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There’s a Speed Limit to the Pace of Evolution


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#1 C1ay

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Posted 03 November 2009 - 06:54 AM

Researchers at the University of Pennsylvania have developed a theoretical model that informs the understanding of evolution and determines how quickly an organism will evolve using a catalogue of “evolutionary speed limits.” The model provides quantitative predictions for the speed of evolution on various “fitness landscapes,” the dynamic and varied conditions under which bacteria, viruses and even humans adapt.

A major conclusion of the work is that for some organisms, possibly including humans, continued evolution will not translate into ever-increasing fitness. Moreover, a population may accrue mutations at a constant rate –- a pattern long considered the hallmark of “neutral” or non-Darwinian evolution -– even when the mutations experience Darwinian selection.

While much is known about the qualitative aspects of evolutionary theory — that organisms mutate and these mutations are selected by the environment and are gradually absorbed by the entire population, very little is known about how, or how quickly, this is accomplished. Information on evolution between consecutive generations is hard to come by, and the lack of understanding has real-world implications. Public-health officials would have an easier time preparing targeted vaccinations, or combating drug resistance, if they understood the evolutionary speed limits on viruses and bacteria such as influenza and M. tuberculosis.

Penn researchers presented a theory of how the fitness of a population will increase over time, for a total of 14 types of underlying landscapes or “speed limits” that describe the consequences of available genetic mutations. These categories determine the speed and pattern of evolution, predicting how a population’s overall fitness, and the number of accumulated beneficial mutations, are expected to increase over time.

Researchers compared the theory to the data from a two-decades study of E. coli to investigate how the bacterium evolves. Organisms of that simplicity and size reproduce more rapidly than larger species, providing 40,000 generations of data to study.

“We asked, quantitatively, how a population’s fitness will increase over time as beneficial mutations accrue,” said Joshua B. Plotkin, principal investigator and an assistant professor in the Department of Biology in Penn’s School of Arts and Sciences. His research focuses on evolution at the molecular scale.

“This was an attempt to provide a theoretical framework for studying rates of molecular evolution,” said first-author Sergey Kryazhimskiy, also of the Department of Biology. “We applied this theory to infer the underlying fitness landscape of bacteria, using data from a long-term bacterial experiment.”.

In some theoretically conceivable landscapes, fitness levels are expected to increase exponentially forever because of an inexhaustible supply of beneficial mutations. But in more realistic landscapes the rate of adaptive substitutions (mutations that improve an organism’s fitness) eventually lose steam, resulting in sub-linear fitness growth. In some of these landscapes, the fitness eventually levels out and the organism ceases to adapt, even though mutations may continue to accrue.

E. coli, for example, has been observed to increase its rate of cellular division by roughly 40 percent during the course of 40,000 generations. Initially, the bacterial fitness increased rapidly, but eventually the fitness leveled out. These data have allowed the research team to infer that early mutations, while conferring large beneficial effects, also diminish the beneficial effects of subsequent mutations.

According to the study, a population’s fitness and substitution trajectories —t he mutations acquired to achieve higher fitness — depend not on the full distribution of fitness effects of available mutations but rather on the expected fixation probability and the expected fitness increment of mutations. This mathematical observation greatly simplifies the possible trajectories of evolution into 14 distinct categories.

Researchers demonstrated that linear substitution trajectories that signify a constant rate of accruing mutations, long considered the hallmark of neutral evolution, can arise even when mutations are strongly beneficial. The results provide a basis for understanding the dynamics of adaptation and for inferring properties of an organism’s fitness landscape from long-term experimental data. Applying these methods to data from bacterial experiments allowed the researchers to characterize the evolutionary relationships among beneficial mutations in the E. coli genome.

The study, appearing in the current issue of the journal Proceedings of the National Academy of Sciences, was performed by Plotkin and Kryazhimskiy along with Gašper Tkacik of the Department of Physics and Astronomy at Penn.

The study was funded by the Burroughs Wellcome Fund, the David and Lucille Packard Foundation, the James S. McDonnell Foundation, the Alfred P. Sloan Foundation, a Defense Advanced Research Projects Agency grant and the National Science Foundation.

Source: University of Pennsylvania

#2 UncleAl

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Posted 03 November 2009 - 11:34 AM

Samuel Adams "Utopias" single stage ferments to 54 proof. Common beer yeast die by 20 proof, wine yeast by 30 proof. Samuel Adams did not have a lab filled wth gene-gineer PhDs. They fermented high sugar aliquots until 99% of the yeast died, then cultured the survivors another round, round and round. Think of it as evolution in action.

#3 HydrogenBond

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Posted 09 November 2009 - 08:33 AM

Evolution has a connection to the context of the environment. Sam Adam's continued to stress the yeast environment with high levels of sugar to create their utopian yeast. If we took a sample of yeast, that never saw this stress, the lack of necessity for this higher sugar level, would not have given any selective advantage to that culture evolving extreme sugar yeast. Instead, the yeast will steady state around the level of their lower environmental stress. If we took that culture, and increased the sugar stress, then we can get their evolution moving again. The new goal will be fitness with respect to the higher sugar.

Once an eco-system reaches steady state, the goal aspect of evolution doesn't change all that quickly and evolution works on optimization. Once Sam Adams gets the yeast they need, it won't change much, since the environment will under strict quality control, so their product is consistent. The yeast might be only exhibit slight improvements and/or some adaptations based on changes in their raw materials. But if they use it to make a brand new beer, they would create a new stress for change, since the yeast not only have to deal with the sugar but the sugar in the context of other chemicals. They stay in business due to product consistency, which would be hard to achieve, if the yeast were mutating randomly out of any context to their process goals.

#4 Galapagos

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Posted 09 November 2009 - 10:52 PM

Evolution has a connection to the context of the environment.

Evolution necessarily involves adaptation to the immediate environment, so of course evolution "has a connection to the context of the environment". Natural selection is the bridge between genes and the environment- genes that work well in the environment are represented in subsequent generations due to selection.

Sam Adam's continued to stress the yeast environment with high levels of sugar to create their utopian yeast. If we took a sample of yeast, that never saw this stress, the lack of necessity for this higher sugar level, would not have given any selective advantage to that culture evolving extreme sugar yeast.


I think what you mean to say here is that if the population in question has not experienced the necessary mutation and subsequent selection in the environment the adaptations to that environment would not exist(in your example it was a high sugar environment).
Why you would be posting this here or what that has to do with this thread is beyond me, but I thought I would offer some corrections anyhow.

Instead, the yeast will steady state around the level of their lower environmental stress. If we took that culture, and increased the sugar stress, then we can get their evolution moving again. The new goal will be fitness with respect to the higher sugar.
Once an eco-system reaches steady state, the goal aspect of evolution doesn't change all that quickly and evolution works on optimization.

Evolution is not some entity that does things like "work on optimization" or have goals. That sounds like the job of an agent, like a creator deity. :wub:
To be clear, evolution is the process of genes in a population changing from generation to generation. No more, no less.
And there are no goals in evolution in the sense of progress, or directionality.

Once Sam Adams gets the yeast they need, it won't change much, since the environment will under strict quality control, so their product is consistent.
The yeast might be only exhibit slight improvements and/or some adaptations based on changes in their raw materials. But if they use it to make a brand new beer, they would create a new stress for change,
They stay in business due to product consistency, which would be hard to achieve, if the yeast were mutating randomly out of any context to their process goals.

As long as there isn't excessive UV or other mutagens in the environment, mutations will occur at the same rate, and the mutations will always be random with respect to the environment or fitness, regardless of whether or not Sam Adams or anybody else wants to use it to make beer. Yeast cultures used by brewers have random mutations just like any other population of yeast.

Just FYI, the mutation rate for yeast actually happens to have been studied extensively. This is a paper(open access) with some estimates and information about mutation rates in yeast:
Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae -- Lang and Murray 178 (1): 67 -- Genetics

And I have recommended this book to you before Hydrogenbond, and you apparently ignored me(because otherwise you would not be making the conceptual mistakes you continue to make), so I will recommend it again:
Amazon.com: The Selfish Gene (9780192860927): Richard Dawkins: Books http://www.amazon.com/Selfish-Gene-Richard-Dawkins/dp/0192860925
You seem to be very confused by the relationship between the phenotype, the genotype, natural selection, and the environment in evolution. This book would serve as a general introduction to natural selection and evolutionary theory and you would benefit greatly from a careful reading of it.

#5 lawcat

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Posted 10 November 2009 - 12:11 AM

This is a funny thread. What are we talking about: fitness increase per hour? mutations per day? That is speed of evolution? That is some funny stuff. (reminds of fallowing the stock market movement.)

#6 Larv

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Posted 10 November 2009 - 10:44 AM

If an increase in the number of marine families over the last 245 million years (since the Permian Extinction) is a valid measure of evolutionary "pace" or "speed" then that statistic shows a punctuated rate of increase of about three families per million years.

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From: Raup, D. and J. Sepkoski, 1984, Periodicity of extinctions in the geologic past. Proc. Natl. Acad. Sci. U.S.A., 81,801-805.