Evolutionary process more detailed than previously believed, study shows

January 16, 2009

New evidence from a study of yeast cells has resulted in the most detailed picture of an organism's evolutionary process to date, says a Texas A&M University chemical engineering professor whose findings provide the first direct evidence of aspects, which up until now have remained mostly theory.

Working with populations of yeast cells, which were color-coded by fluorescent markers, Katy Kao, assistant professor in the Artie McFerrin Department of Chemical Engineering, and Stanford University colleague Gavin Sherlock were able to evolve the cells while maintaining a visual analysis of the entire process.

Their research, which appears in the December edition of Nature Genetics, shows the evolutionary process to be much more dynamic than initially thought, with multiple beneficial adaptations arising within a population. These adaptations, Kao explained, triggered a competition between these segments, known as "clonal interference."

It's the first direct experimental evidence of this phenomenon in eukaryotic cells, or cells with nuclei, and it contrasts the widely accepted classical model of evolution, which doesn't account for simultaneously developing beneficial adaptations, she said. Instead, that model adopts a linear approach, theorizing that a population acquires such adaptations successively, one after another. Rather than a competition occurring, the model posits a complete replacement of one generation by another better-adapted generation.

That wasn't the case in Kao's sample.

Observing the color-coded yeast populations as they evolved to respond to their environment, Kao saw some colors expand while others contracted - a sign that adaptations were occurring. But rather than one segment of the population continuing to shrink until it was completely replaced, some segments were able to compete long enough to acquire further adaptations. When this happened, Kao explained, these populations of cells - once apparently less-fit - began to swell while once-dominant populations started to shrink. This constant reduction and burgeoning of populations signaled the development of multiple beneficial adaptations and a subsequent competition by the cells that acquired them, Kao said.

"Essentially, we were watching evolution in action," Kao said. "We're watching evolution in real time. We're actually seeing a mutation that shows these things have adapted and seeing their population thrive and expand from this adaptation. This is how evolution works.

"In one of our experiments we were able to see five independent population expansions. We had one adaptive mutation that allowed a population to expand, but before it was able to completely take over another un-mutated population of the same cells acquired a different mutation that allowed it to succeed and impede the expansion of the first population."

In addition to determining if and when a population acquired an adaptation, Kao also identified the specific adaptations that were acquired. She accomplished this using a DNA-based technology that enabled her to determine the specific locations on the genes of the yeast cells that expressed beneficial adaptations.

What she found was that as populations rise and fall, some of these beneficial adaptations factor into the continued evolution of the organism; others don't.

"Due to the possibility of this competition, beneficial mutations that have been lost during the evolution of an organism will not be identified from just the final generation of that organism," Kao explained. "Indeed, we found that several of the mutations were nearly lost in the population by the end of the experiment due to this competition."

In other words, as Mother Nature sorts things out, some adaptations go by the wayside, with the latest generation of an organism sometimes showing no traces of them.

"Think of this as another piece of the evolution puzzle," Kao said. "We're gaining a comprehensive understanding of the way a microorganism adapts to its environment as it fights to survive. We're demonstrating that the evolutionary journey has many more 'twists and turns' than we once thought."

The knowledge of those twists and turns ultimately could prove to be very important, Kao explained, because it helps paint a complete picture of an organism's evolution. With that picture intact, scientists stand to gain a better understanding of the way certain highly resistant infections develop and progress.

One such infection, Kao noted, occurs within the bodies of people with weakened immune systems. In such cases, a fungus that is normally kept in check increases to dangerous infectious levels, prompting doctors to prescribe antifungal treatments. Sometimes these treatments become ineffective, and Kao says that one of the reasons for that ineffectiveness is that the human body becomes a vessel for evolution, much like what occurred in her laboratory experiment.

"The fungus is being subjected to a selected pressure, in this instance drugs," Kao said. "As it fights for its survival, mutations occur that help make this fungus resistant to the drug treatments. Most of the clinical studies of these patients isolate just one sample of the mutation at one point in time. But a recent study that isolated these samples from different periods in time suggested that some of the later ones were not derived from earlier ones."

Understanding how this fungus evolves from its initial stages to its most recent stage could lead to the development of better treatments for it, Kao said.

The knowledge of an organism's complete "adaptive landscape" also is likely to benefit the rapidly growing field of metabolic engineering, Kao noted.

As scientists attempt to enhance cells so that they perform such beneficial activities as producing energy or disposing of waste, they'll need to know all of the particular pathways where genes are involved in the expression of a particular trait, Kao said. This is especially important as scientists work to enhance microorganisms so that they possess a higher tolerance to the products they produce, Kao said.

For example, a microorganism might be genetically enhanced to produce butanol as a potential biofuel, she said. The problem however, Kao explained, is these microorganisms generally have a low tolerance to butanol, and at very low concentrations they will start to die from what they are producing.

One way to address this problem is to evolve these microorganisms into forms with a higher tolerance, Kao noted. By examining the entire evolutionary process of such a microorganism, scientists could discover a once-overlooked beneficial adaptation that arose somewhere along the way that would help enhance tolerance. That adaptation might otherwise not be apparent if only the current generation of the microorganism is examined, she said.

Source: Texas A&M University

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1.6 / 5 (7) Jan 16, 2009

If the only way to observe 'evolution' is by manufacturing 'evolution' is it really 'evolution'?
3 / 5 (2) Jan 16, 2009
If the only way to observe 'evolution' is by manufacturing 'evolution' is it really 'evolution'?

In what way did this study 'manufacture' evolution?
not rated yet Jan 16, 2009
These scientests are doing a great work! Only at this level are we humans able to SEE how it works! Those who work with mice are WAY over their heads! Given enough time and money they could MAKE a mouse out of a cake of yeast and understand its problems!
not rated yet Jan 17, 2009
its manufacturing evolution in that they were able to subject different "life pressures" on the yeast cells to force mutations to adapt to its new environment (evolution in a nutshell right there really if you ask me...when added together and taken as a whole..the big picture), which have a short lifetime, which they then pass this mutation onto the "child" cells, and like a chain, as expected, mutations kept occurring due to the outside influence being pushed on the cells. In my mind, not all that unlike, say, a mudfish "walking" across the mud for the very first time in its evolution due to outside influcences such as predators, feeding needs....survival needs basically.
Anyways things like small cell cultures make excellent ways to monitor evolution in action because their lifespan is predictably short, and they make more of themselves :)
Just using sample numbers here...think about an average of 70 yrs we live, and lets say an average of 25 yrs old average before human reproduction, so a new generation every 25 yrs. Now picture that 70 yrs as 7 days, and human reproduction occurring on average at an age of 2.5 days. Now lets say an outside influence or two, or more, occurs...use your imagination (mine says something that makes our species live underground for quite a long time)...that causes changes in our species (in my example for instance, possibly weaker eyesight, but better hearing combined with extremely pale and frail skin pigmentation). Anyhoo, now we pass these traits off to lower generations, who adapt even more to their surroundings..and so on and so forth.
This is no different than what the yeast cells are doing, which means they are effectively evolving.
Now the real question and testing is, in my mind, what would happen if we cloned different species and introduced outside influences at the fetal cellular level to force mutations to see possible evolutionary outcomes. That would probably open the book, or pandoras box depending on how you look at it, on mapping the changes that would occur in humans if we were artifically advanced in the same fashion. If we get this mapping down, the its a matter of WHEN we begin genetically engineering our superior selves :)
2.5 / 5 (2) Jan 17, 2009
Re Stanford, But Applies Here Too

On Humans (And Other Materials) Evolution
And On The Sad State Of Life Sciences In 2009

Re "Stanford researchers show adaptation plays a significant role in human evolution"

1) "For years researchers have puzzled over whether adaptation plays a major role in human evolution or whether most changes are due to neutral, random selection of genes and traits."

- I have been presenting evidence for years that adaptation, i.e. culture, is the driver of evolution of all life including human and, yes, of all other materials, and that genetic evolution is generally biased, not random.

2) "Geneticists at Stanford now...show adaptation, the process by which organisms change to better fit their environment, is indeed a large part of human genomic evolution."

- Shortly after retiring from industrial consulting (1956 - 1998) I started investigating the state of comprehension of the nature of life and of its evolution and I published evidence and conclusion that culture is the driver of all genomic evolution.

3) "Others have looked for the signal of widespread adaptation and couldn't find it...now...we were able to detect the adaptation signatures quite clearly"

- I found the evidence many years ago and presented it clearly in my postings.

4) "All genetic mutations start out random, but those that are beneficial to an organism's success in their environment are directly selected for and quickly perpetuate throughout the population, providing a uniform, traceable signature."

- NO NO NO. The drive of evolution is NOT RANDOM followed by survival selection. It is biased, as explained in my "Life's Manifest" and elaborated in my posts about the role of culture in evolution.

5) "Humans have a very complex history from traveling around the globe, and the human genome is also highly structured, making it complicated and difficult to work with, he said."

- The human genome, like all other genomes, is complicated, being a multi-genes organism, an organism that consists of a cooperative commune of the smaller Earth's primal organisms, namely of genes.

6)"Adaptation becomes widespread in the population very quickly," Petrov said. "Whereas neutral random mutation doesn't and would not have the selective sweep signature."

- Bravo. This happens to be a correct statement. Random mutations are mechanical accidents that the organism may or may not overcome to survive.

I stop here. No patience nor interest to continue picking at each of the following paras. Just sadly frustrated at The Sad State Of Life Sciences In 2009...

Respectfully yours,

Dov Henis

(Comments From The 22nd Century)

Life's Manifest
3 / 5 (2) Jan 17, 2009
its manufacturing evolution in that they were able to subject different "life pressures" on the yeast cells to force mutations to adapt to its new environment...

That's a non-sequitur. Subjecting a cell culture to environmental stress and observing what happens doesn't force the cells to do anything and isn't qualitatively different than environmental stresses these cells will be put under in nature.

They happen to compete, random mutations happen to occur, useful mutations happen to be more likely to survive and spread. This is merely an observation that they are indeed evolving.
not rated yet Jan 17, 2009
RE: Natural Evolution (NE) vs. Artificial Evolution (AE)!?

If the only way to observe 'evolution' is by manufacturing 'evolution' is it really 'evolution'?

I thought this is a very sharp observation, and let me try to break up your question of 'evolution' into 2 processes: natural evolution (NE) and artificial evolution (AE) -- where NE also includes cosmic evolution (CE) and Darwinian evolution (DE); and where DE concerns the evolution of organisms (but not the origin of life) on Earth, whereas CE encompasses the evolution of everything in the universe, including the origin of life and DE.

In the NE situation, everything in nature -- or the cosmos -- can only evolve once at any point in time and space in the universe (including all life organisms on Earth -- eg, you and me: we each can only live once after wherever we were born as living organisms or beings); whereas AE is a scientific method that is man-made or created in the laboratory, so as to mimic and test the products and/or the processes of NE in the cosmos.

As such, in the AE situation, every experiment of a product or a process is repeatable as long as it is to be treated and tested under a same set of controlled conditions in the lab or in nature; whereas everything on Earth can only evolve once into existence -- like you and me as example above -- under any one particular condition of time and space, among the infinite conditions of the space, time, energy, matter, etc that are present in the universe since the accretion and evolution of our planet Earth over 4 billion years ago.

The origin of species (of organisms) as the 19th-century naturalist Charles Darwin observed and proposed (in 1859, thus dubbed DE or the tree of life) has had begun to sprout and evolve on Earth since over 3 billion years ago. And, the DE of organisms still persists on Earth.

Thus, any competent scientists today must begin to delineate, understand, and differentiate AE from NE, and CE from DE, and DE from the origin of life thesis, as discussed above; otherwise the true scientific and intellectual spirits of Charles Darwin's would have had been ill-twisted and vanquished by the now, pseudoscientific, neo-Darwinist reductionism of the 20th century!

So, my short answer to your sharp question above is YES; but you have to more refine your question of 'evolution' to those processes of 'evolution' that I qualified and defined above.

Best wishes, Mong 1/17/9usct3:40p; author "Decoding Scientism" and "Consciousness & the Subconscious" (works in progress since July 2007), "Gods, Genes, Conscience" (2006: http://www.iunive...95379907 ) and "Gods, Genes, Conscience: Global Dialogues Now" (blogging avidly since 2006: http://www2.blogg...50569778 ).
not rated yet Jan 18, 2009
life pressures is meant to mean anything. Whether that be a harmful or good environmental change, a massive disease outbreak...I meant that more to mean "any outside influence that can or will cause a change"
sry for any confusion there :)

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