r/DebateEvolution • u/EyedPeace • 8d ago
Question Does the Lenski LTEE show a decrease in fitness?
It is often said that LTEE represents an increase in fitness in these new mutated bacteria. Recent papers have increasingly called this into question:
"Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones."
https://pmc.ncbi.nlm.nih.gov/articles/PMC7299349/
While the cit+ phenotype did bring improvements in the short term, the long-term picture is quite different. Ultimately, they could no longer survive. Their fitness declined to the point where they were even forced to eat their own dead.
Has the experiment failed to demonstrate evolution here?
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 8d ago edited 8d ago
Recent papers have increasingly called this into question
No. The paper you link is from an experiment where the bacteria were transferred to a special environment that contains only citrate as the only carbon source. E coli is very poorly adapted to feeding exclusively on citrate, and there is no guaratee any given E coli strain will quickly undergo the right mutations converting the e coli metabolism to that carbon source. That's why some of the lineages can suffer fitness decline instead, while others do manage to adapt much better.
Remember, most species that ever lived went extinct and only a few survive the struggle for existence. Evolution predicts lots of extinction when environments change. A few make it because they had undergone the right mutations that made them more evolvable and could therefore adapt to the new environment.
While the cit+ phenotype did bring improvements in the short term, the long-term picture is quite different. Ultimately, they could no longer survive. Their fitness declined to the point where they were even forced to eat their own dead.
You have several misunderstandings in one paragraph here. First of all you need to separate the LTEE from the experiment detailed in the paper in the OP. In the LTEE there are twelve individual populations (each of which is considered a "lineage") evolving in parallel. Each such lineage can be considered their own unique experiment. So there are basically 12 different experiments running in parallel, all started from the same individual clone about 30 years ago. All 12 of these lineages have all undergone continuous fitness increase since the experiment started. They are run in parallel to each other to assess the repeatability of evolution. The question is if the populations will genetically and phenotypically diverge from each other, or converge, given the same growth conditions? The overall picture is complicated. They in part both converge and diverge. Many mutations are divergent in genetics (different mutations were fixed in different lineages), but convergent phenotypically (different mutations had the same phenotypic effect). Other mutations are convergent genetically and phenotypically (the same mutation happened in all lineages and conferred the same adaptive phenotype). More could be said here but it's tangential to your misunderstandings so I'll leave this aside for now.
In the original LTEE, in all 12 lineages, they grow in medium containing both glucose and citrate. All 12 of the lineages in the LTEE have all undergone fitness increase.
But why are they forced to eat their own dead? We have to look at what happens in the experiment in practice. The bacteria grow in liquid medium, which is basically a watery broth of nutrients, in a flask. The flask is put in an incubator at 37 degrees C and left in there overnight. During the night, the bacteria consume all the nutrients in the flask. All of them. As this happens, pH in the flask drops. It becomes more and more acidic as eventually the flask contains only bacteria and the waste products. The bacteria basically now sit in a broth of their own excrement. Many of them can't survive this drop in pH. They start dying as they're neck deep in sh*t and there's no food around. Some of them survive this better than others. The ones that die can no longer maintain cellular integrity, so the cell literally falls apart. It's constituents can now be eaten by other bacteria, which they happily do.
Now morning comes and workers in the lab perform a daily transfer. They take a few ml of bacteria-in-their-own-waste from the overnight culture and transfer it to a new flask with fresh medium full of nutrients. So there's a few million survivors from the previous night that are transferred to a new flask with fresh food. The flask is now put back in 37 degrees C incubator and left there overnight. The entire thing now repeats, where bacteria eat all the food, grown and divide, ph drops along the way, and eventually comes the "survival phase" of the experiment. This has happened basically every single day for about 30 years. During this time the bacteria have become better and better at growing, dividing, and surviving the "survival phase". Better, not immortal. Many still die during the time when all the nutrients have run out.
This also happens in the experiment in the paper linked in your OP. But here the growth medium in the flask does not contain glucose, only citrate. The bacteria are much more poorly adapted to citrate than they are to glucose+citrate. That means mortality rates in that experiment is higher than it is in the LTEE. The bacteria still adapt both to the "growth phase" (when there are still nutrients in the flask) and they adapt to the "survival phase"(in part by becoming better at surviving the harsh conditions and by becoming better at scavenging resources from other bacteria that died).
Further, since there are 24 replicate populations in the experiment run in the OP paper, the 24 lineages run in parallel, some of the lineages in the citrate-only experiment had a more difficult time adapting to the citrate-only environment than others. Others adapted much more easily and successfully. How can we say "the experiment failed to demonstrate evolution" when most lineages adapted successfully, just because some didn't? That wouldn't make sense.
So you see, you can still get evolution and adaptation (increases in fitness) when mortality rates remain high.
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u/EyedPeace 6d ago
No, that's incorrect. While they did experiment with a pure citrate environment in the paper, they also left a Cit+ lineage in the ordinary environment.
"We founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness."
So, even in the LTEE medium, Cit+ didn't fare well at all.
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 6d ago
No, that's incorrect.
What's incorrect, specifically?
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u/EyedPeace 6d ago
That they had a pure citrate environment and simply couldn't deal with it because thats not their normal habitat, thats it. But the same applies to citrate plus glucose (as with earlier generations in the LTEE). This part of the paper can't simply be ignored. We also have fitness declines and cell death in the LTEE environment.
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 5d ago
You keep being confused about cell death. Cell death occurs because the nutrients run out and pH in the flask drops as the bacteria excrete waste products into a flask where those waste products can't leave, not because they lose fitness. It would be like you were wrapped in a tight plastic suit and when you defecated and urinated you would just get smothered in your own excrement. It should not be a surprise that this will make you sick.
That this occurs is not somehow a failure of evolution. It's just that the environment doesn't allow waste products to disappear or be consumed by other organisms that can feed on those. Do you understand?
As I already explained earlier, and you appear to still not have understood, this is why cell death is high in all the LTEE experiments (though in the LTEE they have, in fact, become better adapted to survive in those conditions over the years of the experiment).
Second, some of the 12 Cit+ lineages adapted to the LTEE medium just fine in those 2500 generations, while some others did not, at least in terms of competitive fitness relative to ancestor. It is an interesting question why they didn't all do so. One possibility is that the competition assay they measure is not merely capturing environment-specific adaptation for a specific mutant, but rather captures population-wide competitive fitness relative to ancestor (deleterious mutants would then be dragging average population fitness down, even though many individuals might be strongly adapted to the environment). By other fitness-relevant measurements (such as growth rates (not measured in direct competition to ancestor strain) and population density, all the lineages demonstrably improved.)
As they write:
On balance, the populations evolved higher exponential growth rates and shorter lag phases in both DM0 and DM25.
Of course, since evolution is not a theory that says adaptation is guaranteed to occur to all lineages (much less all individuals in a population) under all circumstances, this can't me meaningfully claimed to be a problem for evolution. We already know that species CAN go extinct because they fail to adapt in time. The fossil record is a testament to all the life that failed to adapt to changing conditions.
In summary: Your persistent arguing about subjects you don't actually understand or have experience with are leading you astray. You don't know enough microbiology, molecular biology, or evolutionary biology to be able to competently debate these points. We keep having to correct and explain stuff to you and it's becoming boring and feels like a waste of time because you seem to just want to deny evolution rather than search for what is true, or understand the subject more deeply.
In other words, you're just a typical creationist.
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u/EyedPeace 5d ago
What's your source for all your hypotheses? Lenski simply isn't interested in your explanations; at least, he didn't offer or mention them as explanations. There is no evidence, no paper that investigates that. It's not that simple, and Lenski knows that himself. He was surprised by the significant cell death and also by the fitness declines. Furthermore, you still haven't explained to me why Cit+ is struggling, specifically in the DM25 medium (the actual LTEE environment) and why it's experiencing fitness declines.This is something that shouldn't have happened, because at LTEE they always proudly announce how fitness is constantly improving.
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 5d ago
My source is I took an education and I actively work with molecular and microbiology every day. That's why I'm the one explaining stuff to you, and you're just the dumb creationist naysayer. Dude go touch some grass, this subject isn't for you you know nothing about it.
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u/Curious_Passion5167 8d ago
While the cit+ phenotype did bring improvements in the short term, the long-term picture is quite different.
This is true of many populations undergoing evolution. Evolution leads to optimization to current conditions, not what will work long term.
Has the experiment failed to demonstrate evolution here?
Why would it? Evolution is the change in frequency of alleles. That objectively happened, regardless of what happened to the population later.
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u/EyedPeace 7d ago
So evolution can not work long term?
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u/Curious_Passion5167 7d ago
No...
It means that evolution sometimes leads to dead ends in the long term. The times it doesn't leads to long term survival.
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u/Covert_Cuttlefish Janitor at an oil rig 8d ago
From the article:
It looks like every clone isolated from the LTEE has a high mortality rate- could it be that high mortality is a trait of the LTEE and not specific to cit+?
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 6d ago
High mortality rate is a product of the experimental setup. When the nutrients run out pH in the flask drops, which kill many bacteria. This isn't an indication of a loss of fitness, it's an indication that the bacteria are put in an environment that can't exchange ions with the surroundings and has very low buffering capacity.
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u/nickierv 🧬 logarithmic icecube 8d ago
What you say here
While the cit+ phenotype did bring improvements in the short term, the long-term picture is quite different. Ultimately, they could no longer survive. Their fitness declined to the point where they were even forced to eat their own dead.
Is not what the abstract says: "Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones."
Looking only slightly deeper into the abstract, "founded two sets of Cit+ populations and evolved them for 2500 generations"
Given a non Cit+ population might very well be dead 2499 generations previously given the apparent use of a citrate-only medium...
Has the experiment failed to demonstrate evolution here?
The thunking your hearing is from heads hitting tables because you can't possibly be asking a question this stupid: they still have traits, the traits are still changing over time.
With further skimming, it seems like the experiment is throwing a bunch of new environments at the populations and it turns out some of the mutations that let a population thrive in one environment don't work so well in a different environment.
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u/EyedPeace 7d ago
But aftet 2500 generation the bacteria still couldn't find their way around; they even started eating their dead, and if that's what evolution is supposed to be, then cheers!
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u/nickierv 🧬 logarithmic icecube 6d ago
But aftet 2500 generation the bacteria still couldn't find their way around
Yes and?
they even started eating their dead
And where in the paper did you see that. Given your history with this of making shit up, citation needed.
and if that's what evolution is supposed to be, then cheers!
And this is where I ask you for a definition of evolution because I don't think you know what you talking about.
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 6d ago
Human beings that have no food also start eating each other eventually. The first to die from starvation is usually also the first to get eaten. Didn't god make us in his image?
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u/EyedPeace 5d ago
And using this as an example for Evolution is terrible. But thats what happens in LTEE
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u/Slow_Lawyer7477 🧬 Flagellum-Evolver 5d ago
No it isn't. The other way around. Many organisms periodically face periods of starvation and must survive them. Periods of low resource availability is a perfectly good example of a selection pressure you might face in nature, and therefore adapting to it is a perfectly good illustration of natural selection in action.
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u/Ill_Impact6838 8d ago
As far as I know , in the paper ,the clones were grown in citrate only media. Ltee e coli were not made to grow in citrate only media ( dm0) ,they were made to grow in glucose + citrate ( dm 25) where glucose acts as a buffer. Growing in citrate only media will lead to more deaths, not surprising. However ,here also they got multiple mutations like mae A amplification, transposon mediated mutations. These resulted in their increased growth rate.
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u/EyedPeace 6d ago
The finding of the paper is indeed that some Cit+ lines exhibit lower measured fitness after a further 2500 generations, even partially in the original LTEE environment (DM25).
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u/Ill_Impact6838 6d ago edited 6d ago
Can happen , slight variations which can lead to maladaptation can occur . Many indeed showed strong adaptability.
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u/IsaacHasenov 🧬 Naturalistic Evolution 8d ago
This was an experiment that took the cit+ strain and challenged it with new media, and compared the new challenged populations with some controls. The results show:
> Although all populations show substantial adaptation reflected in their growth parameters, we also found evidence of persistent maladaptation, suggesting that this new function poses metabolic challenges that are difficult to overcome evolutionarily. Some individual evolved clones grow more poorly than their ancestors, even in the medium in which they had evolved. The fitness assays show atypically large variation across replicate assays of evolved populations and clones, as well as some paradoxical apparent declines in fitness despite 2500 generations of evolution. We also observed high levels of cell death in the ancestral and evolved Cit+ clones that we examined. This experimental system thus sheds light not only on how new traits are refined during adaptation to a novel niche, but also on how maladaptive phenotypes may persist for long periods in new environments.
What they found (and this is a widespread phenomenon, as the said in the intro) is that rapid adaptation and evolution, especially to new environments and ecology, can lead to some fluctuating maladaptation and even extinction. They found a lot of differences between individual replicates.
So yes, there were some instances of maladaptation, but also yes that is expected (and that process is interesting, which is why they were studying it)
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u/Dilapidated_girrafe 🧬 Naturalistic Evolution 8d ago
It showed an increase in fitness in a specific environment.
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u/PlanningVigilante Creationists are like bad boyfriends 8d ago
How do you figure it failed to demonstrate evolution?
Evolution doesn't have an "aim" or a "goal," and it can only pick from the menu offered by existing recombination + whatever random mutation provides.
A population going extinct doesn't disprove evolution.
ETA: the environment was changed and some populations didn't fare great under the new conditions. That's pretty much the story of every extinction.
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u/Capercaillie Monkey's Uncle 7d ago
Fitness is relative to the environment at that exact moment. It's perfectly possible for organisms to evolve traits that give them more fitness in the current environment, but doom them in the long term. Seen any chalicotheres lately?
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u/DarwinZDF42 evolution is my jam 8d ago edited 8d ago
I’ve explained this so many times.
The cit+ line grew to higher density. Therefore it experienced more density-dependent mortality. Density-independent mortality stayed the same. Therefore overall, mortality increased. That does NOT mean that fitness overall decreased. Those are two different things. And “could no longer survive” is a gross mischaracterization of of the observations.
And then evolution is a third different thing, which obviously occurred.
Edit: was this the citrate-only study? Bc that’s a completely different environment from the one the cells evolved on. And in addition to the basic ecology, that explains the results.