Genetic evidence for punctuated equilibrium

Phylogenetic trees reveal traces of rapid evolution at speciation, a new study says

Melissa Lee Phillips
Oct 5, 2006
Evidence for punctuated equilibrium lies in the genetic sequences of many organisms, according to a study in this week's Science. Researchers report that about a third of reconstructed phylogenetic trees of animals, plants, and fungi reveal periods of rapid molecular evolution."We've never really known to what extent punctuated equilibrium is a general phenomenon in speciation," said Douglas Erwin of the National Museum of Natural History in Washington, D.C., who was not involved in the study. Since its introduction by Stephen Jay Gould and Niles Eldredge in the 1970s, the theory of punctuated equilibrium -- that evolution usually proceeds slowly but is punctuated by short bursts of rapid evolution associated with speciation -- has been extremely contentious among paleontologists and evolutionary biologists.While most studies of punctuated equilibrium have come from analyses of the fossil record, Mark Pagel and his colleagues at the University of Reading, UK, instead examined phylogenetic trees generated from genetic sequences of closely related organisms.Based on the number of speciation events and the nucleotide differences between species in each tree, the researchers used a statistical test to measure the amount of nucleotide divergence likely due to gradual evolution and the amount likely due to rapid changes around the time of speciation.They found statistically significant evidence of punctuated evolution in 30% to 35% of the phylogenetic trees they examined. The remaining trees showed only evidence of gradual evolution.Among the trees showing some evidence of punctuated equilibrium, the authors performed further tests to determine the size of the effect. They found that punctuated evolution could account for about 22% of nucleotide changes in the trees, leaving gradual evolution responsible for the other 78% of divergence between species.Pagel and his colleagues were surprised that rapid evolution appears to contribute so much in some lineages, he said. "I would have maybe expected it to be half that much," he told The Scientist.The researchers also found that rapid bursts of evolution appear to have occurred in many more plants and fungi than animals. Genetic alterations such as hybridization or changes in ploidy could allow rapid speciation, Pagel said, and these mechanisms are much more common in plants and fungi than in animals."Their result is pretty interesting, particularly the fact that they got so much more from plants and fungi than they did from animals, which I don't think most people would expect," Erwin told The Scientist.However, it's possible that the analysis could be flawed, because the authors didn't take into account extinction rates in different phylogenetic trees when they determined the total number of speciation events, according to Douglas Futuyma of the State University of New York at Stony Brook, who was not involved in the study. But "they've got a very interesting case," he added. "I certainly think that this warrants more attention."According to Pagel, the results suggest that other studies may have misdated some evolutionary events. Dates derived from molecular clocks assumed to have a slow, even tempo will place species divergences too far in the past, he said, since genetic change assumed to take place gradually may have happened very quickly. "These kinds of events could really undo any notion of a molecular clock -- or at least one would have to be very careful about it," Futuyma told The Scientist.Well known evolutionary mechanisms could account for rapid genetic change at speciation, Pagel said. Speciation often takes place when a population of organisms is isolated, which means that genetic drift in a small population or fast adaptation to a new niche could induce rapid evolutionary change.Melissa Lee Phillips Links within this article:M. Pagel et al., "Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level," Science 314:119-121, October 6, 2006. http://www.sciencemag.orgJ.P. Roberts, "New Growth in Phylogeny Programs," The Scientist, December 20, 2004. Erwin Palevitz, "Love Him or Hate Him, Stephen Jay Gould Made a Difference," The Scientist, June 10, 2002. Gould, N. Eldredge, "Punctuated equilibrium comes of age," Nature, November 18, 1993. PM_ID: 8232582 L. Pray, "Mechanisms of Speciation," The Scientist, November 17, 2003. Pagel Toma, "Fast track hybrid speciation," The Scientist, November 29, 2002. Adams et al., "Polyploidy and genome evolution in plants," Current Opinion in Plant Biology, April 2005. Futuyma