Human Evolution-Bacteria Conjugation

[PhysicsFan11]

So evolution is based on the premise that successive mutations lead to phenotypic changes ultimately resulting in varied species. This despite the fact that many mutations in nature are actually deleterious to that species.

The question I have then, is that if mammalian evolution produced successive varied generations of species, starting from a common origin, why have bacteria not done the same.?Particularly with conjugate reproduction, E.coli for example, despite >10 to the 12th [Observed] generations have not essentially been transformed though there are species specific variations, particularly antibiotic resistance. (in other words, E,coli have not evolved into paramecia , for example) So then how can mammals, from their common point of therapsids, have evolved so many species with only about 6 million new generations from point of origin to current?

 

[Simon Bridge]

E.coli for example, despite >10 to the 12th [Observed] generations have not essentially been transformed though there are species specific variations, particularly antibiotic resistance. (in other words, E,coli have not evolved into paramecia , for example)

Well that would contradict the theory of evolution for a start.
Modern creatures do not evolve into each other... they share a common ancestor.
All modern life forms are at the same level in evolutionary terms.

Speciation happens at different speeds in different lines because the organisms are different and are subject to different circumstances. Biology is messy. Why would you expect mammal evolution to occur at a similar rate to bacteria evolution?

 

[Drakkith]

So evolution is based on the premise that successive mutations lead to phenotypic changes ultimately resulting in varied species. This despite the fact that many mutations in nature are actually deleterious to that species.

Most mutations are actually neutral, having no beneficial or detrimental effect. Those that are deleterious are either not passed on, or are passed on with a reduced frequency compared to the non-deleterious alleles. Note that many mutations that appear deleterious can actually have a 'hidden' beneficial effect. For example, sickle cell anaemia is a result of a mutation in the gene that controls the type of hemoglobin produced and used by red blood cells. Two copies of this mutation give rise to the disease, but a single copy of the mutated gene paired with a single copy of the non-mutated gene confers resistance to malaria and explains its persistence in the genome of populations in malaria-prone areas.

The question I have then, is that if mammalian evolution produced successive varied generations of species, starting from a common origin, why have bacteria not done the same.?

There are great differences between primates and bacteria at many different levels that contribute to this, such as genome size, details of their cellular machinery, environmental pressures, and many, many others.

Particularly with conjugate reproduction, E.coli for example, despite >10 to the 12th [Observed] generations have not essentially been transformed though there are species specific variations, particularly antibiotic resistance. (in other words, E,coli have not evolved into paramecia , for example)

For one, these bacteria are not under the kind of environmental pressure that would lead to such drastic changes in their forms. In addition, a change of that kind of magnitude represents an enormous evolutionary jump (ignoring the fact that bacteria wouldn't evolve into paramecia anyways, but into another unique type of lifeform).

 

[mfb]

Particularly with conjugate reproduction, E.coli for example, despite >10 to the 12th [Observed] generations have not essentially been transformed

Is "using a completely new energy source" sufficient?
E. coli long-term evolution experiment

We did not observe 10¹² generations, that would take millions of years.

 

[PhysicsFan11]

Actually, and this is well established with multiple sources, E.coil and many other bacteria actually can replicate at such a prodigious rate (and exponentially) that in [One] day they are able to (with binary fission) produce from a single bacteria , well greater than 10 9th or >1 billion progeny. One would then think that in that [vast] amount of replication, we would observe much more mutational change that [is] observed in vitro.

 

[PhysicsFan11]

Above should read 'than is observed in vitro'.

 

[PhysicsFan11]

Further, with regards to above responses, my understanding is that most mutations that are observed are harmful (or possibly neutral) but not beneficial. Thus, in relation to my main point, beneficial mutations have not been seen in vitro. I could be wrong on this but please convey any research findings/literature where beneficial mutations have been observed in the laboratory or experimental setting. This essential fact I think we can say with clarity , therefore is not replicable in an observational setting such as a field experiments or the laboratory.

 

[mfb]

You can edit your posts if you want to change them.

Actually, and this is well established with multiple sources, E.coil and many other bacteria actually can replicate at such a prodigious rate (and exponentially) that in [One] day they are able to (with binary fission) produce from a single bacteria , well greater than 10 9th or >1 billion progeny. One would then think that in that [vast] amount of replication, we would observe much more mutational change that [is] observed in vitro.

That is not a generation. Your parents are one generation earlier than you, not billions, although billions of humans were born between your parents and you.

E. coli, under ideal conditions, has a few tens of generations per day.

One would then think that in that [vast] amount of replication, we would observe much more mutational change than [is] observed in vitro.

What exactly do you expect and where does this expectation come from?

my understanding is that most mutations that are observed are harmful (or possibly neutral) but not beneficial.

So what? The beneficial ones lead to a larger reproduction, the harmful don't spread. That is natural selection.

Thus, in relation to my main point, beneficial mutations have not been seen in vitro.

I linked an example in my previous post. In case you meant "in vivo", see Drakkith's post. And there are more published examples than you can ever study in detail.

 

[PhysicsFan11]

So with regards to: "There are great differences between bacteria and primates genetically" ... we need to answer the question of : Paramecia (which are Eukaryotes and protozoa , not bacteria) have 23 chromosomes. Primates vary of course, but are in the 46-48 number of chromosome range. Then, protozoa and bacteria , in terms of DNA mass, can be in the 10 to the 9th Dalton and 10/ 10th Dalton range, and primate DNA >10 to 12th Daltons but not much more. So I not clear on any great differences...

 

[PhysicsFan11]

Also, yes it may be correct that bacteria/protozoa are not under the kinds of environmental pressure (leading to beneficial mutations) that may have contributed to primate evolution. Or may be someone can add to this; in other words, I am not clear about environmental pressure occurring or not occurring with regards to bacteria/protozoa/fungi?
Can this pressure be applied in a field or laboratory setting?

 

[PhysicsFan11]

mfb,
The link to E.coli evolution is fascinating...thank you...

 

[DaveC426913]

Can this pressure be applied in a field or laboratory setting?

Sure. That's how we get antibiotic resistant bacteria.

 

[jim mcnamara]

Consider that your biology assumptions need some help. The amu mass of DNA in a cell varies, it also varies within a species - switchgrass - Panicum virgatum is polyploid meaning it has multiple copies of the same (not necessarily identical ) copies of each chromosome - DNA mass per cell varies over an order of magnitude.
The number of genes (places on chromosomes where active DNA lives) varies wildly as well across species.

Differences between E. coli and humans are legion. It is the context and implementation of the gene expressed as a phenotype (ex: blue eyes vs brown eyes) that matters in natural selection. Not DNA mass. A large fraction (under study) of DNA present on mammalian cells seems to contribute little to the active phenotype of individuals. FWIW.

Where did you come up with your point of view? In other words can you please cite a textbook or article or something like that as the source?

As to: 'pressure' - that is simply differential survival of individuals because of varying genes - and environmental changes. Fiddle with the environment -> force changes over time and generations. In the paper mfb cited, citrate was present in the growth medium. Two mutations occurred randomly. The cells with those two mutations are then able to extract more energy from the growth medium than their cohorts in the same flask of growth medium. They breakdown citrate more efficiently into energy than their buddies... Eventually they took over the flask(s). Because they had a bioenergetic 'edge' - in this case.

 

[PhysicsFan11]

Valid points Jim,
However I do think DNA mass does relate to the process of natural selection. Introns, or non sense DNA, (a component of that mass) initially thought to be irrelevant, have been found to be important (and perhaps critical) to genetic variation and there may not be much essential difference between bacteria, fungi and mammals (with regards to Introns).

In respect to pressure on DNA, my question (E.coli evolution experiment) is about your statement 'two mutations occurred randomly', which then led to +Citrate extractors and better able to withstand environmental challenges. How can random mutations [predict] the nutritional need in this case..how many random mutations would it take to get to the 'right one'? So were they truly random or was there a signal sent into the transcription process guiding the development of that mutation? I just want to be clear about the wording of [random]. I appreciate your detailed addition to this.

 

[Ygggdrasil]

A common fallacy in these types of arguments is to assume humans are the pinnacle of evolution. The truth is that bacteria are just as evolved as humans, but they are evolved to fill a different environmental niche. In fact, one could argue that bacteria are much more evolved than humans. If you put a human cell and a bacterial cell together in a test tube, the bacteria cells will multiply much faster than the human cells and outcompete the human cells for resources. Bacteria will also outcompete other types of eukaryotic cells like yeasts or paramecia; almost no other type of organism can match the speed with which bacteria can multiply. Bacteria can be found in almost any environment on Earth and in many extreme environments (extremely high/low temperatures, extreme pH, the presence of poisonous elements like arsenic, etc.). Bacteria are capable of performing many biosynthetic reactions that no other organisms are known to perform. For example, all of the biological nitrogen on Earth comes from bacteria as only bacteria are capable of fixing atmospheric nitrogen (N₂) into forms useable by other organisms (e.g. amino acids, ammonia, nitrates, etc.). Humans, on the other hand, can't even synthesize all 20 amino acids by themselves. Eukaryotes would not be able to perform cellular respiration had they not stolen the necessary genes from the bacterium that would eventually become the mitochondrion.

In evolutionary terms, it's easy to argue that bacteria are the most successful class of organisms on Earth given the wide variety of bacteria and their ubiquity. In fact, inside the human body, there are ten times as many bacterial cells as there are human cells. From this point of view, perhaps we are nothing more than large incubators for bacteria.

Further, with regards to above responses, my understanding is that most mutations that are observed are harmful (or possibly neutral) but not beneficial. Thus, in relation to my main point, beneficial mutations have not been seen in vitro. I could be wrong on this but please convey any research findings/literature where beneficial mutations have been observed in the laboratory or experimental setting. This essential fact I think we can say with clarity , therefore is not replicable in an observational setting such as a field experiments or the laboratory.

On this point, here's a nice review article discussing the distribution of effects of mutations: http://www.nature.com/nrg/journal/v11/n8/full/nrg2808.html Here's a relevant exerpt:

Approximately 30% of TEM1 mutations cause a partial reduction in fitness, primarily owing to mildly destabilizing mutations that reduce the levels of soluble, folded protein. The remaining fraction (~62%) has no immediate measurable effects on fitness (Box 1). Although this detailed distribution is available for only one protein, experiments with other proteins show similar trends; approximately 40% of mutations reduce or completely abolish the activity of the mutated proteinhttp://www.nature.com/nrg/journal/v11/n8/full/nrg2808.html#B8

It's worth noting that whether a mutation is beneficial, neutral, or deleterious depends on the particular environment in which the organism resides. In many in vitro evolution experiments (such as the Lenski experiment that others have cited), one can often find beneficial mutations by adapting an organism to a new environment.

 

[DaveC426913]

In evolutionary terms, it's easy to argue that bacteria are the most successful class of organisms on Earth given the wide variety of bacteria and their ubiquity.

+1

 

[Drakkith]

How can random mutations [predict] the nutritional need in this case..how many random mutations would it take to get to the 'right one'?

They can't predict anything. The mutations were truly random. DNA is always being damaged, and repair processes, while very, very good, are not 100% effective at repairing the damage. The two specific mutations that led to the bacteria's ability to utilize citrate were only two of many, many mutations incurred over years of time. Most of these mutations had little to no effect on the cell population, some were detrimental, and some were beneficial. Note that this is a case of several separate mutations which, by themselves, had little effect on the cell. But combined these mutations allowed the cell to utilize citrate which allowed the first cell with both of these mutations to rapidly reproduce, taking over the sample with its progeny.

As to how many mutations it would take to get the 'right one', that depends on the specific mechanisms affected by any given mutation and how they enable the organism to interact with its environment. There simply isn't a a single answer. Sometimes a single-nucleobase mutation can have a profound effect on an organism and sometimes a mutation that deletes, replaces, or changes hundreds to thousands of bases can have essentially no effect.

Consider the following hypothetical example:

Let's say that a mutation changes a single nucleobase involved in making opsins, light sensitive molecules involved in vision, that significantly reduces a predatory diurnal mammal's ability to see. This is, obviously, a hugely detrimental mutation that greatly reduces the survivability of the organism. This organism would be unlikely to survive and reproduce, so the mutation is unlikely to be passed on.

Now consider an organism whose population has recently moved into a very low-light environment and uses its other senses much more than its vision, much like cave-dwelling organisms do. If this organism's offspring has a mutation that completely deletes several critical genes involved in vision, this mutation would have little effect on the offspring's survivability since it isn't using it's vision much anyways. If this mutation is heritable, then it can be passed on to future offspring and the proportion of organisms in this species that are effectively blind can increase over time since there is little to no detrimental effect by losing these genes. In fact, this mutation can eventually spread to all of the species progeny if it happens to confer some beneficial effect, such as a reduction in energy expenditure. Even if it doesn't confer an advantage, it can still spread to the majority of a species offspring through genetic drift.

 

[Evo]

Valid points Jim,
However I do think DNA mass does relate to the process of natural selection. Introns, or non sense DNA, (a component of that mass) initially thought to be irrelevant, have been found to be important (and perhaps critical) to genetic variation and there may not be much essential difference between bacteria, fungi and mammals (with regards to Introns).

In respect to pressure on DNA, my question (E.coli evolution experiment) is about your statement 'two mutations occurred randomly', which then led to +Citrate extractors and better able to withstand environmental challenges. How can random mutations [predict] the nutritional need in this case..how many random mutations would it take to get to the 'right one'? So were they truly random or was there a signal sent into the transcription process guiding the development of that mutation? I just want to be clear about the wording of [random]. I appreciate your detailed addition to this.

Please link to the sources for your statements that Jim requested, furnishing requested citations is not an option here. When you furnish the sources of your information, we can tell if you are reading misinformation or just misunderstanding what you are reading, it really helps the discussion, we don't have to try to guess about what you might have read.

Thank you.

 

[PhysicsFan11]

Ok, so multiple mutations must have occurred as noted in the E.coli evolution link noted on prior posts,; most of these mutations were non-consequential but some of which actually potentiated the final point mutations for the Citrate+ E.coli. The link also describes how the [entire] realm of the E.coli genome, over time, developed mutations. This is a remarkable observation. The inference then [could] be that there is a limit to the observed traits of the E.coli in the study...is there a [finite limit] to its evolutionary phenotype if indeed the entire genotype has already had the full spectrum of individual mutations? I believe this is a very important question and I am sure there is someone who can answer it. The exact wording used in the link is "that every possible single point mutation in the E.coli genome has occurred multiple times".
This quote then references : Blount, Zachary D.; Borland, Christina Z.; Lenski, Richard E. (2008). "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli". Proceedings of the National Academy of Sciences 105 (23): 7899–906.Bibcode:2008PNAS..105.7899B. doi:10.1073/pnas.0803151105. JSTOR https://www.jstor.org/stable/25462703.PMC 2430337. PMID 18524956.

 

[Ygggdrasil]

A few notes on long term evolution experiments (LTEE):

1. Subsequent to the 2008 PNAS paper describing the Cit+ strain, the Lenski lab published a follow up paper identifying some of the actualizing mutations behind the Cit+ phenotype: http://www.nature.com/nature/journal/v489/n7417/full/nature11514.html. We discussed the paper in the following PF thread: https://www.physicsforums.com/threads/long-term-evolution-experiment.638509/

2. In the 2008 PNAS paper, the authors note that all each of the 12 cultures in the LTEE had grown for long enough times such that each culture would sample all single point mutations possible in the genome. However, many evolutionary studies showed that epistasis plays very important roles in evolution. The same point mutation can have different effects on an organism's phenotype depending on what other mutations are present. Thus, sampling every single point mutation cannot tell you the effect of every possible pair of single point mutations. Even though the experiment sampled all single point mutations, it has not sampled all combinations of mutations, so much of the evolutionary landscape still remains unexplored.

3. In many cases, the evolution of beneficial traits require certain permissive mutations to precede acquisition of the actualizing mutations that confer the beneficial phenotype. In the absence of the permissive mutations, the actualizing mutations can be deleterious instead. This situation appears to be the case for the evolution of the Cit+ phenotype in the Lenski experiment, and this phenomenon has also been observed in the evolution of steroid receptors: http://www.ncbi.nlm.nih.gov/pubmed/17702911

4. In some cases, the permissive mutations confer an evolutionary benefit to the organism, so there exists an adaptive path toward the evolution of the beneficial trait (i.e. the fitness of the organism increases at all steps along the way). For example, this has been seen in the evolution of antibiotic resistance: http://www.sciencemag.org/content/312/5770/111.long However, in the cases of the Cit+ and steroid receptor evolution, the permissive mutations seem to be neutral. Thus, evolution of these new phenotypes depended not only on natural selection, but also neutral drift. More broadly, given the pervasive roles of epistasis in evolution, neutral drift is likely continually opening and closing various potential adaptive paths towards new phenotypes, consistent with previous thoughts about the role of historical contingency on evolution. If true, this would suggest that evolution, to some extent, is fundamentally unpredictable.

5. Finally, with regard to the limits of mutation to improve the fitness of an organism, various long term evolution experiments have encountered a phenomenon known as "diminishing returns epistasis" (for example see http://www.sciencemag.org/content/342/6164/1364.long and http://www.sciencemag.org/content/344/6191/1519.long). At first, the population acquires mutations that greatly increase the reproduction rate of the population, but the rate at which the fitness increases diminishes over time. These observations may suggest some rate limiting metabolic processes in the cell that defines the maximum growth rate of the organisms.

 

[mfb]

5. Finally, with regard to the limits of mutation to improve the fitness of an organism, various long term evolution experiments have encountered a phenomenon known as "diminishing returns epistasis" (for example see http://www.sciencemag.org/content/342/6164/1364.long and http://www.sciencemag.org/content/344/6191/1519.long). At first, the population acquires mutations that greatly increase the reproduction rate of the population, but the rate at which the fitness increases diminishes over time. These observations may suggest some rate limiting metabolic processes in the cell that defines the maximum growth rate of the organisms.

That shouldn't be surprising. If initial adaption is poor there are more possible improvements. And there is no way a cell can reproduce in milliseconds, so there has to be some limit.

 

[PhysicsFan11]

All valid points...I am still intrigued, in reference to the E.coli evolution experiment, about the odds of the Citrate + ( mutation resulting in E.coli that are able to utilize Citrate in aerobic conditions) occurring. There are 4288 genes found to be coding for proteins in E.coli (see https://en.wikipedia.org/wiki/Escherichia_coli#Genomics). If we conservatively estimate that it requires 2 potentiating mutations to allow for a final actuating mutation to develop, which then results in a new trait (such as the Citrate utilizing protein), then the number of potential mutations would be described by the permutation formula. C representing the maximum number of possible combinations and n the total subjects in a field, r the number of subsets, thus based on the formula C = n!/ (r! ( n-r )! ), we arrive at 13,131,343,936 possible combinations/ mutations! The Citrate + mutation seems to have developed very early in the total pathway of the C number of possible mutations. How did that happen?! by anyones understanding of this?

 

[PhysicsFan11]

To summarize above, for the Citrate + mutation to occur randomly in the E.coli evolution experiment, it certainly beat the odds for it to occur so early in the total universe of possible mutations that could have occurred instead. Random or another process such as an unknown signaling mechanism for this mutation?

 

[Drakkith]

If we conservatively estimate that it requires 2 potentiating mutations to allow for a final actuating mutation to develop, which then results in a new trait (such as the Citrate utilizing protein), then the number of potential mutations would be described by the permutation formula. C representing the maximum number of possible combinations and n the total subjects in a field, r the number of subsets, thus based on the formula C = n!/ (r! ( n-r )! ), we arrive at 13,131,343,936 possible combinations/ mutations! The Citrate + mutation seems to have developed very early in the total pathway of the C number of possible mutations. How did that happen?! by anyones understanding of this?

After 30,000 generations, the number of bacteria had to be staggeringly huge. Much greater than the maximum number of possible combinations. In addition, DNA isn't static. A mutation can happen at any time during the cell's life, not just when it is dividing. Under these circumstances, I don't know if it's accurate to say that it occurred very early on.

 

[PhysicsFan11]

The question is an important one. Perhaps someone very familiar with the intricacies of the E.coli evolution study can add to this? If the mutation indeed occurred early on, then the implications are as prior noted. If conversely, the mutation occurred in the latter part of the mutation spectrum, then this too has implications. Namely, that the E.coli are still very phenotypically recognizable as the progenitor E.coli. i.e., they have not evolved into something in any way unrecognizable from the original.

 

[mfb]

All valid points...I am still intrigued, in reference to the E.coli evolution experiment, about the odds of the Citrate + ( mutation resulting in E.coli that are able to utilize Citrate in aerobic conditions) occurring. There are 4288 genes found to be coding for proteins in E.coli (see https://en.wikipedia.org/wiki/Escherichia_coli#Genomics). If we conservatively estimate that it requires 2 potentiating mutations to allow for a final actuating mutation to develop, which then results in a new trait (such as the Citrate utilizing protein), then the number of potential mutations would be described by the permutation formula. C representing the maximum number of possible combinations and n the total subjects in a field, r the number of subsets, thus based on the formula C = n!/ (r! ( n-r )! ), we arrive at 13,131,343,936 possible combinations/ mutations! The Citrate + mutation seems to have developed very early in the total pathway of the C number of possible mutations. How did that happen?! by anyones understanding of this?

I don't know where your number comes from, but the approach does not work.
All the bacteria accumulated many mutations. Mutations that don't change fitness can easily stay in the pool, so you always have a huge amount of different DNA sets in the sample. It's not like the bacteria need exactly two changes and no changes anywhere else.

 

[Ygggdrasil]

It's not necessarily the case that the Cit+ phenotype requires a unique genotype. In other words, there may be more than one combination of potentiating mutations that enable the identified actualizing mutations to work, and there could be entirely different actualizing mutations that work via a different biochemical mechanism. It is difficult to estimate the probabilities involved.

 

[PhysicsFan11]

Yes, the study references 2 potentiating mutations and 1 actualizing mutation leading to the Cit+ phenotype, and the estimate number of total potential mutations, utilizing the permutation formula, may actually be a very conservative one with the r or subset number, being 3 only.

 

[Drakkith]

If the mutation indeed occurred early on, then the implications are as prior noted.

Or, if it did indeed occur 'early', it could simply have been due to plain old probability. An event with a one-in-a-million chance of happening can certainly occur the first time. People win the lottery every day.

If conversely, the mutation occurred in the latter part of the mutation spectrum, then this too has implications. Namely, that the E.coli are still very phenotypically recognizable as the progenitor E.coli. i.e., they have not evolved into something in any way unrecognizable from the original.

I don't see how the mutations occurring 'later' as apposed to 'earlier' has anything to do with whether or not the bacteria have evolved into something beyond the original species.

 

[PhysicsFan11]

Or, if it did indeed occur 'early', it could simply have been due to plain old probability. An event with a one-in-a-million chance of happening can certainly occur the first time. People win the lottery every day.

Well, yes but realistically...one can say still understand that probability wise, an early onset Cit + mutation has remarkable implications.

 

[PhysicsFan11]

I don't see how the mutations occurring 'later' as apposed to 'earlier' has anything to do with whether or not the bacteria have evolved into something beyond the original species.

If indeed the mutation occurred in the latter phase of the full spectrum of possible mutations, then there really are not many mutations 'left' so to speak...Very logical...
If it did occur in the latter phase, then we also can interpret that there is a a finite limit of possible phenotypic variation, that being the case since there is an X amount of maximum possible mutation combinations per aforementioned computation.

 

[mfb]

Yes, the study references 2 potentiating mutations and 1 actualizing mutation leading to the Cit+ phenotype, and the estimate number of total potential mutations, utilizing the permutation formula, may actually be a very conservative one with the r or subset number, being 3 only.

Assuming only three mutations underestimates the probability massively.

Take 10 million possible places for a mutation, assume that every cell randomly has 25,000 of them (corresponding to ~.5% genetic difference between cells, the level humans have - probably an underestimate), calculate the probability that a cell has three specific mutations (plus about 25,000 mutations elsewhere). It is about 1 in 60 millions. The experiment had way more cells, so even a much smaller number of mutations is sufficient to get a reasonable chance of three mutations at specific places. In addition, see above: it does not have to be the only combination that leads to the same result.

 

[Ygggdrasil]

The question is an important one. Perhaps someone very familiar with the intricacies of the E.coli evolution study can add to this? If the mutation indeed occurred early on, then the implications are as prior noted. If conversely, the mutation occurred in the latter part of the mutation spectrum, then this too has implications. Namely, that the E.coli are still very phenotypically recognizable as the progenitor E.coli. i.e., they have not evolved into something in any way unrecognizable from the original.

Why would you expect the E. coli to evolve into something unrecognizable from the original? The culture conditions for the LTEE are fairly close to optimal growth conditions for an organism like E. coli. If you were to seed the cultures with E. coli and a number of other species, it's likely, that the E. coli would win out and dominate the culture over time. In these cases, most traits are under purifying selection which in general, will help to disfavor change over time (because most changes are deleterious).

 

[PhysicsFan11]

All the bacteria accumulated many mutations. Mutations that don't change fitness can easily stay in the pool, so you always have a huge amount of different DNA sets in the sample.

Ok but the question remains, where in the spectrum of all of the possible mutations (let us call this the X amount) did the Citrate +[set] of mutations occur? [If] it was earlier on (in this pathway of total possible mutations), then it stretches probability theory for such a beneficial trait to emerge in the time that it did. It was mentioned by Drakkith earlier that it would be analogous to winning the lottery.

The experiment had way more cells, so even a much smaller number of mutations is sufficient to get a reasonable chance of three mutations at specific places.

I understand with more clarity your point.

The culture conditions for the LTEE are fairly close to optimal growth conditions for an organism like E. coli.

Yes, near optimal environment and growth medium for the E.coli experiment. It would be quite interesting to implement and then observe the effects of varied and more challenging environments for the E.coli to evolve in a way that is phenotypically different than their progenitors.
Respects to all...

 

[mfb]

Ok but the question remains, where in the spectrum of all of the possible mutations (let us call this the X amount) did the Citrate +[set] of mutations occur? [If] it was earlier on (in this pathway of total possible mutations), then it stretches probability theory for such a beneficial trait to emerge in the time that it did. It was mentioned by Drakkith earlier that it would be analogous to winning the lottery.

I don't see any indication that it would have occurred very early or very late. Estimating the probability precisely looks like a huge challenge.

You can edit your posts if you want to add something. I merged your posts.