studies like it) is that it doesn't just take us back to a 1970-vintage view of human evolution. Humans really did expand out of Africa, as Wilson had claimed. But their expansion didn't prevent some genes from the hominids that were already there from surviving until today. Templeton doesn't have much to say on what happened when Africans moved into Eurasia--was interbreeding rare, or did the populations of pioneers and natives fuse together? Whichever is the case, Templeton would like people to think about human evolution less as a tree and more as a trellis. To that end, I've reproduced a figure from his new paper. (The thin lines show the flow of genes between different regions of the world, and the black arrows show major expansions of human populations from one region to another.)

[Update: Templeton's paper is now online.]



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Has any other genetic research backed up Templeton's claims?

As far as I understand from your comment, there is a little bit of multiregionalism in Templeton research. Or is it just the evidence of gene flow among various populations of (strictly) sapiens? Last but not least, who went out of Africa more than half a million years ago?

Thanks for the blog.


By Marco Ferrari (not verified) on 07 Dec 2005 #permalink

Iwould say what Templeton writes IS multiregional evolution

It's good to see anthropologists starting to think more deeply about the nature of phylogeny near the species level. When we stand far away from the evolutionary tree the branches are clear; when we get up close the tree resolves itself into a genealogical network that is exceedlingly complex. Problems of historical inference interact with problems of historical representation to create a circle of questions that look simple on the surface but are in fact quite difficult.

Phylogenetic problems near the species level have been discussed widely in the general systematics literature, and anthropologists could benefit from an examination of that literature. The phylogeny of Homo sapiens is neither more nor less complex than that of any species. These two papers might be of interest to people working on these issues; the first is a general introduction and the second is more technical:

"Evolutionary history and the species problem" (HTML text only) (pdf with diagrams)

"Systematic generalization, historical fate, and the species problem" (HTML text only) (pdf with diagrams)

Interesting, interesting. I really wonder where man first came from? Did cosmic radiation produce mutants which eventually produced us? What were we like l.5 million years ago? Would I recognize my self as a human? Could I talk to me? The greatest question is Why am I here?? Is there a reason or am I just a genetic mistake that has gone horribly wrong? Will I kill my self off before I event make a dent on history of the earth ? After all, the dinosaures were here for millions of years and us, maybe one milliion years of which these last 3000 years have produced something that is destructive to the earth and its inhabitants including itself? Are we going to have another genetic explosion in the future that will make us different than we are today? Is life so maluable that it can be anything, depending on the era of time uncountable? So many questions and to think we are waging war at great expense on our fellow man.

By Jimmy Porter (not verified) on 07 Dec 2005 #permalink

I would say what Templeton writes IS multi regional evolution

I see it as more of a hybrid between "out of Africa" and a multi regional view. Several waves of out migration with some returning movement. The major changes seem to be radiating out of one place quickly rather than the slow mixing of multi regionalism (assuming I understand multi regionalism correctly).

Just as with "punctuated equilibrium" and gradual evolution, it would make sense that neither "out of Africa" and multi regionalism are absolutes. In fact there seem to me to be similarities between the "out of Africa" view and punctuated equilibrium. But why should Africa be the source of more disequilibrium periods. Maybe the population of early hominids was larger there due to their longer history there or maybe the climate of Africa changes more often.(?)

From the trellis diagram, it looks like the Southern European hominids were the product of steady gene flow between the Africans & the South Asians. But where does that put the Neandertals? And which Homo species was it who produced the "Acheulean Out of Africa Expansion"? That one was a bit early for Homo sapiens.

says Milford (Wolpoff?) I would say what Templeton writes IS multiregional evolution

One interpretation is that the data conform to some multiregional positions. It is also consistent with an "out of africa then back again" idea. (After all, early humans did not have a map or itinerary, so movement was not one-directional.)

It is plausibly consistent only with ... 'soft' multiregionalist and 'soft' out-of africa positions.

I have observed the 'out-of-africa' and 'multiregionalism' hypotheses transformed into a false dichotomy.

My analogy uses a chessboard: the extreme multiregionalism concept has humans evolving independently on each square, with little gene exchange with adjacent squares.

The extreme out-of-africa concept has only the humans from square a-1 spreading over the entire board and exterminating previous tenants.

Surely the truth is somewhere in between.

By Anonymous (not verified) on 08 Dec 2005 #permalink

Interesting. I had never read anywhere about the "Out of Asia" part. Unfortunately, there is not date on the diagram for that part.

The "Acheulean out of Africa" also is news to me. Is this Neanderthal?

I guess the treillis part indicates that the population of humans was somehow linked all the way from Africa to Asia, for example tribes distributed all along the territory, that would exchange mates, and thus allow gene flow. Is there any way to deduce from this whether it's the males or the females that would be more mobile? That would be terrific information about the culture of the early human societies!

[The "Acheulean Out of Africa" probably denotes the migrations of ergaster/erectus.]

This is very intersting material. As we all know, "Out of Africa" has been propounded without respite -- longevity due in no smaller measure to an apropos compound of egalitarian thought and nascent science. However, we now know that those population histories adduced from singular sources of information (mtDNA, Y-chromosome) are too simplistic.

That's what makes this issue so intractable, yet so intriguing: information forever beyond our investigation.

For example, the common belief at the moment is that the Neanderthals contributed very little to our genepool by virtue of the fact that we have yet to find a definitive Neanderthal lineages. Yet, we know that lineages can be quickly lost or dispersed -- evolution is seemingly nothing but a chaotic jumble of stochastic events: founder effects, bottlenecks, drift, end-/exogamy (migration), selective sweeps, population expansions -- or any concurrent combination of these! Piecing together population histories is a difficult task indeed, compounded by the fact that mutation rates are themselves very suspect, the consequent confidence intervals on coalescence dates even more so, and that experts have yet to agree on whether mtDNA is even neutral (the fundament of all timeline work therefrom).

Invariably, interpreting the paleoanthropological material is certainly somewhat more subjective than analyzing allele frequencies and distributions, but how can it be ignored? The fact remains that some (ostensibly "modern") Upper Palaeolithic European remains possess the mandibular nerve canal sheath found in Neanderthals but absent among Africans and Asians; that many fossil finds (attributed to sapiens due to their age) possess intermediate morphologies between "archaic" and "modern" hominids; that no distinct and recent "African" hominid material has been found in other areas of the world; that many extant humans have many features attributable to archaics; that hominid fossils in Asia suggest not invasion but instead in-situ gradational evolution from archaic to modern forms. And the list goes on...

If I were a betting man, I would hedge my bet on reticulated multi-regional evolution (not Coon-esque independent speciation). What is for sure is that the singular African exodus of convention is a gross simplification that resonates most strongly with the public, but discordantly with the genes and bones we have scrutinized hitherto.

By The Ice Titan (not verified) on 09 Dec 2005 #permalink

Is the long distance dispersal arrows indicative of large scale migration or is it evidence of the 'stronger evolutionary fitness'* of a variant of a gene?

* By this, I mean a variant of a gene that increases the likelihood of survival of the individual that carries it.

Tempelton's trellis doesn't support (nor refute) multiregionalism, as the major past expansions occur within African populations. The question is, (1) are there signals of admixture at later dates with archaic populations in Eurasia and out going modern humans? And (2) signals of admixture with back migrations to Africa after lengthy periods of time? So far molecular evidence does not seem to support affirmative answers. This doesn't mean some don't see in the fossils evidence of such admixture. But such conclusions can be tricky. Human variability may be greater due to selection and/or plasticity than assumed. Consider all those robust looking Australian fossils at Kow Swamp--H. erectus? or just sapiens enduring harsh and drier conditions? Also diversity of loci will exceed 200,000 years for some regions. That is only to be expected. We shouldn't expect all our DNA to date back to some 200,000 years, as though it was wiped clean. Afterall, the assumed effective size of the ancestral human population may have been somewhere around 10,000 individuals (maybe more?). Survival of ancestral loci depends on population history.

The "tangled bush" view of human evolution resulting from a focus on populations and genes rather than on species is perhaps less neat but more in keeping with the actual complexity of things. A "tree diagram" may be more neat than a web, and it may even tell some kind of bird's eye view of the truth, but things are always more complicated. This reminds me of Stephen Jay Gould's emphasis on the growing complexity of our view of the human evolutionary lineages. There is a major issue, however, which needs to be clarified, namely the possibility first and then the degree of interbreeding between different human species -- supposing that is the right word in any case. A fascinating post, Carl.

Given the new finding of 700,000 years ago migration into Britain, one might be led to believe this should have left some genetic signature/expansion somewhere. It would be a good test of Templeton's 'trellis' if that expansion were found now that we know what we are looking for.

whew, the comments on this blogpost alone bring up so much material. Templeton's work is both fascinating and yet another example of excessive reductionism by geneticists. It's a trend we've seen time and time again, and yet it continues. If I ever meet Templeton I owe him a beer for so definitively exposing one of their little lies. But enough of the rantings of a 'phenotypist' (no better word for my school of thought).

One of the things that always bothered me about the strict Out Of Africa school is that it just don't pass the common sense test: I brought these objections up both as an undergrad and as a grad student in paleoanth. I mean, there are people out there that have carnal relations with their [i]sheep[/i]. And they want me to believe that Early Moderns didn't have intercourse with either Homo erectus or neanderthalensis? Sorry, not going to believe it. Having seen 'scientific' reconstructions based on skulls such as Kabwe (broken hill), I can tell you that until I was told which skull it was, I might not have placed it as outside of H sapiens...and I'm supposed to be trained to see those differences. Also, I don't know if anyone here has had a chance to read Wolpoff et al.'s review articles on the subject, but they're brilliant, as even rabid Out Of Africa people will concede.

I'd have to agree with Milford that what Templeton demonstrates IS INDEED multiregional evolution. It is gene flow across continents, in both directions, throughout the lineage. Multiregionalism merely says that local populations continued to be part of the gene pool over time, rather than being supplanted by migrations.

Also, the Acheulean expansion looks like the perfect chronology to be the Homo antecessor expansion (the caves in Spain...those guys). antecessor is considered the best candidate for the neanderthal ancestral population. And indeed as the lead scientists at the spain sites will contend, potentially for moderns as well (i dunno how much I credit that).

The Templeton Trellis gives an elegant, simple (and multiregionalist) explanation for the gradual trend in H erectus toward some gracilization and increased brain size over time. THese are definitive trends seen whether we refer to H ergaster in Africa or H erectus in asia (specifically Mapa and Dali). A continued gene flow across the two 'species' would easily explain that, as one would expect such traits as increased brain size to spread rapidly due to conferred fitness benefits.

The gene/populationf flow chart is nothing particularly new. It appeared in Dawkins 2004 book, The Ancestor's Tale.

I'd just like to point out that I was the 502,357th visitor to The Loom. Very proud of it. Never thought it would happen to ME.

By JB "The Middleman" (not verified) on 09 Jan 2006 #permalink

"In any local (ââ¬Ånon-dimensionalââ¬Â) situation species are usually well-defined, but across space and time the grouping of populations into species is often problematic. Three views of species are in common use today, the biological species concept, the evolutionary species concept, and the phylogenetic species concept. Each of these has strengths and weaknesses, but no matter which is applied, exact counts of the number of species in any extended area will always be ambiguous no matter how much factual information is available."
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