Highlight: Family Ties--New Evidence Simplifies Human Evolutionary Tree

Abstract

Rest easy, it seems our ancestors were not the interspecies Casanovas once supposed. After humans went their separate way from chimpanzees, we made a clean break of it, each group mating within its species, a new analysis suggested by geneticist Tadashi and coworkers. This is a thorough rewrite of the evolutionary narrative told by David Reich, Nick Patterson, and colleagues at the Broad Institute in Cambridge, MA. In 2006, the popular press rang with near-salacious headlines such as “Late swinging in the evolutionary tree?” from The Philadelphia Inquirer and “Grandpa! Leave that chimp alone! Who knows what it might lead to?” from The Times of London. That year in Nature, Reich and Patterson presented evidence that, following an initial genetic split 6 million years ago, humans and chimpanzees interbred for a time as a hybridized species. The analysis was not universally well received. “We’d like to have a more Victorian view of our genome,” David Page of the Whitehead Institute in Cambridge told the New York Times. ”This reminds us that we are really animals.” However, beyond the giggle-inducing implications, a number of phylogenists did not like it for more practical reasons. The explanation was complicated and based on thin evidence. “In it very small numbers were given large importance,” said Dan Graur, who studies molecular evolution at the University of Houston. “This very complicated model has been making its way into literature and textbooks. But the problem is that people have ignored the fact of recombination.” During meiosis, matching chromosomes can swap whole sections of material, leaving Junior with new-sprung genetic diversity, but phylogenists with a newly complicated picture. However, in a new study published in Genome Biology and Evolution (Hara et al. 2012), researchers from Japan’s National Institute of Advanced Science and Technology in Tokyo and the Graduate University for Advanced Studies in Kanagawa managed to sidestep this problem entirely. “What was done in this case this was quite amazing,” said Graur, who was not involved in the work. “The limits are not contaminated by half-maternal, half-paternal material.” By comparing shorter segments that are unlikely to have recombined since humans shared a common ancestor with the great apes, they were able to trace evolutionary history without seeing any hint that different linages had once converged into one. “Everyone who is doing primate evolution will be affected by this,” Graur said. When asked how much their work negates previous work in the field, Imanishi was modest: “Our estimates of human-ape divergence times and the ancestral population sizes are not much different from those of previous works,” he wrote. “However, by using the largest dataset of genome sequences and applying a much better model to the data, we succeeded in presenting the most accurate estimates ever.” Their work, so far, has been warmly received by colleagues. “It seems that many evolutionary biologists, including Dr. Naruya Saitou of National Institute of Genetics of Japan […] did not like the hypothesis by Patterson et al. and wanted to deny it. We could demonstrate what they intuitively thought.” In addition, the researchers are intrigued by several other aspects of their study. They were also surprised by the finding that each chromosome seems to have an intrinsic mutation rate. “We concluded that variation in tau [speciation time] across the chromosomes would be due to the difference in mutation rate across the chromosomes,” writes Yuichiro Hara. “But we could not find the cause of the variation in mutation rate. We are interested in the mechanisms of genome evolution in closely related lineages (Hara and Imanishi, 2011, BMC Evol. Biol.), too, and thus clarification of this is our next goal.” And beyond that the team is also interested in seeing their novel analytical method applied to other species. Graur is similarly eager to see this method become more widespread, “These days complicated models are used as a first resort rather than a last resort. It’s nice to see such a straightforward and ingenious approach to solve a problem that was quite complicated.” He is especially interested in seeing the relationship between humans, Neanderthals, and Denisovians explored. Some claim that modern Papua New Guineans carry fragments of the Denisovian genome and paleolithic hominids believed to exist based on a tiny amount of DNA extracted from a finger bone found several years ago in a Siberian cave. Graur did have one criticism. “If I was writing up this work, I would have said that everything that was said before about the speciation was junk. The authors are very polite. They could have been more forceful.”