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.)