Bacteria such as Escherichia coli can acquire predictable mutations to adapt to a changing environment.
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Although mutations, the driver of evolution, occur at random, a study of the bacterium Escherichia coli reveals that nature often finds the same solution to the same problem again and again.
Over time, random mutations enable organisms to adapt and diversify, often when geographically separated groups of the same species grow better suited to their local environment and less like members of the other group.
But that's not the only way that genetic diversity can arise. Researchers have reported cases of cichlid fish, palm trees and finches adapting to different ecological niches and splitting into different species despite living in the same place. In 2008, evolutionary biologist Michael Doebeli of the University of British Columbia (UBC) in Vancouver and colleagues reported that E. coli bacteria can also diversify while sharing a test tube.
In that study, they fed easy-to-digest glucose and a harder-to-stomach acetate to homogeneous populations of the bacteria, and let the bacteria chomp away. E. coli can switch between the two foods, but the team found that in each test tube two groups emerged, specialized in consuming either glucose or acetate. What they did not know was which genetic path each group took to achieve its specialization.
Mapping evolution
In the new study, published online today in Public Library of Science Biology, Doebeli and colleague Matthew Herron, also at UBC, went back to the frozen samples from three of their test tubes and sequenced 17 gene samples from various stages of the experiment. The DNA showed that in some cases identical mutations appeared independently in all three test tubes: despite the random nature of mutations, the same changes in the environment favored the same genetic solutions.
Doebeli and Herron also found that some mutations occurred only in a specific order: after one group had become specialized for glucose and the other for acetate, both groups evolved to switch better between meal types. That last mutation would not have been useful until after the emergence of the first, which helped exhaust food supplies faster. That finding is novel, says systems biologist Michael Stumpf of Imperial College London. Although biologists have observed traits appearing in a particular order, until now no one had documented the genetic basis for those changes.
"It's of interest to know how often the genes that change are the same or different," says biologist Jerry Coyne of the University of Chicago, Illinois. "That tells us how much constraint there is on evolution." Insects often evolve resistance to insecticides through the same common mutations, he notes.
Evolutionary constraint
Coyne adds, however, that it may not be practical to extrapolate very much from an asexually reproducing species such as E. coli to organisms that reproduce sexually.
And Stumpf warns that because bacteria live in such large populations, their evolution in aggregate may be more predictable than that of larger, more dispersed species.
Environments also change faster than most species can evolve, Stumpf says, so he would be interested in future studies that examine how predictable evolution is in changing environments. Doebeli agrees: he has dozens of other frozen lines of bacteria, which evolved in environments of varying complexity, waiting for their genomic snapshots.
This article is reproduced with permission from the magazine Nature. The article was first published on February 19, 2013.
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32 Comments
Add CommentThis is not evolution happening. These are traits already existing in their DNA, dormant or 'hidden in the junk DNA' so to speak. These are capabilities the bacterium has developed along the way and kept in their survival arsenal. In the lab, they just saw E. Coli reach for some of the tricks in their bag, not evolve them.
Reply | Report Abuse | Link to thisInteresting experiment, but IMO their conclusions are way off...
As I understand, genetic mutations may occur entirely randomly, but they are generally selected for reproduction on the basis of the benefits they infer upon the organism. As a result, beneficial mutations (in prevailing conditions) are more likely to be perpetuated... In this study, it seems that many other mutations might have occurred but those that offered benefits in the (likely similar) conditions of each population were commonly selected for promotion.
Reply | Report Abuse | Link to thisWhat is the process by which the bacterium developed those hidden capabilities along the way?
Reply | Report Abuse | Link to thisAs far as I understand Evolution (BS Cellular & Molecular Biology), Evolution is the change in allele frequencies over time. Since the specifying alleles were not present at the beginning (no glucose or acetate proteins), and they appeared over time, Evolution had occurred. Regardless of whether the genes had evolved earlier and become deactivated or were novel. I agree with you that the genes reactivating is way easier and much more statistically likely than the genes appearing randomly, but all still evolution nonetheless.
Reply | Report Abuse | Link to thisEdit to my previous comment, they were able to digest glucose and acetone in the beginning, but they made new proteins or altered their existing proteins (and also their DNA) and became specialized, but still evolution.
Reply | Report Abuse | Link to this"they just saw E. Coli reach for some of the tricks in their bag" how exactly did they "reach" for them?
Reply | Report Abuse | Link to thisRe: "...[M]utations, the driver of evolution...enable organisms to adapt and diversify..."
Reply | Report Abuse | Link to this"...[M]utations...must be eliminated in nature, which would otherwise present a spectacle entirely different from the reality. This is partly due to the fact that mutations are not adaptive. If we say that it is only by chance that they are useful, we are still speaking too leniently. In general, they are useless, detrimental, or lethal. Darwin himself did not think that the races of domesticated animals were capable of surviving in nature but the modern Darwinians are obliged to explain evolution as the result of mutations."
[Prof. W. R. Thompson. 1956. Introduction. In: Charles Darwin. Origin of Species. Everyman Library No. 811. London: J. M. Dent and Sons. Reprinted with permission. Evolution Protest Movement. 1967. NEW CHALLENGING ‘INTRODUCTION' TO THE ORIGIN OF SPECIES. Selsey, Sussex: Selsey Press Ltd., p. 10]
Which cell has the randon mutation?
Reply | Report Abuse | Link to this@Bill_Crofut, as usually you haven't troubled yourself to understand the subject before criticizing. You are obviously unaware of non-coding regions, endogenous retroviruses, gene duplication, enhancers, pseudogenes, etc. All of these permit mutations to occur without disabling functional genes. In fact, mutations to gene regulation can have significant affects on evolution without changing any genes. Of course you would know this if you had any interest in understanding evolution. But like all the other sciam trolls your only interest is in sharing your ignorance.
Reply | Report Abuse | Link to this"The DNA showed that in some cases identical mutations appeared independently in all three test tubes: despite the random nature of mutations, the same changes in the environment favored the same genetic solutions."
Reply | Report Abuse | Link to thisI was taught the wrong definition of random apparently somewhere along the line.
8) - TES
As I understand, many genetic mutations could have randomly occurred, but the preponderance of cells that successfully reproduced we those that contained beneficial traits (for their current conditions) selectively incurred from some subset of mutations.
Reply | Report Abuse | Link to thisRSchmidt (comment 9),
Reply | Report Abuse | Link to thisFirstly, "my" criticism is really Prof. Thompson's criticism.
Secondly, regarding my ignorance, you'll get no argument from me.
Thirdly, my ignorance also includes no knowledge of any mutation that is useful. Please dispell some of my ignorance by sharing that knowledge with me.
Fourthly, regarding an understanding of evolution (specifically related to the fossil record in this case), allow me to share the published view of the late Prof. Stephen Jay Gould:
“The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology....Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never "seen" in the rocks.
Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study.”
[1977. Evolution's Erratic Pace. NATURAL HISTORY, May, p. 14]
Example of a beneficial mutation: the ancestral state of humans is lactose tolerance in infancy and lactose intolerance in adulthood. Mutations appeared independently in three populations which practiced animal husbandry (eastern Africa, northern Europe, and the Middle East). The mutations keep the lactase gene turned "on", allowing those with the mutation to consume the nutritious, sterile fluid throughout life.
Reply | Report Abuse | Link to thisAnother beneficial mutation (depending on prevailing environmental conditions) is that presence/absence of dark skin pigmentation. Please see/hear:
Reply | Report Abuse | Link to this"Human Skin Depigmented More Than Once,"
http://www.scientificamerican.com/podcast/episode.cfm?id=human-skin-depigmented-more-than-on-13-02-21
I'm waiting for the transcript, but having dark pigmentation in upper latitudes inhibits the production of vitamin D and increases the risk of developing rickets. Having insufficient dark pigmentation in equatorial regions exposes one to excessive UV-A absorption and increases the risk of developing skin cancer. That populations from varying latitudes eventually develop appropriate levels of pigmentation is a beneficial adaptation produced by random mutation.
Mtgilbert,
Reply | Report Abuse | Link to thisRe: "Before the evolution of lactase persistence, humans typically lost their ability to digest lactose around the age of five. (This is thought to have helped motivate weaning.) Still today, most of the world's population can only tolerate milk for the first few years of life. But, through at least four parallel evolutions starting several thousand years ago, lactase persistence spread throughout human populations. One of these, the earliest, is known to have originated in Europe."
http://www.scientificamerican.com/article.cfm?id=lactose-toleraence
That quote brings to mind the following questions:
How were our human ancestors able to survive prior to the "evolution" of lactase persistence?
Is one mutation responsible for lactose tolerance as well as intolerance?
Jtdwyer,
Reply | Report Abuse | Link to thisRe: http://www.scientificamerican.com/podcast/episode.cfm?id=human-skin-depigmented-more-than-on-13-02-21
Prof. Jablonski’s commentary consists of a short series of assertions without the provision of any evidence. Granted, nothing more than that could be expected in the time she was allotted. There is text available on the topic (see comment 15).
Are you suggesting then that the presence/absence of skin pigmentation is not the product of a beneficial mutation?
Reply | Report Abuse | Link to thisAll mammals are able to digest milk in infancy - the very name comes from the mammary tissue which produces it. I do not know the origin of the enzyme lactase, but it is probably the result of gene duplication of another sugar-digesting enzyme followed by point mutations (i.e., a paralog). In paralogs, original sequences retain their functions and mutations in duplicates can lead to the evolution of new functions. In lactase persistence, mutations in the promoter region of the lactase gene cause production of the enzyme past infancy. The advantage in this is the ability to get nutrition from milk *in addition* to meat, plants, etc. You ask good questions, Bill.
Reply | Report Abuse | Link to thisJtdwyer (comment 17),
Reply | Report Abuse | Link to thisThe phrase, “beneficial mutation,” seems to me a contradiction in terms. If not, why do x-ray technicians go to such lengths to protect themselves from the substance of their trade? Why is not the characteristic simply genetic rather than mutagenic?
mtgilbert (comment 18),
Reply | Report Abuse | Link to thisThank you for the compliment, but you give me far too much credit. My questions could not be asked without the source material in the web page text.
Would someone define for me what a species is?
Reply | Report Abuse | Link to thisI mean, I went to a museum that displayed how Darwin identified 13 species of Finch on the Gallapagos based on their beak sizes. That sure seems stupid to me. If my nose is bigger or smaller than yours, it does not mean I am a different species than you.
In a similar way it seems like nonsense to me when people say that genetic changes of E. Coli over time is evolution. I am genetically different than my father and grandfather. I have overcome different challenges in my environment than they did. It no way does that represent evolution.
http://en.wikipedia.org/wiki/Species
Reply | Report Abuse | Link to this"A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring."
secretagent3180,
Reply | Report Abuse | Link to thisProf. W. R. Thompson offered very little encouragement regarding the definition of species:
"What we call the natural system of classification is a proof of evolution since it can only be explained as a result of evolution....The argument specifically implies that nothing is exempt from this evolutionary process. Therefore, the last thing we should expect on Darwinian principles is the persistence of a few common fundamental structural plans. Yet this is what we find...[T]here is often controversy and, uncertainty about the definitions of genera. species, and varieties; but taking the taxonomic system as a whole, it appears as an orderly arrangement of clear-cut entities which are clear cut because they are separated by gaps. These gaps Darwin explained by the hypothesis that the intermediates are constantly eliminated by natural selection. I do not think that we can be expected to accept this unproved supposition as an argument for Darwinism."
[1956. Introduction. In: Charles Darwin. Origin of Species. Everyman Library No. 811. London: J. M. Dent and Sons. Reprinted with permission. Evolution Protest Movement. 1967. NEW CHALLENGING ‘INTRODUCTION' TO THE ORIGIN OF SPECIES. Selsey, Sussex: Selsey Press Ltd., p. 13]
Jtdwyer,
Reply | Report Abuse | Link to thisThe url you provided also contains the following disclaimer:
"While in many cases this definition is adequate, the difficulty of defining species is known as the species problem."
I may be the only participant here who has published on nutrient-dependent pheromone-controlled adaptive evolution and modeled it based on what is currently known about molecular epigenetics with the use of animal models of epigenetic effects in species from microbes to man. See, for example, "Nutrient-dependent / Pheromone-controlled Adaptive Evolution" at http://dx.doi.org/10.6084/m9.figshare.155672
Reply | Report Abuse | Link to thisThere are links from the model to my peer-reviewed publications.
Despite the claims, no scientific evidence suggests that mutations cause adaptive evolution. Adaptive evolution obviously occurs via 4-stages of niche construction: 1)ecological 2) social 3) neurogenic and 4) socio-cognitive. Is is not possible for any mutation to cause fixation/epistasis via step 1 (the ecological niche is nutrient-dependent). Step 2 is required for control of nutrient-dependent adaptive evolution. Ecological niche construction is controlled by the metabolism of nutrients to species specific pheromones in species from microbes to man. Pheromones establish constraints of the social niche.
Those who are trapped in the statistics of population genetics where selection somehow occurs for phenotype may need to start with the basic principles of biology and levels of biological organization that link olfaction and odor receptors to the epigenetic tweaking of immense gene networks portrayed in my model of systems biology. But because that's the only way to understand adaptive evolution it may be worth it to learn. Minimally, you won't be caught discussing mutation-driven adaptations, or redefining your terms to make it appear that a theory represents the biological facts. It never has, and we can see now that it never will. Adaptive evolution has always been nutrient-dependent and pheromone-controlled, and always will! That's probably as predictable as anything that's ever been believed, which makes it somewhat unbelievable that so many people believe in mutations theory.
So what?
Reply | Report Abuse | Link to thisIf you really wanted to develop a meaningful argument (I'm not interested - I merely responded to secretagent3180's taunting request), try a little more extensive research - for example read
Reply | Report Abuse | Link to thishttp://en.wikipedia.org/wiki/Species_problem
It includes the quotation:
"... I was much struck how entirely vague and arbitrary is the distinction between species and varieties"
- Charles Darwin, On the Origin of Species (p. 48)
Consider continuing your research:
Darwin, C. (1859). "On the origin of species by means of natural selection." London: Murray. ISBN 84-206-5607-0.
Jtdwyer,
Reply | Report Abuse | Link to thisSince you’re not interested, your lack of interest will be honored.
So what I'm hearing is that in order to get the Sea Monkeys pictured on the package, you have to subject them to the proper environment and then just wait for the adaptive mutations to occur naturally.
Reply | Report Abuse | Link to thisI think it is quite probable that evolutionary theory is incomplete, and that the mutation process is not as random as has been believed. There is probably some type of self organization process that is taking place that eventually results in the emergence of new genetic traits. Although pure Lamarckian ideas are clearly wrong, it is possible that repetitive (collective) exposure to environmental stresses over time can indirectly influence the aforementioned self organization process.
Reply | Report Abuse | Link to this@christinaak: Yes, you're pointed in the right direction, Christina, but the process is not only very simple, its right in front of us. Darwin was right, but we have to think in rather more abstract terms about the dynamics.
Reply | Report Abuse | Link to thisOur fascination with the notion of "information" has us, in our attempts to dig into the issues, holding the shovel by the wrong end. We overlook the fact that Mendel describes the (static) _result_ of the process, not the (dynamic) process of evolution; Mendel's insight, while interesting, has no connection with that process.
@Bill_Crofut: Your insight and questions are aimed in the right direction, Bill. Even though organisms change -- nature always finds a way -- science, like all human groups, is entirely geared toward stasis, i.e., maintaining its structure, doctrine and paradigms.
What we see in this study is what one might call probabilistic vectoring of the organism's response to its (average) environment. The crisis in biology, including evolution, is that we lack an overarching theory that embraces all subdisciplines, but we have all the data we need. Currently we find that the same organism's change depends on which subdiscipline is describing it (and, of course, the part of it addressed by the subdiscipline). Like sex in the church, this is yet another scandal we deny as extant.
mounthell,
Reply | Report Abuse | Link to thisRe: "We overlook the fact that Mendel describes the (static) _result_ of the process, not the (dynamic) process of evolution; Mendel's insight, while interesting, has no connection with that process."
According to Franciscan Fr. Valentine Long, Fr. Mendel's contribution had more of an impact on the science of genetics than you seem to have indicated:
“It was...Gregor Johann Mendel, a Catholic priest from Austria, who discovered the now accepted laws of heredity. With Darwinism all the rage at the time, however, his painstaking work went unrecognized for thirty-five years....But Mendel's laws, once they became well known, altered the whole general concept of inheritance to disprove Darwin.”
[Rev. V. Long, O.F.M.. 1978. Evolutionism—A fairy tale for adults. HOMILETIC & PASTORAL REVIEW, April, pp. 30-31]