Long-term evolution is 'surprisingly predictable,' experiment shows

Mar 18, 2013 by Bjorn Carey
Dr. Michael Palmer, left, and Professor Marcus Feldman, with co-author Arnav Moudgil (not pictured), found that the long-term evolutionary dynamics were surprisingly predictable in a model of protein folding and binding.

(Phys.org) —A protein-folding simulation shows that the debated theory of long-term evolution is not only possible, but that the outcomes are predictable. The Stanford experiment provides a framework for testing evolutionary outcomes in living organisms.

Two birds are vying for food. One bird's beak is shaped, by virtue of a , such that it's slightly more adept at cracking seeds. This sets the bird on the road toward acquiring more food, a better chance of scoring a mate and, most important, passing on its genetic endowment.

This individual's success is an example of short-term evolution, the widely accepted Darwinian process of by which individual organisms that have better adapted to their surroundings prevail.

In recent years, however, some scientists have argued that natural selection occurs not just at the individual organism level, but also between lineages over the course of many generations. In a new study, Stanford have demonstrated that not only is this long-term evolution possible, but that long-term evolutionary outcomes can be surprisingly predictable.

The group set up a computer simulation in which 128 lineages of proteins continuously folded into new shapes, competing to bind with other molecules, called , in each new configuration. The better each protein could attach itself to the ligands, the more ligands it would scoop up, and the higher its fitness – that is, its average number of "offspring" – would be. The simulation was run for 10,000 generations.

Although the chaos of 128 lineages – a total of more than 16,000 individual proteins – mutating over thousands of generations might seem unpredictable, and that it would be nearly impossible for the same thing to happen twice, it's actually the opposite.

"Even though things look complicated, the possible are quite constrained," said lead author Michael Palmer, a computational biologist at Stanford. "There are only a few viable mutations at any point, which makes the dynamics predictable and repeatable, even over the long term."

The study, co-authored by Marcus Feldman, a biology professor at Stanford, and Stanford research biologist Arnav Moudgil, was recently published in the Journal of the Royal Society Interface.

In some experiments, the lineages that consistently came out on top in the long term were not initially the best adapted at binding to ligands. "The immediate fitness is not the only important thing," Palmer said. "Yes, a lineage does have to survive in the short term. But just as important is how it is able to adapt to new and potentially variable environments over the longer term."

A good example of this scenario is Darwin's famous finches. It's thought that individuals – perhaps just a single pair of birds – from a South American species ended up on the Galápagos Islands about 1 million years ago. Today their descendants have diversified into about 15 modern species. Some eat seeds, some eat insects, or flowers. Some eat ticks, or even drink the blood of other birds.

"If there was some catastrophe that removed one of those food sources, it might wipe out one or more of the 15 species, but the rest of the lineage – the descendants of that initial pair of birds – would persist," Palmer said. "Now say there was a competing lineage that was great at cracking seeds, but unable to evolve to other diets due to some prior genetic constraint. The same catastrophe could wipe it out."

The finding, and others like it, could represent a significant shift in viewpoint for biologists. For one thing, it means that in certain situations, scientists should look beyond the details at the level of the individual organism, as the evolutionary dynamics can be accurately understood as lineage selection.

It also has implications on a species' genomic architecture, or how a genome is organized on the lineage level. While a lineage's genome might primarily select for a particular set of traits in order for individuals to survive in the short term, in order to out-compete other , it must also be able to adapt to new conditions over the long term.

"An individual can have a lucky mutation that produces an immediate adaptation," said Palmer. "Or a lineage can have a lucky mutation that happens to position it to adapt to the range of environments it will experience over the next thousand generations. A single mutation can have a distinct short-term and long-term fitness."

The authors believe that the work can be replicated in microorganisms, and are now hoping that microbiologists will apply the new metrics of selection in vitro.

"There is already some evidence in vitro that there is a lot of constraint on evolutionary trajectories," Palmer said, "and we think we've come up with a good framework to quantify evolutionary predictability and long-term fitness."

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

More information: Paper: rsif.royalsocietypublishing.or… 130026.full.pdf+html

Related Stories

When plants go polyploid

Sep 13, 2011

(PhysOrg.com) -- Plant lineages with multiple copies of their genetic information face higher extinction rates than their relatives, researchers report in Science magazine.

Slower evolving bacteria win in the end

Mar 18, 2011

(PhysOrg.com) -- Scientists in the US have found bacteria that evolve slowly are more likely to survive in the long term than those evolving more quickly.

Interacting mutations promote diversity

Jun 28, 2012

Genetic diversity arises through the interplay of mutation, selection and genetic drift. In most scientific models, mutants have a fitness value which remains constant throughout. Based on this value, they compete with other ...

The genetics of molecular evolution

Nov 06, 2012

A team of scientists researching the effect of long-term molecular evolution (the study of DNA, RNA and proteins) have produced findings which suggest most amino-acid substitutions have different fitness ...

Recommended for you

Team defines new biodiversity metric

2 hours ago

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

6 hours ago

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 : 25

Adjust slider to filter visible comments by rank

Display comments: newest first

Shelgeyr
1.4 / 5 (9) Mar 18, 2013
We've experimented with "long-term" evolution?

Wow. They must have come a LONG, LONG way from those mutant-inbred fruitfly experiments we did 30 years ago... Those were fun though.
Infinum
2.1 / 5 (7) Mar 18, 2013
In terms of long term survival generality > specialization
In terms of short term best fit specialization > generality

Simple truth of life.
Torbjorn_Larsson_OM
4.3 / 5 (12) Mar 18, 2013
Creationists shouldn't comment on science, it is hilarious and makes deconverts from religion as seen on Dawkins's Convert's Corner.

Of course there are limits on evolution as on every other natural mechanism. If the environment changes too fast, the population genome can't adapt. But if not it will, as we know have happened. Biology is the best tested science we have due to its complexity, demonstrated in the article.

There are no restrictions in the genome, genes appear and disappear all the time, as seen in junk-DNA (former, now dead genes). Again demonstrated in this very article, 128 initial proteins (genes) made 16 000.

Only a laughable creationist can then say "genes already exist" - because he/she didn't even read the research. Basic fallacy of red herring, not responding to the situation. And again, this is why religion fails, magic is not the answer as demonstrated by each and every creationist commenting on science.
C_elegans
4.6 / 5 (11) Mar 18, 2013
Seriously? We first began to understand the molecular basis for genetic inheritance over 100 years ago, not 30. Yes, we've come a long way.

Genes are created ALL THE TIME.
Molecular Biology shows that genome replication is very good, but not perfect. Random mutations, translocations and transversions spontaneously occur during replication. Not to mention transposons, lncRNAs, and viruses: all of which are designed to move DNA from one place to another.

This is why exons exist. Blocks of protein-coding DNA (exons) are surrounded by less important introns. Breaks are likely to occur in introns, and can be used like building blocks that are mix and matched to create new genes ALL THE TIME.

As a scientist, I regularly mutate every gene in the entire genome of c. elegans in an afternoon, and nature has ALOT more DNA available to mutate. All combinations of DNA are possible, so the best combination will be selected.

---____-_____----___---____- (-exon, _intron)
verkle
1 / 5 (16) Mar 19, 2013
Creationists shouldn't comment on science...


Torbjorn_Larsson_OM, your pride is suffocating, and your knowledge and application of historical science is almost nil.

If creationists couldn't comment on science, let alone engage in it, the world would not be what it is today. You would not be in your place where you are today. Because it would mean taking away the science base you depend on. Go ahead and study how many of the great scientists in history took the Bible as fact.

A very partial list includes Copernicus, Kepler, Galileo, Descartes, Pascal, Newton, Bayes, Euler, Faraday, Mendel, Joule, Hertz, Pasteur, Kelvin, Planck...

You really want to erase their contribution to science?

Sinister1811
1 / 5 (6) Mar 19, 2013
If it's predictable, then it should be possible to predict what certain types of animals or plants will look like in the distant future, and what types of adaptations they'll develop.
nowhere
4.7 / 5 (12) Mar 19, 2013
Creationists shouldn't comment on science...


Go ahead and study how many of the great scientists in history took the Bible as fact.

A very partial list includes Copernicus, Kepler, Galileo, Descartes, Pascal, Newton, Bayes, Euler, Faraday, Mendel, Joule, Hertz, Pasteur, Kelvin, Planck...

You really want to erase their contribution to science?


Irrelevant. A man preaching creationism is a creationist and a man employing the scientific method is a scientist. In all instances where those men acted as creationist we have in fact done as you say and ignored their input. Where are their great works on religion? discarded, if any. But their work as scientists? Why that is, as you pointed out, what makes them great, and all that's remembered of them.
JVK
1 / 5 (7) Mar 19, 2013
Darwin's "conditions of existence" predict that the epigenetic effect of a novel nutrient will alter the cell wall and permit its receptor-mediated entry. If intracellular thermodynamically-controlled protein biosynthesis is positively effected, the nutrient may result in de novo gene expression via protein folding that enables amino acid substitutions.

If the amino acid substitution does not positively effect organism level thermoregulation, adaptive evolution does not occur. Clearly, however, adaptive evolution does not occur via random mutations.

Nutrient-dependent "conditions of existence" must be established via ecological niche construction before Natural Selection can occur. Compare: "Two birds are vying for food. One bird's beak is shaped, by virtue of a random mutation..." to this: Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation http://dx.doi.org...e.643393

How does a random mutation enable selection for beak morphology?
JVK
1 / 5 (7) Mar 19, 2013
As a scientist, I regularly mutate every gene in the entire genome of c. elegans in an afternoon, and nature has ALOT more DNA available to mutate. All combinations of DNA are possible, so the best combination will be selected.


This may give others the wrong idea about what's selected and how selection occurs. Here's a realistic approach:

Differences in the behavior of nematodes that enable natural selection are determined by nutrient-dependent rewiring of their primitive nervous system (Bumbarger, Riebesell, Rödelsperger, & Sommer, 2013). Species incompatibilities are associated with cysteine-to-alanine substitutions (Wilson et al., 2011), which can be expected to alter thermoregulation via the same molecular mechanisms of microbes.

Some people can't seem to grasp the fact that the molecular mechanisms (e.g., the amino acid substitutions) are conserved in species from microbes to man. Please help them to grasp the biological facts and dispense with ridiculous theory!
Canadianwilson
4.2 / 5 (5) Mar 19, 2013
verkle:"If creationists couldn't comment on science, let alone engage in it, the world would not be what it is today"

No kidding the world wouldn't be what it is today because if religion prevailed over science then many scientist would have been put to death/jailed for challenging the so called "facts" set forth by the church. That's the basic premise of religion control by way of fear.

If you check your facts Galileo was imprisoned for challenging the blindly followed facts of the bible. Ecclesiastes 1:5,Psalm 104:5, Psalm 93:1, 96:10 all state that heliocentrism is the true structure of the solar system.

Please remove yourself from these threads as you provide no sensible input. I guess you are just filling your duties as a good old Christian fear monger on the latest contribution science until the can no longer be denied? As they say history repeats itself. Science will continue to disprove religion and the bible as it has done for centuries.
JVK
1 / 5 (7) Mar 19, 2013
Science will continue to disprove religion and the bible as it has done for centuries.

Darwin told us, "conditions of existence" during past centuries have a higher priority in the context of explanatory power. The nutrient-dependent pheromone-controlled "conditions of existence" have since been largely ignored to favor the ever-more apparently ridiculous assumption that it was Darwin who proposed the theory of random mutations to explain natural selection.

Not only is random mutations theory not representative of science, it should have never been assumed to explain anything about species divergence, which is clearly nutrient-dependent. What is it that you think has been disproved by science about religion and the Bible? You seem to be horribly under-informed.

Conditions of existence (proof):
Excerpt: "Two birds are vying for food. One bird's beak is shaped... such that it's slightly more adept at cracking seeds. This sets the bird on the road toward acquiring more food...
Canadianwilson
5 / 5 (2) Mar 19, 2013
"What is it that you think has been disproved by science about religion and the Bible? You seem to be horribly under-informed."

I think you need a history lesson and need to read a post before you comment. I am quite unclear of how you didn't get this from my previous post but I will bring it down to your level of understanding. The bible states in Ecclesiastes 1:5,Psalm 104:5, Psalm 93:1, 96:10 that heliocentrism(that means the earth is the center of the solar system) is the true structure of the solar system. I'm not sure how in your mind this is not an example of how science disproved the bible? The only conclusion I can make from your comment is that you believe the earth is still the center of the solar system and that its only 6000 years old and dinosaurs fossils are here to challenge your blind faith. If that's the case then I truly feel sorry for you.

antialias_physorg
4.2 / 5 (5) Mar 19, 2013
If it's predictable, then it should be possible to predict what certain types of animals or plants will look like in the distant future, and what types of adaptations they'll develop.

Only if the envionment remains static (which it doesn't). At the very least the changing organisms also alters its environment (e.g. by more efficiently depriving it of nutrients it gobbles up).

And even though the above suggests that the number of paths are limited they are not necessarily limited to a set of one. A choice very early on can lead to rather drastically different evolutionary paths (each of which can be constrained themselves).

Think about the simple choice of some animal species evolving to be able to live on dry land vs. water. Only two choices...but the long term outcomes are rather different.
Claudius
2.6 / 5 (5) Mar 19, 2013


How does a random mutation enable selection for beak morphology?


You are ignoring the natural variation within species. There is a bell-shaped curve describing natural variation of traits withing species. That means that beak morphology would not be identical between different members of the same species, there would be variation, and some members would have beaks that were better suited for certain conditions. These members would be selected for in future generations.
aroc91
not rated yet Mar 19, 2013


How does a random mutation enable selection for beak morphology?


You are ignoring the natural variation within species. There is a bell-shaped curve describing natural variation of traits withing species. That means that beak morphology would not be identical between different members of the same species, there would be variation, and some members would have beaks that were better suited for certain conditions. These members would be selected for in future generations.


inb4 "is there a model for that?"
JVK
1 / 5 (5) Mar 19, 2013
...some members would have beaks that were better suited for certain conditions. These members would be selected for in future generations.

What enables the selection of those members?
See, for comparison: Ben-Sahra et al, Stimulation of de novo pyrimidine synthesis by growth signaling through mTOR and S6K1. Science 339, 1323–1328 (2013)

Excerpt: "...mTORC1 and S6K1 are not essential for de novo pyrimidine synthesis...in response to growth-promoting signals, such as insulin and nutrients. The direct regulation ... by S6K1 serves as a mechanism to increase the pool of nucleotides available for the RNA and DNA synthesis that accompanies cell growth. ...pyrimidine synthesis represents another major anabolic process that is responsive to changes in cellular growth conditions through mTORC1 signaling."

There is a model of selection for amino acid substitutions for comparison to theories of "somehow selected" beak morphology. http://dx.doi.org...e.643393
C_elegans
5 / 5 (1) Mar 21, 2013
Sorry JVK, you lost me. Some nucleotide changes are more likely, because depending on the mutagen only certain nucleotide replacements are allowed. You keep quoting things but I don't understand what your point is.
JVK
1.2 / 5 (6) Mar 21, 2013
I apologize; I do not know how to put this succinctly because I don't know how much you already understand.

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes: http://linkinghub...12015000

The change is due to divergent feeding behavior (i.e., nutrient driven). Nutrient-dependent pheromone production controls reproduction. My point is that mutagens do not cause nucleotide replacements that result in adaptive evolution, which is nutrient-dependent and pheromone-controlled in species from microbes to man.
C_elegans
5 / 5 (1) Mar 22, 2013
What? Why? I promise you, mutations are happening. Sure, behaviors may influence evolutionary trajectories, but that is to be expected. As you might say, only the most nutritious survive.

As to your paper: this is about two related species of nematodes. You see, nematodes grow from larva to adults when food is around. When there isn't, an alternate developmental step is entered, the dauer stage. Dauers are hardy, long-lived, and specialized to conditions of little food. Once food returns, they continue on to grow into adults.

That is what that paper is talking about. This other species of nematode has a dauer-stage that is predatory. Remarkably, they find that most of the original neurons are present in the diverged species, but that they have repurposed their firing capabilities to control novel behaviors. This is caused by individual mutations in many genes that ultimately change the ratio of proteins in these neurons. I agree, it was a very cool paper.
JVK
1 / 5 (4) Mar 22, 2013
This is caused by individual mutations in many genes that ultimately change the ratio of proteins in these neurons. I agree, it was a very cool paper.


You seem to be arguing for mutation-caused adaptive evolution via ecological, social, and neurogenic niche construction in nematodes at a time when we know that a nutrient-dependent amino acid cysteine-to-alanine substitution represents pheromone-controlled species incompatibilities.

Is there a mutation that concurrently directs or controls adaptive from the bottom up (nutrition) and from the top down (by pheromone controlled reproduction), or are you representing less than half of what's required to get from pleiotropy to epistatis across species from microbes to man. For example, a mutation that results in better nutrient utilization might cause something adaptive, but nothing that shows up in phenotype that can be naturally selected.

You seem to be saying that mutations are somehow selected. Is there a model for that?
C_elegans
not rated yet Mar 22, 2013
Natural selection is the model.

I still don't follow. Why does cysteine-to-alanine represent species 'incompatabilities'. That's an amino acid, not a nucleotide. Amino acids are not typically inherited. Are you referring to the mutation in the DNA sequence that causes Cys->Ala? That paper is not a documentation of two species diverging, it's a comparison of two diverged species that have a similar life-stage (dauers). The authors mention pheromones because that is the signal to enter a dauer or normal developmental cycle. If the environment is crowded (lots of pheromones around), then pheromones become detected by receptors on neurons. Those detected pheromones cause the nematode to deviate towards the alternate dauer state during development.

Also, please define epistasis? It means to 'cover up'. This is often a term used by geneticists to identify gene in the same pathway, as one gene's phenotype will be epistatic to all other genes downstream in that genetic pathway.
C_elegans
5 / 5 (1) Mar 22, 2013
For example, a mutation that results in better nutrient utilization might cause something adaptive, but nothing that shows up in phenotype that can be naturally selected.


That's not true. If the effect of the mutation is 'better nutrient utilization', then that is the phenotype! Natural selection chooses mutations that drive fecundity.

Imagine a plate of 500 worms. One of them has a mutation (genotype) for better nutrient utilization (phenotype). That worm will be able to metabolize its food better, make more progeny than its competitors, and the gene will spread to fixation over time.
JVK
1 / 5 (5) Mar 22, 2013
There is no scientific evidence that mutations are selected and no molecular mechanisms that would allow their selection. Mutations theory is a statistical misrepresentation of Darwin's conditions of existence. Those conditions must be met before natural selection occurs. For the role of amino acid substitutions see: Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation http://dx.doi.org...e.643393
C_elegans
not rated yet Mar 23, 2013
Ok, thanks.
CQT
1 / 5 (2) Mar 23, 2013
Only if the envionment remains static (which it doesn't). - AP


If nothing else planetary evolution ends a DNA-based information transfer eventually. Unless a planetary evolution leads to a non-DNA information transfer DNA-based life must relocate.

Although the universe bears much evidence for planets able to support DNA-based information transfer the distances to relocate to other DNA-friendly planets presently appears insurmountable.

Humans have always imagined life forms independent from the environments and molecules that brought them and all life known forth.

We provide the conditions and selections for our existence and our long-term evolution now.

The 'experiment' labeled 'humans' has become surprisingly predictable.
We will not be saving planets from their eventual demise.
This couples with the following prediction:
You will not find any evidence that saves a static universe.