How Does Mullers ratchet affect the Lenski E. coli experiment?

[Darwin123]

How does Mullers ratchet affect the of the Lenski E. coli experiment?


The E. Coli in Lenski's experiment have been chosen so that there is no conjugation among the bacteria. This basically stops lateral gene transfer between cells. These bacteria are about as sexless as a organism can get.

Mullers ratchet is the hypothesis that without gene transfer, deleterious mutations have to accumulate. Without some form of gene exchange, no gene in a cell can escape the harmful effects of mutations in the another cell. Natural selection doesn't help because a gene is stuck with the other genes in the genome. Eventually, a completely asexual population has to die.

So why aren't these bacteria in Lenski's experiment dying off? Why is natural selection continuing to improve the bacteria in the environment?

Does this mean that Muller ratchet is sometimes invalid? Does it mean that there hasn't been enough time for deleterious mutations to accumulate? How do these eunuchs keep evolving with 'improved' fitness'?

You would think 60,000 generations of asexual reproduction would result in a decrease in fitness, not in new innovations. However, there are asexual animals that have been around a long time. I thought that parathenogensis was a dead end for animals. However, if the bacteria can keep on evolving then maybe parthenogenesis is not such a dead end.

Here is a link on the Lenski experiment

http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment
'Lenski chose an E. coli strain that reproduces only asexually, without bacterial conjugation; this limits the study to evolution based on new mutations and also allows genetic markers to persist without spreading except by common descent.[4]'

Here is a link on Mullers ratchet.
http://en.wikipedia.org/wiki/Muller's_ratchet
In evolutionary genetics, Muller's ratchet (named after Hermann Joseph Muller, by analogy with a ratchet effect) is the process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner.

[William L Hunt]

On Sat, 12 Jul 2014 23:20:55 -0400 (EDT), Darwin123 <drose...@yahoo.com> wrote:

>How does Mullers ratchet affect the of the Lenski E. coli experiment?
>
>
> The E. Coli in Lenski's experiment have been chosen so that there is no conjugation among the bacteria. This basically stops lateral gene transfer between cells. These bacteria are about as sexless as a organism can get.
>
> Mullers ratchet is the hypothesis that without gene transfer, deleterious mutations have to accumulate. Without some form of gene exchange, no gene in a cell can escape the harmful effects of mutations in the another cell. Natural selection doesn't help because a gene is stuck with the other genes in the genome. Eventually, a completely asexual population has to die.
>
> So why aren't these bacteria in Lenski's experiment dying off? Why is natural selection continuing to improve the bacteria in the environment?
>
> Does this mean that Muller ratchet is sometimes invalid? Does it mean that there hasn't been enough time for deleterious mutations to accumulate? How do these eunuchs keep evolving with 'improved' fitness'?
>
> You would think 60,000 generations of asexual reproduction would result in a decrease in fitness, not in new innovations. However, there are asexual animals that have been around a long time. I thought that parathenogensis was a dead end for animals. However, if the bacteria can keep on evolving then maybe parthenogenesis is not such a dead end.

There are completely asexual lineages of rotifers that have existed for millions of years, so
"Muller's ratchet" doesn't have to lead to extinction.
Also the importance of occassional conjugation is in bringing genes from separate lineages together
(with some fitness benefit), it probably has little or no effect on Muller's ratchet.
Sexual recombination is much more effective in removing slightly deleterious mutations but with and
without sexual recombination there will some equilibrium point reached where the rate new slightly
deleterious mutations are added to the population equals the rate they are removed. This varies with
population size, mutation rate and genome size (meaning the number of bases where a point mutation
has some fitness effect).
In asexual lineages as the number of slightly deleterious point mutations present increases, the
mutation rate for new slightly deleterious point mutations goes down as more are already in this
state. Likewise, the back muation rate (the rate bases mutate back from the slightly deleterious
state) increases. Eventually there will be an equilibrium point reacted.
But lineage selection also operates to keep the number of slightly deleterious mutations down.
Lineages with more slightly deleterous mutations go extinct to be replaced by lineages with fewer.
The greater the population size the more effective is this lineage selection and the lower the
equilibrium point.
William L Hunt

[Darwin123]

On Tuesday, July 15, 2014 2:41:55 PM UTC-4, William L Hunt wrote:

> On Sat, 12 Jul 2014 23:20:55 -0400 (EDT), Darwin123 wrote:
>
>
>
> >How does Mullers ratchet affect the of the Lenski E. coli experiment?
>
> >
>
> >
>
> > The E. Coli in Lenski's experiment have been chosen so that there is no conjugation among the bacteria. This basically stops lateral gene transfer between cells. These bacteria are about as sexless as a organism can get.
>
> >
>
> > Mullers ratchet is the hypothesis that without gene transfer, deleterious mutations have to accumulate. Without some form of gene exchange, no gene in a cell can escape the harmful effects of mutations in the another cell. Natural selection doesn't help because a gene is stuck with the other genes in the genome. Eventually, a completely asexual population has to die.
>
> >
>
> > So why aren't these bacteria in Lenski's experiment dying off? Why is natural selection continuing to improve the bacteria in the environment?
>
> >
>
> > Does this mean that Muller ratchet is sometimes invalid? Does it mean that there hasn't been enough time for deleterious mutations to accumulate? How do these eunuchs keep evolving with 'improved' fitness'?
>
> >
>
> > You would think 60,000 generations of asexual reproduction would result in a decrease in fitness, not in new innovations. However, there are asexual animals that have been around a long time. I thought that parathenogensis was a dead end for animals. However, if the bacteria can keep on evolving then maybe parthenogenesis is not such a dead end.
>
> There are completely asexual lineages of rotifers that have existed for millions of years, so
> "Muller's ratchet" doesn't have to lead to extinction.

These rotifers have existed for billions to trillions of generations, so they really broke Meullers ratchet a long time ago.

And let us not forget the mitochondria that live in every extant eukaryote. These guys haven't been laid for at least a billion years. It is difficult to tell how many generations, though. They reproduce in somatic cells. However, they are transmitted in the long term over germ line cells.

You are claiming that the genome reaches equilibrium because of mutations that undue the deleterious mutations. However, these backwards mutations don't seem to me very likely. so it
seems to me this equilibrium is very much weighted toward deleterious mutations.


Gene deletions can't be undone. Eventually, every gene lineage has to eventually get deleted for good and all. It appears to me that this is the extreme case of Haldanes Dilemma. If the size of the population is kept fixed, and the environment homogeneous, eventually each and every gene line has to terminate.

I think gene duplications can delay the fatal our. There have been beneficial gene duplications seen in Lenski's bacteria. One gene mutated and captured a promoter from another gene. So the result was a new way to digest sugar. I also seems to me that the gene from whom the promoter was stolen was effectively deleted. So it seems to me that the number of active genes in Lenski's bacteria should be non increasing.

I wonder if Lenski's genes have or will equilibrate in the way you are describing. How would we tell when the rate of deleterious mutations equals the rate of mutations that cancel out the deleterious mutations? What would that even mean? Could the genes of these castrated E. Coli remain in flux forever?

There is also the possibility that Lenski hasn't entirely eliminated lateral gene transfer. Lenski made sure that they couldn't conjugate like other E. coli. However, there is a process called transformation which may remain viable.

Transformation is when the bacterium incorporate the DNA from chromosomes that the bacterium has 'eaten'. There is a physiological state that some bacteria achieve where they are especial prone to transformation.

I hypothesize that Lenski's bacteria could eventually evolve a 'new' mode of lateral gene transfer. He blacked one channel for transferring genes. However, this lack of gene transfer may be creating an existential threat. An individual bacterium that could occasionally grab another gene may be at an advantage. Maybe more than one way to incorporate genes.

So the genes in these bacteria may find other ways to 'break out' of their cells. Lenski won't find it right away since he is looking at this one gene marker. He is eliminating all bacteria that don't have this gene marker. However, what if there are some bacteria that have two or three of the same marker?

Lateral gene transfer could make one bacterium not have a marker and another bacterium have two copies of the same marker. This would be difficult to separate from the effects of gene duplication, to be sure.

In any case, Lenski's experiment may eventually tell us a little about the origins of conjugation! The bacteria may converge on a pseudo conjugation process.

This is speculation, of course. However, I do wonder what the very long term results of the Lenski experiment will be.

[William L Hunt]

On Fri, 18 Jul 2014 01:33:47 -0400 (EDT), Darwin123 <drose...@yahoo.com> wrote:

>On Tuesday, July 15, 2014 2:41:55 PM UTC-4, William L Hunt wrote:
>> On Sat, 12 Jul 2014 23:20:55 -0400 (EDT), Darwin123 wrote:
>>
>>
>> >How does Mullers ratchet affect the of the Lenski E. coli experiment?
>>
>>
>> > The E. Coli in Lenski's experiment have been chosen so that there is no conjugation among the bacteria. This basically stops lateral gene transfer between cells. These bacteria are about as sexless as a organism can get.
>>
>>
>> > Mullers ratchet is the hypothesis that without gene transfer, deleterious mutations have to accumulate. Without some form of gene exchange, no gene in a cell can escape the harmful effects of mutations in the another cell. Natural selection doesn't help because a gene is stuck with the other genes in the genome. Eventually, a completely asexual population has to die.
>>
>>
>> > So why aren't these bacteria in Lenski's experiment dying off? Why is natural selection continuing to improve the bacteria in the environment?
>>
>>
>> > Does this mean that Muller ratchet is sometimes invalid? Does it mean that there hasn't been enough time for deleterious mutations to accumulate? How do these eunuchs keep evolving with 'improved' fitness'?
>>
>>
>> > You would think 60,000 generations of asexual reproduction would result in a decrease in fitness, not in new innovations. However, there are asexual animals that have been around a long time. I thought that parathenogensis was a dead end for animals. However, if the bacteria can keep on evolving then maybe parthenogenesis is not such a dead end.
>>
>> There are completely asexual lineages of rotifers that have existed for millions of years, so
>> "Muller's ratchet" doesn't have to lead to extinction.
> These rotifers have existed for billions to trillions of generations, so they really broke Meullers ratchet a long time ago.
>
> And let us not forget the mitochondria that live in every extant eukaryote. These guys haven't been laid for at least a billion years. It is difficult to tell how many generations, though. They reproduce in somatic cells. However, they are transmitted in the long term over germ line cells.
>
> You are claiming that the genome reaches equilibrium because of mutations that undue the deleterious mutations. However, these backwards mutations don't seem to me very likely. so it
>seems to me this equilibrium is very much weighted toward deleterious mutations.
>

Mullers ratchet is about how single base point mutations that are only slightly deleterious will
build up. More than slightly deleterious point mutations will be quickly eliiminated due to the
effect on the organism fitness. But slightly deleterious point mutations only have an effect when
taken in aggregate. With nothing else reducing the equilibrium, there will always be some point
where the rate that forward point mutations (to a slightly deleterious base) equals the back
mutation rate (back from the slightly deleterious base). I would roughly estimate this would occur
when 65% are slightly deleterious (and 45% normal). You might hav a different estimate?
With lineage selection in a large population (think asexual rotifers), this will be reduced further
to roughly (my best guess) 55% slightly deleterious. And with some occasional recombination of small
portions a genome it might be reduced another 10%.
But there will always be some equilibrium point.
And I do not think Mullers rachet need ever lead to a death spiral where an increase in the number
of slightly deleterious point mutations leads to a smaller population size. Then the smaller
population size reduces the benefit of lineage selection leading to again to a higher number of
slightly deleterious point mutations. And on and on until extinction.
I don't think that happens.
William L Hunt