Leapfrogging Darwin: Desai lab captures evolution in action

November 21, 2019
Cvijovic and Nguyen Ba

‘Survival of the fittest’ is arguably the most influential concept in modern biology. This week, the Desai group went head-to-head with Darwin’s dogma.

“People used to think species were created as is. Lamarck, Wallace, Darwin, and company convinced people that species evolved,” says B.N. Queenan, Executive Director of Research at Harvard’s NSF-Simons Center for Quantitative Biology. “For the last 150 years, we’ve been living within the Darwinian framework: that in the struggle for survival it’s the fittest who get through. The Desai group has just shown evolution plays by entirely different rules.”

“We figured out a new way to watch evolution in action,” says Michael Desai, professor of Organismic & Evolutionary Biology (OEB) and of Physics. “And as soon as we started watching, we realized it wasn’t doing what it was supposed to under the existing theory.”

“We’re led to believe that evolution is slow, that beneficial mutations are rare,” says Ivana Cvijović, a former Ph.D. student in the Desai lab and one of the lead authors on the paper. “Instead, we see organisms that are tripping over themselves to get better. They can’t even use all their innovations because they are competing so fast with each other.”

“The new model fundamentally changes our ability to predict how things evolve,” says Queenan. “Up until now we haven’t been able to anticipate how the flu will evolve, or the common cold, or how antibiotic resistance will emerge, because we’ve been using a model that doesn’t really account for what happens in nature.”

“Even if you have complete information about a population at a certain time, you actually have a very limited ability to predict who is going to win in the future,” says Artur Rego-Costa, an OEB graduate student with Michael Desai. “That’s to me the most exciting part of the project.”

“To me, the most surprising thing was: mutations and genotypes that seem to have fallen behind can leapfrog and dominate,” says Cvijović, now an Associate Research Scholar at the Lewis-Sigler Institute for Integrative Genomics at Princeton. “There are ‘come from behind victories’ happening constantly.”

The insight into evolution was made possible by a technology developed by Alex N. Nguyen Ba, a postdoctoral fellow in the Desai lab and one of the lead authors on the paper. Nguyen Ba invented a way of “barcoding” DNA. The Desai lab could therefore insert barcodes into yeast cells and then watch what happened as the individual cells evolved over a thousand generations.

“We can identify every single relevant beneficial mutation over a thousand generations,” says Nguyen Ba. “Even in the simplest case – yeast inside a test tube – we’ve learned quite a lot more than what people anticipated.”

“This project is what I love about science,” says Cvijović. “We did seemingly the most boring experiment ever and look what we found.”

“You can imagine that even more interesting things could be observed in the complex environments outside the lab,” says Nguyen Ba. “Who knows what the rules are when multiple species are coexisting or competing, when predators and prey are interacting, or when environmental conditions changing. Previously these sorts of things would be completely impossible to capture, but now we can start to make progress understanding how evolution actually operates.”


Article: https://www.nature.com/nature/volumes/575/issues/7783

Gazette new release: https://news.harvard.edu/gazette/story/2019/11/evolution-more-complex-than-survival-of-the-fittest-had-us-believe/