'Living fossils' and DNA stability

[StringJunky]

Occasionally, I read about creatures that have remained relatively unchanged for a hundred million years or more. Does this mean they have stable DNA or is it due to some other factor?

[DrP]

48 minutes ago, StringJunky said:

Occasionally, I read about creatures that have remained relatively unchanged for a hundred million years or more.

Is this the Chinese salamander thing that was on the radio yesterday?  They said it hadn't changed for over a hundred million years.

48 minutes ago, StringJunky said:

Does this mean they have stable DNA or is it due to some other factor?

I do not know...  I might guess at it being because they are perfectly evolved as they are to survive in the environment they are in?  There design has been good enough to avoid becoming extinct over that time. I think they are good hiders and must be pretty resilient. Presumably any mutations were not improvements to their on-going survival.

.... I was trying to think of an axolotl pun to sign of on but I couldn't quite make it work. Well 'that's all I gotl'.    

Edited April 4, 2019 by DrP

[Ten oz]

1 hour ago, StringJunky said:

Occasionally, I read about creatures that have remained relatively unchanged for a hundred million years or more. Does this mean they have stable DNA or is it due to some other factor?

My understand is that Living Fossil is a superficial label. It simple means a species looks nearly the same to what we assume it did in years past per the fossil record. Fossils however are typically just mineral deposits and not material suitable for DNA testing. More over DNA more that a few thousand year old has seldom been recovered and even in the best natural preserved conditions on earth DNA degrades over time. So when we read about living fossils like the Coelacanth said to have remained the same for 400 million years that assessment is not one being made using DNA. We (humans) actually have no idea how similar the DNA is. 

Quote

Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is of lower quality in comparison with modern genetic material.[3] The damage characteristics and ability of aDNA to survive through time restricts possible analyses and places an upper limit on the age of successful samples Allentoft et al. (2012). There is a theoretical correlation between time and DNA degradation,[23] although differences in environmental conditions complicates things. Samples subjected to different conditions are unlikely to predictably align to a uniform age-degradation relationship.[24] The environmental effects may even matter after excavation, as DNA decay rates may increase,[25]particularly under fluctuating storage conditions.[26] Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for contemporary sequencing technologies. https://en.wikipedia.org/wiki/Ancient_DNA#Degradation_processes

 

[StringJunky]

57 minutes ago, DrP said:

Is this the Chinese salamander thing that was on the radio yesterday?  They said it hadn't changed for over a hundred million years.

I do not know...  I might guess at it being because they are perfectly evolved as they are to survive in the environment they are in?  There design has been good enough to avoid becoming extinct over that time. I think they are good hiders and must be pretty resilient. Presumably any mutations were not improvements to their on-going survival.

.... I was trying to think of an axolotl pun to sign of on but I couldn't quite make it work. Well 'that's all I gotl'.    

Yes, that was the one that triggered the thought last. Yes, being ''optimally'' evolved for their environment, which may be not be accommodating of further mutations could be a reason. Cheers.

18 minutes ago, Ten oz said:

My understand is that Living Fossil is a superficial label. It simple means a species looks nearly the same to what we assume it did in years past per the fossil record. Fossils however are typically just mineral deposits and not material suitable for DNA testing. More over DNA more that a few thousand year old has seldom been recovered and even in the best natural preserved conditions on earth DNA degrades over time. So when we read about living fossils like the Coelacanth said to have remained the same for 400 million years that assessment is not one being made using DNA. We (humans) actually have no idea how similar the DNA is. 

 

Why do you think I  wrote 'living fossils'; it's just an expression to describe something that has changed little over a long time. Taken literally, it's an oxymoron.

Edited April 4, 2019 by StringJunky

[Ten oz]

43 minutes ago, StringJunky said:

Why do you think I  wrote 'living fossils'; it's just an expression to describe something that has changed little over a long time. Taken literally, it's an oxymoron.

Right, my point was that it isn't entirely accurate to say something has changed "little" over time. We don't know. Rather it is more accurate to say that the appearance seems to have changed little overtime.

[dimreepr]

20 minutes ago, Ten oz said:

Right, my point was that it isn't entirely accurate to say something has changed "little" over time. We don't know. Rather it is more accurate to say that the appearance seems to have changed little overtime.

1

If we don't know what we don't know, why is it more accurate to say; antfucking?

3 hours ago, StringJunky said:

Occasionally, I read about creatures that have remained relatively unchanged for a hundred million years or more. Does this mean they have stable DNA or is it due to some other factor?

DNA is the same in all living or once living cells, the variable is the environment.

[Ten oz]

40 minutes ago, dimreepr said:

If we don't know what we don't know, why is it more accurate to say; antfucking?

We do know, per the fossil record, how things probably looked. That is why. 

[dimreepr]

2 minutes ago, Ten oz said:

We do know, per the fossil record, how things probably looked. That is why. 

nitpicking is, at least, useful sometimes.

[Ten oz]

3 hours ago, dimreepr said:

nitpicking is, at least, useful sometimes.

Perhaps not this time though. Living fossil is a superficial title and we all agree. 

The OP is asks about DNA. We don't have testable DNA from a hundred million years ago. 

[StringJunky]

38 minutes ago, Ten oz said:

Perhaps not this time though. Living fossil is a superficial title and we all agree. 

The OP is asks about DNA. We don't have testable DNA from a hundred million years ago. 

I think a modern organism's ancestral story can be gleaned from its DNA. 

[Ten oz]

18 minutes ago, StringJunky said:

I think a modern organism's ancestral story can be gleaned from its DNA. 

Sure, but we do not have multi million year old samples.

 

[CharonY]

16 minutes ago, StringJunky said:

I think a modern organism's ancestral story can be gleaned from its DNA. 

There are very different themes within this topic. When folks refer to an organism being unchanged they refer to their morphology as Ten Oz mentioned, due to the reliance on fossil records. The underlying DNA changes are virtually unknown. We can recreate ancestral history using DNA of extant (i.e. still living) organisms, but they rely on measuring the differences between investigated species and assume that larger distances correlate with an earlier split. It would therefore also assume that a the distance for a given species would be much larger to its ancestor a few million years ago (even with little obvious morphological changes) compared to a different, extant species, who may look different, but had a shared ancestor only a few thousand years ago.

[StringJunky]

Just now, Ten oz said:

Sure, but we do not have multi million year old samples.

 

I think we need CharonY or Arete to say what can be read from it.

[Intrigued]

7 hours ago, Ten oz said:

So when we read about living fossils like the Coelacanth said to have remained the same for 400 million years that assessment is not one being made using DNA.

When we read that we are reading an oversimplified or ill informed statement. Coelacanths are not a species, a genus, or even a family, but an order. None of the extant species were around 400 million years ago, or 200 hundred million, or 100 million. The living fossil name is appropriate because coelacanths were thought to have gone extinct at the end of the Cretaceous, yet some of them managed to avoid the KPg boundary event.

[StringJunky]

1 minute ago, CharonY said:

There are very different themes within this topic. When folks refer to an organism being unchanged they refer to their morphology as Ten Oz mentioned, due to the reliance on fossil records. The underlying DNA changes are virtually unknown. We can recreate ancestral history using DNA of extant (i.e. still living) organisms, but they rely on measuring the differences between investigated species and assume that larger distances correlate with an earlier split. It would therefore also assume that a the distance for a given species would be much larger to its ancestor a few million years ago (even with little obvious morphological changes) compared to a different, extant species, who may look different, but had a shared ancestor only a few thousand years ago.

OK. Cheers.

[peterwlocke]

it could be that their environment has one main problem that if they evolved otherwise it would hurt them or that the gene pool is really small and when mutations do happen they die for one reason or another without getting a chance to mate which I suppose would mean it is bad but idk. also, they could have changed just there fossils don't show all the features.

[CharonY]

19 minutes ago, Intrigued said:

When we read that we are reading an oversimplified or ill informed statement. Coelacanths are not a species, a genus, or even a family, but an order. None of the extant species were around 400 million years ago, or 200 hundred million, or 100 million. The living fossil name is appropriate because coelacanths were thought to have gone extinct at the end of the Cretaceous, yet some of them managed to avoid the KPg boundary event.

What I wanted to add in an edit but will put in here now is that there are different concepts of living fossils. Coelacanths are interesting , as Latimeria species were considered a paradigm of a living fossil for quite some time. With these species a hypothesis of a kind of genetic stasis had been formed, which is in contradiction to the tree-based paradigm I mentioned above. However, a closer view on the molecular level of these species have refuted or at least not supported these claims. I vaguely remember a paper where they (I believe) demonstrated that populations of a Latimeria had low molecular diversity and substitution rates but I also remember that that fell apart in meta-analyses.

14 minutes ago, peterwlocke said:

it could be that their environment has one main problem that if they evolved otherwise it would hurt them or that the gene pool is really small and when mutations do happen they die for one reason or another without getting a chance to mate which I suppose would mean it is bad but idk. also, they could have changed just there fossils don't show all the features.

These are are examples for stabilizing selection and/or low/no mutations as well as no drift. The issue is that there are no good examples where these factors are so strong as to stabilize genomes for a long time frame. Even in artificial systems it is extremely difficult (if not impossible) to reproduce and even the most stable ecological niches to face some kind of fluctuations eventually.

[StringJunky]

9 minutes ago, CharonY said:

What I wanted to add in an edit but will put in here now is that there are different concepts of living fossils. Coelacanths are interesting , as Latimeria species were considered a paradigm of a living fossil for quite some time. With these species a hypothesis of a kind of genetic stasis had been formed, which is in contradiction to the tree-based paradigm I mentioned above. However, a closer view on the molecular level of these species have refuted or at least not supported these claims.

These are are examples for stabilizing selection and/or low/no mutations as well as no drift. The issue is that there are no good examples where these factors are so strong as to stabilize genomes for a long time frame. Even in artificial systems it is extremely difficult (if not impossible) to reproduce and even the most stable ecological niches to face some kind of fluctuations eventually.

I think I was asking if the environmental niche the salamander found itself in restricted expressions of successful  mutations and as such kept a relatively unchanged physiology for a very long time.

[CharonY]

2 minutes ago, StringJunky said:

I think I was asking if the environmental niche the salamander found itself in restricted expressions of successful  mutations and as such kept a relatively unchanged physiology for a very long time.

To elaborate what I mentioned above, in order for that to happen the selective sweep must be so strong (or mutation rate so low) that any mutations would have to be strongly selected against. Especially as most mutations will be neutral this is highly unlikely in principle, which makes it very unlikely to exist in practice.

[StringJunky]

6 minutes ago, CharonY said:

To elaborate what I mentioned above, in order for that to happen the selective sweep must be so strong (or mutation rate so low) that any mutations would have to be strongly selected against. Especially as most mutations will be neutral this is highly unlikely in principle, which makes it very unlikely to exist in practice.

OK. Thanks for elaborating.

[CharonY]

Thinking about it, the only system that could face these conditions would likely to be a fairly simple (single-celled) organism with a small genome (close to the minimum viable set of genes) with very small intergenic regions, perhaps growing under nucleic acid limiting conditions (e.g. low phosphate conditions) in conjunction with other conditions to which the genome is exquisitely tuned to. 

But again, setting that up artificially would be quite a task. Also considering that there are also mutations that are biochemically neutral (redundant codons) or functionally neutral (e.g. certain regions within proteins) I really doubt that such a condition even exists even in principle. Extrapolating that to a complex organism would be even more problematic.

[StringJunky]

1 minute ago, CharonY said:

Thinking about it, the only system that could face these conditions would likely to be a fairly simple (single-celled) organism with a small genome (close to the minimum viable set of genes) with very small intergenic regions, perhaps growing under nucleic acid limiting conditions (e.g. low phosphate conditions) in conjunction with other conditions to which the genome is exquisitely tuned to. 

But again, setting that up artificially would be quite a task. Also considering that there are also mutations that are biochemically neutral (redundant codons) or functionally neutral (e.g. certain regions within proteins) I really doubt that such a condition even exists even in principle. Extrapolating that to a complex organism would be even more problematic.

Akin to winning the national  lottery several times in a row? 

[CharonY]

Perhaps like winning the lottery and getting robbed immediately after every time?

[StringJunky]

4 minutes ago, CharonY said:

Perhaps like winning the lottery and getting robbed immediately after every time?

  I'll put that idea in a box and let it float away into oblivion.

Edited April 4, 2019 by StringJunky

[MigL]

I had read that a certain species of eel-like shark had remained ( relatively ) unchanged for approx. 150 mil yrs.
And a type of shrimp, for about 200 mil yrs.

( just adding to the confusion  )