Time in a bottle: Scientists watch evolution unfold

Oct 18, 2009
E. coli cultures in the laboratory of Michigan State University evolutionary biologist Richard Lenski. Credit: Greg Kohuth, Michigan State University

A 21-year Michigan State University experiment that distills the essence of evolution in laboratory flasks not only demonstrates natural selection at work, but could lead to biotechnology and medical research advances, researchers said.

Charles Darwin's seminal first laid out the case for evolution exactly 150 years ago. Now, MSU professor Richard Lenski and colleagues document the process in their analysis of 40,000 generations of bacteria, published this week in the international science journal Nature.

Lenski, Hannah Professor of Microbial Ecology at MSU, started growing cultures of fast-reproducing, single-celled E. coli bacteria in 1988. If a genetic mutation gives a cell an advantage in competition for food, he reasoned, it should dominate the entire culture. While Darwin's theory of is supported by other studies, it has never before been studied for so many cycles and in such detail.

"It's extra nice now to be able to show precisely how selection has changed the genomes of these bacteria, step by step over tens of thousands of generations," Lenski said.

Lenski's team periodically froze bacteria for later study, and technology has since developed to allow complete genetic sequencing. By the 20,000-generation midpoint, researchers discovered 45 mutations among surviving cells. Those mutations, according to Darwin's theory, should have conferred some advantage, and that's exactly what the researchers found.

The results "beautifully emphasize the succession of mutational events that allowed these organisms to climb toward higher and higher efficiency in their environment," noted Dominique Schneider, a molecular geneticist at the Université Joseph Fourier in Grenoble, France.

Lenski's long-running experiment itself is uniquely suited to answer some critical questions -- such as whether rates of change in a bacteria's genome move in tandem with its fitness to survive.

Michigan State University Richard Lenski, standing, analyzes E. coli cultures with postdoctoral researcher Jeffrey Barrick. Credit: Greg Kohuth, Michigan State University

"The coupling between genomic and adaptive evolution is complex and can be counterintuitive," Lenski concluded. "The genome was evolving along at a surprisingly constant rate, even as the adaptation of the bacteria slowed down a lot. But then suddenly the mutation rate jumped way up, and a new dynamic relationship was established."

A mutation involved in DNA metabolism arose around generation 26,000, causing the mutation rate everywhere else in the to increase dramatically. The number of mutations jumped to 653 by generation 40,000, but researchers surmise that most of the late-evolving mutations were not helpful to the bacteria.

Gene mutations involved in human DNA replication are involved in some cancers. Many of the patterns observed in the experiment also occur in certain microbial infections, "and cancer progression is a fundamentally similar evolutionary process," observed collaborator Jeffrey Barrick. "So what we learn here can help us better understand the course of these diseases."

Barrick, a postdoctoral researcher in MSU's Department of Microbiology and Molecular Genetics, developed computational tools to discover and validate often complex mutations. "We know an astounding amount about the details of evolution in these little Erlenmeyer flasks," he said.

The Nature paper involved collaboration with scientists from South Korea as well as France and MSU. The research, said genomics team leader Jihyun Kim of the Korea Research Institute of Bioscience and Biotechnology, "is not only useful in understanding the tempo and mode of evolution, but can serve as a nice framework for practical applications in biotechnology, such as improving the performance or productivity of an industrial strain."

Thousands of generations later, the MSU experiment continues to evolve. "Like a lot of science, our study answers some questions but raises many others," Lenski said.

Source: Michigan State University (news : web)

Explore further: Walking fish reveal how our ancestors evolved onto land

add to favorites email to friend print save as pdf

Related Stories

Natural selection may not produce the best organisms

Jul 18, 2008

"Survival of the fittest" is the catch phrase of evolution by natural selection. While natural selection favors the most fit organisms around, evolutionary biologists have long wondered whether this leads to the best possible ...

Beyond a 'speed limit' on mutations, species risk extinction

Oct 01, 2007

Harvard University scientists have identified a virtual "speed limit" on the rate of molecular evolution in organisms, and the magic number appears to be 6 mutations per genome per generation -- a level beyond which species ...

Ready, set, mutate... and may the best microbe win

May 18, 2006

Even with modern genomic tools, it's a daunting task to find a smoking gun for Darwinian evolution. The problem lies in being able to say not just when and how a specific gene mutated but also how that one genetic change ...

Recommended for you

Team defines new biodiversity metric

Aug 29, 2014

To understand how the repeated climatic shifts over the last 120,000 years may have influenced today's patterns of genetic diversity, a team of researchers led by City College of New York biologist Dr. Ana ...

Danish museum discovers unique gift from Charles Darwin

Aug 29, 2014

The Natural History Museum of Denmark recently discovered a unique gift from one of the greatest-ever scientists. In 1854, Charles Darwin – father of the theory of evolution – sent a gift to his Danish ...

User comments : 13

Adjust slider to filter visible comments by rank

Display comments: newest first

Fakeer
2 / 5 (4) Oct 18, 2009
Microbial infections involve time cycles that are probably too short for such mutations to have any significant effect. However the reference to the progression of cancer is well appreciated. When this is realised I hope we can revist the term 'war against cancer' for the meaningless outcry that it has become.
E_L_Earnhardt
Oct 18, 2009
This comment has been removed by a moderator.
MNIce
2.4 / 5 (10) Oct 18, 2009
1. It is common to attribute the theory of natural selection to Darwin, but properly, credit belongs to Edward Blyth, who published a series of articles on it in Magazine of Natural History between 1835 and 1837, 22 years before Darwin's book went into print.

2. Nothing in this report suggests that the cultured bacteria have become anything but the same critters selectively bred for the conditions of Lenski's flask. There is no evidence that they are a new species, nor is there any report of a new survival advantage under more natural conditions. Indeed, most of the mutations were harmful, as any creationist would predict.

This is a demonstration of "micro-evolution" within a species under specific conditions, but not the Darwinian molecules-to-man story. There is no new support for big-E Evolution here, despite the headline. It may re-affirm the faith of evolutionists, but won't convince their opposition.
nilbud
Oct 18, 2009
This comment has been removed by a moderator.
malapropism
Oct 18, 2009
This comment has been removed by a moderator.
malapropism
4.3 / 5 (6) Oct 18, 2009
2. Nothing in this report suggests that the cultured bacteria have become anything but the same critters selectively bred for the conditions of Lenski's flask.

Well, that depends on the initial, intermediate conditions and final conditions (although I do not think that the experiment has been terminated as yet and if so even the current "final" conditions are only intermediate). If the researchers maintained a static set of conditions in some flasks, and btw I believe there are multiple experiments (flasks) running concurrently, then changes due to mutation are not adaptive for an environmental change so some should display inter-strain competitive advantage.

In other cases where conditions are altered over time then yes, adaptation is to environmental change. The better-fit strain has advantage. This demonstrates selection quite nicely in a time-frame we can easily watch. So your point would be...?
malapropism
5 / 5 (6) Oct 18, 2009
There is no evidence that they are a new species, nor is there any report of a new survival advantage under more natural conditions. Indeed, most of the mutations were harmful, as any creationist would predict.

I do not think they claimed finding a new species. At least, I did not read this into the research discussion. From where in the article do you take that assumption?

Similarly, how do you make the assumption that most of the mutations were harmful? ("Not helpful" does not necessarily mean "harmful".) And even if they were, what of it and why would this be claimed by creationists? (I presume that your unstated claim is that the presence, at some points in time across the generations of the e. coli, of harmful mutations somehow support a creationist viewpoint?)
malapropism
4.3 / 5 (6) Oct 18, 2009
And finally,
This is a demonstration of "micro-evolution" within a species under specific conditions, but not the Darwinian molecules-to-man story. There is no new support for big-E Evolution here, despite the headline. It may re-affirm the faith of evolutionists, but won't convince their opposition.

You confuse, or mischievously seek to conflate, biogenesis with evolution through natural selection.

Nowhere in this article did the researchers claim to have seen biogenesis, nor was this the object of their studies. They do claim good evidence for observable ongoing mutation of the genome of an organism through generations and, by virtue of some of those mutations, evolution of the overall phenotype of the organism by natural selection of advantageous genomic mutations.

(NB. with reference to your other comment about "harmful" mutations, in some environmental contexts a mutation that is beneficial in another context may be considered "harmful".)
jgelt
4.8 / 5 (5) Oct 19, 2009
Recording the genetic drift of a population on a gene by gene basis over 40K generations (under whatever selective influence) is a prodigious observational achievement.
Showing a mutation that controls rate of mutation is very interesting, too.
SteveL
not rated yet Oct 19, 2009
Being a somewhat more complex genome, I imagine quite a few mutations have occoured over the last 40,000 human generations.

I'd be interested in knowing if any stressors were applied to the samples and if so what they were and what the genetic response was. That would give us a more informative example of how genetics reacts and adapts to environmental changes and at what rate - at least for these samples.
rab96
not rated yet Oct 19, 2009
Although the results of the research are interesting, the title of the article is misleading; since no new species have developed, there is no question of evolution. Maybe it will happen after a million years...
mabarker
2 / 5 (4) Oct 19, 2009
I agree. The title is indeed misleading. I suggest: *News Flash - bacteria remain bacteria!*
Please show this darwinian skeptic how E. coli can change into some other prokaryote (a different genus would do nicely). *Advantageous genomic mutations* malapropizzim? I read in this article, *but researchers surmise that most of the late-evolving mutations were not helpful to the bacteria* Kinda goes along with creation-basher Paul Ehrlich, who said, *. . . mutations normally are either neutral or harmful; only very rarely are they helpful - just as random change made by poking a screwdriver into the guts of your computer will rarely improve its performance* (2000, p. 21). E. coli remains E. coli, as I taught my medical microbiology students for 9 years. That's right, I did not teach my students to genuflect before darwin's altar.
SteveL
not rated yet Oct 20, 2009
Perhaps with no reason to change, there is none? Or at least any detectible change is miniscule.

I'd imagine that in far less than 40,000 generations under difficult environmental conditions that may force the genome to adapt it will. How much mutation would be required to "evolve" and become a new gene? I don't know and likely that point would be hotly debated far longer than needed.
Ethelred
5 / 5 (6) Oct 20, 2009
The title is indeed misleading. I suggest: *News Flash - bacteria remain bacteria!*

The title is 100% accurate. The bacteria adapted via mutation and natural selection to the environment they are in. That is evolution. You have a religious problem with it which has nothing to do actual facts.

Please show this darwinian skeptic how E. coli can change into some other prokaryote (a different genus would do nicely).

That isn't all there is to evolution. Using your own private definitions doesn't change the facts.

{q}Paul Ehrlich, who said, *. . . mutations normally are either neutral or harmful; only very rarely are they helpful {/q}
The key word is NORMALLY and in the previous statement it was MOST. Occasionally they are helpful and you clearly are ignoring the FACT that the bacteria adapted via mutation to the new environment. You ignored NORMALLY and MOST as you must to support your religion.

Ethelred
malapropism
5 / 5 (3) Oct 20, 2009
Please show this darwinian skeptic how E. coli can change into some other prokaryote (a different genus would do nicely).

Unfortunately there are some problems with your suggestion:

Regardless of the mutation it seems extremely unlikely that an organism could effectively move between Genera except by evolution over geological time scales. This is unlikely to be seen directly. A species-level (or sub-species/strain level) change is much more likely to be observed.

E. coli transfer DNA horizontally through 3 mechanisms, none of which is a direct analogue of sexual reproduction as they do not create gametes or a fusion zygote (the closest is donation of DNA, usually a copy of some sort, from one bacterial cell to another while they are in contact - termed conjugation). I think it would be difficult, though perhaps not impossible, to devise an experiment to determine that this transfer could not occur after some notional evolutionary change (i.e. demonstrating speciation).
malapropism
5 / 5 (2) Oct 20, 2009
*Advantageous genomic mutations* malapropizzim? I read in this article, *but researchers surmise that most of the late-evolving mutations were not helpful to the bacteria*

Yes, indeed - advantageous (for the ecological conditions in the flask). Note that I did not comment about the number of these - it could have been just 1 mutation that was advantageous; the number is irrelevant as it is the fact of selection happening under competitive pressure while also finding the mutational change involved that is the core issue. And that demonstrates an important facet of evolution occurring and being observed.

As Ethelred said, the keywords are "normally" and "most" - these leave the possibility of the abnormal and the least. ("Only very rarely are they helpful," is a quite acceptable statement that sometimes something useful happens, that you seem to conveniently ignore.)

By the way, I do not genuflect at anything, let alone at an altar, if that was your implication.