https://www.science.org/content/article/these-gars-are-ultimate-living-fossils

Open access article:
https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false

These researchers looked at Gar, but it also applies to sturgeons.
These two bony fish lineages seem to have a very slow rate of molecular
evolution. The changes in their DNA accumulate so slowly that two
lineages separated for over 100 million years can still form fertile
hybrids. 3 million years is pushing it for species like lions and
tigers that can still form hybrids, but the hybrids are sterile.
Bonobos and chimps are around 3 million years divergent and can still
form fertile hybrids, but the claim is that these fish evolve orders of
magnitude more slowly than mammals.

The Science news article claims that mammals accumulate 0.02 mutations
per site per million years, while these fish averaged only 0.00009
mutations per million years. For the 1100 coding exons that they looked
at for this study these fish evolve much more slowly than mammals.

The news article notes that other "living fossils" such as coelacanths
(0.0005) evolve faster, but slower than amphibians (0.007). It sounds
like terrestrial animals evolve faster than fish.

Ron Okimoto

On 3/11/24 4:17 PM, RonO wrote:
> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>
> Open access article:
> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>
> These researchers looked at Gar, but it also applies to sturgeons. These
> two bony fish lineages seem to have a very slow rate of molecular
> evolution.  The changes in their DNA accumulate so slowly that two
> lineages separated for over 100 million years can still form fertile
> hybrids.  3 million years is pushing it for species like lions and
> tigers that can still form hybrids, but the hybrids are sterile. Bonobos
> and chimps are around 3 million years divergent and can still form
> fertile hybrids, but the claim is that these fish evolve orders of
> magnitude more slowly than mammals.
>
> The Science news article claims that mammals accumulate 0.02 mutations
> per site per million years, while these fish averaged only 0.00009
> mutations per million years.  For the 1100 coding exons that they looked
> at for this study these fish evolve much more slowly than mammals.
>
> The news article notes that other "living fossils" such as coelacanths
> (0.0005) evolve faster, but slower than amphibians (0.007).  It sounds
> like terrestrial animals evolve faster than fish.

If it's repair mechanisms they hypothesize as the cause of slow
evolution, they really should be looking at junk sequences rather than
just 4-fold degenerate sites. I suggest introns. And if the introns
aren't alignable, well, that kills the theory right there.

RonO wrote:

> These researchers looked at Gar, but it also applies to sturgeons. These
> two bony fish lineages seem to have a very slow rate of molecular
> evolution.  The changes in their DNA accumulate so slowly that two
> lineages separated for over 100 million years can still form fertile
> hybrids.

I'd like to see some of their 100 million year old DNA!

> 3 million years is pushing it for species like lions and
> tigers that can still form hybrids, but the hybrids are sterile. Bonobos
> and chimps are around 3 million years divergent and can still form
> fertile hybrids, but the claim is that these fish evolve orders of
> magnitude more slowly than mammals.

The oldest Chimp fossils are only like 1/6th that age.

Kind of puts everything into perspective, right there...

> The Science news article claims that mammals accumulate 0.02 mutations
> per site per million years, while these fish averaged only 0.00009
> mutations per million years.  For the 1100 coding exons that they looked
> at for this study these fish evolve much more slowly than mammals.

There's no such thing as a molecular clock.

I personally don't believe in your Intelligent Design. No,
I believe in evolution. And in evolution we have this thing
called "Natural Selection."

Ill named, granted, "Natural Selection" simply means that an
organism, it's DNA, changes in response to it's environment.
Thus, if the environment is stable -- it's not putting any
pressure on DNA to change -- you're not going to see a lot
of changes. And if the environment is putting a lot of
pressure on an organism to change, you're going to see a lot
of changes accumulate in their DNA.

This is where it turns weird: If one population, say, goes
somewhere else, moves to a different environment and the
other stays put, but you assume that they are accumulating
changes at the exact same rate, you end up with a wildly
exaggerated age estimate.

I know you're going to claim that you're an expert on all this
and know it like the back of your hand, but nothing you posted
here makes the slightest sense if that were true.

"May a cat poop in your underwear drawer."

--
http://jtem.tumblr.com

On 11/03/2024 23:28, John Harshman wrote:
> On 3/11/24 4:17 PM, RonO wrote:
>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>
>> Open access article:
>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>
>> These researchers looked at Gar, but it also applies to sturgeons.
>> These two bony fish lineages seem to have a very slow rate of
>> molecular evolution.  The changes in their DNA accumulate so slowly
>> that two lineages separated for over 100 million years can still form
>> fertile hybrids.  3 million years is pushing it for species like lions
>> and tigers that can still form hybrids, but the hybrids are sterile.
>> Bonobos and chimps are around 3 million years divergent and can still
>> form fertile hybrids, but the claim is that these fish evolve orders
>> of magnitude more slowly than mammals.
>>
>> The Science news article claims that mammals accumulate 0.02 mutations
>> per site per million years, while these fish averaged only 0.00009
>> mutations per million years.  For the 1100 coding exons that they
>> looked at for this study these fish evolve much more slowly than mammals.
>>
>> The news article notes that other "living fossils" such as coelacanths
>> (0.0005) evolve faster, but slower than amphibians (0.007).  It sounds
>> like terrestrial animals evolve faster than fish.
>
> If it's repair mechanisms they hypothesize as the cause of slow
> evolution, they really should be looking at junk sequences rather than
> just 4-fold degenerate sites. I suggest introns. And if the introns
> aren't alignable, well, that kills the theory right there.
>

Tree species thought to be separated by tens of millions of years are
known to hybridise. For example Platanus orientalis and Platanus
occidentalis, and also with Tilia, Quercus and Aesculus. In the case of
Tilia I suspect that multiple rounds of introgression has served to
limit the amount of divergence between species. However Tilia does
appear as a short branch in cladograms, supporting the hypothesis that
forest trees have a lower rate of evolution.

--
alias Ernest Major

On 3/12/24 3:50 AM, Ernest Major wrote:
> On 11/03/2024 23:28, John Harshman wrote:
>> On 3/11/24 4:17 PM, RonO wrote:
>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>
>>> Open access article:
>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>
>>> These researchers looked at Gar, but it also applies to sturgeons.
>>> These two bony fish lineages seem to have a very slow rate of
>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>> that two lineages separated for over 100 million years can still form
>>> fertile hybrids.  3 million years is pushing it for species like
>>> lions and tigers that can still form hybrids, but the hybrids are
>>> sterile. Bonobos and chimps are around 3 million years divergent and
>>> can still form fertile hybrids, but the claim is that these fish
>>> evolve orders of magnitude more slowly than mammals.
>>>
>>> The Science news article claims that mammals accumulate 0.02
>>> mutations per site per million years, while these fish averaged only
>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>> they looked at for this study these fish evolve much more slowly than
>>> mammals.
>>>
>>> The news article notes that other "living fossils" such as
>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>
>> If it's repair mechanisms they hypothesize as the cause of slow
>> evolution, they really should be looking at junk sequences rather than
>> just 4-fold degenerate sites. I suggest introns. And if the introns
>> aren't alignable, well, that kills the theory right there.
>>
>
> Tree species thought to be separated by tens of millions of years are
> known to hybridise. For example Platanus orientalis and Platanus
> occidentalis, and also with Tilia, Quercus and Aesculus. In the case of
> Tilia I suspect that multiple rounds of introgression has served to
> limit the amount of divergence between species. However Tilia does
> appear as a short branch in cladograms, supporting the hypothesis that
> forest trees have a lower rate of evolution.
>
Then again, ducks that are thought to be separated by tens of millions
of years are also known to hybridize, and their rate of evolution isn't
particularly slow.

On 3/12/24 6:44 AM, John Harshman wrote:
> On 3/12/24 3:50 AM, Ernest Major wrote:
>> On 11/03/2024 23:28, John Harshman wrote:
>>> On 3/11/24 4:17 PM, RonO wrote:
>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>
>>>> Open access article:
>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>
>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>> These two bony fish lineages seem to have a very slow rate of
>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>> that two lineages separated for over 100 million years can still
>>>> form fertile hybrids.  3 million years is pushing it for species
>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>> and can still form fertile hybrids, but the claim is that these fish
>>>> evolve orders of magnitude more slowly than mammals.
>>>>
>>>> The Science news article claims that mammals accumulate 0.02
>>>> mutations per site per million years, while these fish averaged only
>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>> they looked at for this study these fish evolve much more slowly
>>>> than mammals.
>>>>
>>>> The news article notes that other "living fossils" such as
>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>
>>> If it's repair mechanisms they hypothesize as the cause of slow
>>> evolution, they really should be looking at junk sequences rather
>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>> introns aren't alignable, well, that kills the theory right there.
>>>
>>
>> Tree species thought to be separated by tens of millions of years are
>> known to hybridise. For example Platanus orientalis and Platanus
>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>> of Tilia I suspect that multiple rounds of introgression has served to
>> limit the amount of divergence between species. However Tilia does
>> appear as a short branch in cladograms, supporting the hypothesis that
>> forest trees have a lower rate of evolution.
>>
> Then again, ducks that are thought to be separated by tens of millions
> of years are also known to hybridize, and their rate of evolution isn't
> particularly slow.
>
All sorts of seemingly long-separated species (both plant and animal)
are observed. What determines whether the hybrid offspring are fertile,
infertile or sterile? I found an article on Big Think
https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
describing an unsuccessful attempt to produce a "humanzee". Fortunately
it didn't work. The chromosome count is different in humans and
chimpanzee, but does this imply that it's essentially impossible?

On 3/12/24 9:04 AM, erik simpson wrote:
> On 3/12/24 6:44 AM, John Harshman wrote:
>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>> On 11/03/2024 23:28, John Harshman wrote:
>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>
>>>>> Open access article:
>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>
>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>> that two lineages separated for over 100 million years can still
>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>> are sterile. Bonobos and chimps are around 3 million years
>>>>> divergent and can still form fertile hybrids, but the claim is that
>>>>> these fish evolve orders of magnitude more slowly than mammals.
>>>>>
>>>>> The Science news article claims that mammals accumulate 0.02
>>>>> mutations per site per million years, while these fish averaged
>>>>> only 0.00009 mutations per million years.  For the 1100 coding
>>>>> exons that they looked at for this study these fish evolve much
>>>>> more slowly than mammals.
>>>>>
>>>>> The news article notes that other "living fossils" such as
>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>
>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>> evolution, they really should be looking at junk sequences rather
>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>> introns aren't alignable, well, that kills the theory right there.
>>>>
>>>
>>> Tree species thought to be separated by tens of millions of years are
>>> known to hybridise. For example Platanus orientalis and Platanus
>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>> of Tilia I suspect that multiple rounds of introgression has served
>>> to limit the amount of divergence between species. However Tilia does
>>> appear as a short branch in cladograms, supporting the hypothesis
>>> that forest trees have a lower rate of evolution.
>>>
>> Then again, ducks that are thought to be separated by tens of millions
>> of years are also known to hybridize, and their rate of evolution
>> isn't particularly slow.
>>
> All sorts of seemingly long-separated species (both plant and animal)
> are observed.  What determines whether the hybrid offspring are fertile,
> infertile or sterile?  I found an article on Big Think
> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/ describing an unsuccessful attempt to produce a "humanzee".  Fortunately it didn't work.  The chromosome count is different in humans and chimpanzee, but does this imply that it's essentially impossible?
>
It's not chromosome count that's the problem. Fission and fusion don't
prevent reproduction. major translocations can prevent reproduction, as
can differential gene gain or loss. Consider, for example, a gene
duplication in which, as usually happens, one copy is eventually lost.
If it's a different copy in different species, a hybrid could through
recombination produce gametes with zero copies.

On 12/03/2024 16:04, erik simpson wrote:
> On 3/12/24 6:44 AM, John Harshman wrote:
>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>> On 11/03/2024 23:28, John Harshman wrote:
>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>
>>>>> Open access article:
>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>
>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>> that two lineages separated for over 100 million years can still
>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>> are sterile. Bonobos and chimps are around 3 million years
>>>>> divergent and can still form fertile hybrids, but the claim is that
>>>>> these fish evolve orders of magnitude more slowly than mammals.
>>>>>
>>>>> The Science news article claims that mammals accumulate 0.02
>>>>> mutations per site per million years, while these fish averaged
>>>>> only 0.00009 mutations per million years.  For the 1100 coding
>>>>> exons that they looked at for this study these fish evolve much
>>>>> more slowly than mammals.
>>>>>
>>>>> The news article notes that other "living fossils" such as
>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>
>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>> evolution, they really should be looking at junk sequences rather
>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>> introns aren't alignable, well, that kills the theory right there.
>>>>
>>>
>>> Tree species thought to be separated by tens of millions of years are
>>> known to hybridise. For example Platanus orientalis and Platanus
>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>> of Tilia I suspect that multiple rounds of introgression has served
>>> to limit the amount of divergence between species. However Tilia does
>>> appear as a short branch in cladograms, supporting the hypothesis
>>> that forest trees have a lower rate of evolution.
>>>
>> Then again, ducks that are thought to be separated by tens of millions
>> of years are also known to hybridize, and their rate of evolution
>> isn't particularly slow.
>>
> All sorts of seemingly long-separated species (both plant and animal)
> are observed.  What determines whether the hybrid offspring are fertile,
> infertile or sterile?  I found an article on Big Think
> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/ describing an unsuccessful attempt to produce a "humanzee".  Fortunately it didn't work.  The chromosome count is different in humans and chimpanzee, but does this imply that it's essentially impossible?
>

No. Hybrids between species with different chromosome counts are common.
(The mule is the classic example.) They're commonly, but not universally
sterile. There are even hybrids between Indian (2n=6/7) and Chinese (2n=

There are even hybrids between Indian (2n=6/7) and Chinese (2n=46) muntjacs.

Beyond that there are species which are polymorphic for chromosome
count. (Even humans, where there are a few individuals with chromosomal
fusions. They result in reduced fertility with individuals with the
normal karyotype, but they're not completely sterile.)

I studied the literature on chromosomal race some decades back. My
conclusion was that most chromosomal races are cryptic species, but some
represent genuine polytypic species. (That was before the latest period
of ascendancy of taxonomic splitters.) The classical cases are Mus
musculus and Nannospalax ehrenbergi.

Plant high polyploids often have variable chromosome counts. One could
ascribe this to inaccuracy in counting the chromosomes, or explain it as
the genome being tolerant of aneusomy (not caring whether there are 8, 9
or 10 copies of a gene).

In the case of a chromosomal fusion, during meiosis the fused chromosome
will pair up with the two unfused chromosomes. If the right two
chromosomes go the same way as the chromosomes separate then meiosis is
successful. The tolerance of deviations from the regular diploid state
during meiosis seems to vary between taxa - there are even plant species
that manage to separate triploid genomes into diploid and haploid sets.

--
alias Ernest Major

On 3/12/24 12:41 PM, Ernest Major wrote:
> On 12/03/2024 16:04, erik simpson wrote:
>> On 3/12/24 6:44 AM, John Harshman wrote:
>>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>>> On 11/03/2024 23:28, John Harshman wrote:
>>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>>
>>>>>> Open access article:
>>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>>
>>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>>> molecular evolution.  The changes in their DNA accumulate so
>>>>>> slowly that two lineages separated for over 100 million years can
>>>>>> still form fertile hybrids.  3 million years is pushing it for
>>>>>> species like lions and tigers that can still form hybrids, but the
>>>>>> hybrids are sterile. Bonobos and chimps are around 3 million years
>>>>>> divergent and can still form fertile hybrids, but the claim is
>>>>>> that these fish evolve orders of magnitude more slowly than mammals.
>>>>>>
>>>>>> The Science news article claims that mammals accumulate 0.02
>>>>>> mutations per site per million years, while these fish averaged
>>>>>> only 0.00009 mutations per million years.  For the 1100 coding
>>>>>> exons that they looked at for this study these fish evolve much
>>>>>> more slowly than mammals.
>>>>>>
>>>>>> The news article notes that other "living fossils" such as
>>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>>
>>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>>> evolution, they really should be looking at junk sequences rather
>>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>>> introns aren't alignable, well, that kills the theory right there.
>>>>>
>>>>
>>>> Tree species thought to be separated by tens of millions of years
>>>> are known to hybridise. For example Platanus orientalis and Platanus
>>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>>> of Tilia I suspect that multiple rounds of introgression has served
>>>> to limit the amount of divergence between species. However Tilia
>>>> does appear as a short branch in cladograms, supporting the
>>>> hypothesis that forest trees have a lower rate of evolution.
>>>>
>>> Then again, ducks that are thought to be separated by tens of
>>> millions of years are also known to hybridize, and their rate of
>>> evolution isn't particularly slow.
>>>
>> All sorts of seemingly long-separated species (both plant and animal)
>> are observed.  What determines whether the hybrid offspring are
>> fertile, infertile or sterile?  I found an article on Big Think
>> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/ describing an unsuccessful attempt to produce a "humanzee".  Fortunately it didn't work.  The chromosome count is different in humans and chimpanzee, but does this imply that it's essentially impossible?
>>
>
> No. Hybrids between species with different chromosome counts are common.
> (The mule is the classic example.) They're commonly, but not universally
> sterile. There are even hybrids between Indian (2n=6/7) and Chinese (2n=
>
> There are even hybrids between Indian (2n=6/7) and Chinese (2n=46)
> muntjacs.
>
> Beyond that there are species which are polymorphic for chromosome
> count. (Even humans, where there are a few individuals with chromosomal
> fusions. They result in reduced fertility with individuals with the
> normal karyotype, but they're not completely sterile.)
>
> I studied the literature on chromosomal race some decades back. My
> conclusion was that most chromosomal races are cryptic species, but some
> represent genuine polytypic species. (That was before the latest period
> of ascendancy of taxonomic splitters.) The classical cases are Mus
> musculus and Nannospalax ehrenbergi.
>
> Plant high polyploids often have variable chromosome counts. One could
> ascribe this to inaccuracy in counting the chromosomes, or explain it as
> the genome being tolerant of aneusomy (not caring whether there are 8, 9
> or 10 copies of a gene).
>
> In the case of a chromosomal fusion, during meiosis the fused chromosome
> will pair up with the two unfused chromosomes. If the right two
> chromosomes go the same way as the chromosomes separate then meiosis is
> successful. The tolerance of deviations from the regular diploid state
> during meiosis seems to vary between taxa - there are even plant species
> that manage to separate triploid genomes into diploid and haploid sets.
>
Thanks, both you and John. I'd never even heard of muntjacs.

On 3/11/2024 6:28 PM, John Harshman wrote:
> On 3/11/24 4:17 PM, RonO wrote:
>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>
>> Open access article:
>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>
>> These researchers looked at Gar, but it also applies to sturgeons.
>> These two bony fish lineages seem to have a very slow rate of
>> molecular evolution.  The changes in their DNA accumulate so slowly
>> that two lineages separated for over 100 million years can still form
>> fertile hybrids.  3 million years is pushing it for species like lions
>> and tigers that can still form hybrids, but the hybrids are sterile.
>> Bonobos and chimps are around 3 million years divergent and can still
>> form fertile hybrids, but the claim is that these fish evolve orders
>> of magnitude more slowly than mammals.
>>
>> The Science news article claims that mammals accumulate 0.02 mutations
>> per site per million years, while these fish averaged only 0.00009
>> mutations per million years.  For the 1100 coding exons that they
>> looked at for this study these fish evolve much more slowly than mammals.
>>
>> The news article notes that other "living fossils" such as coelacanths
>> (0.0005) evolve faster, but slower than amphibians (0.007).  It sounds
>> like terrestrial animals evolve faster than fish.
>
> If it's repair mechanisms they hypothesize as the cause of slow
> evolution, they really should be looking at junk sequences rather than
> just 4-fold degenerate sites. I suggest introns. And if the introns
> aren't alignable, well, that kills the theory right there.
>

The article claims that these fish have better control of their
transposons, and that chromosomal structural changes are also
accumulating more slowly. The decrease in structural mutations is
likely what is allowing the interbreeding and interfertility to be
extended back to such a distantly lineages. Structural changes are a
big reason why functional gametes do not form from hybrids. If their
chromosomal number is different or they have too many translocations
very few viable gametes can form complete haploid genomes.

Ron Okimoto

On 3/12/2024 11:04 AM, erik simpson wrote:
> On 3/12/24 6:44 AM, John Harshman wrote:
>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>> On 11/03/2024 23:28, John Harshman wrote:
>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>
>>>>> Open access article:
>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>
>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>> that two lineages separated for over 100 million years can still
>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>> are sterile. Bonobos and chimps are around 3 million years
>>>>> divergent and can still form fertile hybrids, but the claim is that
>>>>> these fish evolve orders of magnitude more slowly than mammals.
>>>>>
>>>>> The Science news article claims that mammals accumulate 0.02
>>>>> mutations per site per million years, while these fish averaged
>>>>> only 0.00009 mutations per million years.  For the 1100 coding
>>>>> exons that they looked at for this study these fish evolve much
>>>>> more slowly than mammals.
>>>>>
>>>>> The news article notes that other "living fossils" such as
>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>
>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>> evolution, they really should be looking at junk sequences rather
>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>> introns aren't alignable, well, that kills the theory right there.
>>>>
>>>
>>> Tree species thought to be separated by tens of millions of years are
>>> known to hybridise. For example Platanus orientalis and Platanus
>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>> of Tilia I suspect that multiple rounds of introgression has served
>>> to limit the amount of divergence between species. However Tilia does
>>> appear as a short branch in cladograms, supporting the hypothesis
>>> that forest trees have a lower rate of evolution.
>>>
>> Then again, ducks that are thought to be separated by tens of millions
>> of years are also known to hybridize, and their rate of evolution
>> isn't particularly slow.
>>
> All sorts of seemingly long-separated species (both plant and animal)
> are observed.  What determines whether the hybrid offspring are fertile,
> infertile or sterile?  I found an article on Big Think
> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/ describing an unsuccessful attempt to produce a "humanzee".  Fortunately it didn't work.  The chromosome count is different in humans and chimpanzee, but does this imply that it's essentially impossible?
>

The chromosome number difference would just reduce the number of viable
gametes. Other chromosomal differences like translocations are just as
bad. Translocations that are not reciprocal like moving genes from the
X chromosome to an autosome is fine within a species, but it results in
imbalanced sex chromosomes. For mammals hybrid females are fine because
it has copies of all the genes, but male hybrids only get one X
chromosome and if it is missing some genes you can have male infertility
and even missing male hybrids because they do not develop properly.
Equids scramble their karyotypes. Mule hybrids are essentially
infertile, but they have some weird meiotic mechanism that seems to get
all the chromosomes from one species into the same gamete often enough
to produce some offspring in the backcross. It seems crazy, but you can
get a horse back by crossing a stallion to a mule.

Ron Okimoto

On Tue, 12 Mar 2024 09:04:22 -0700, erik simpson
<eastside.erik@gmail.com> wrote:

>On 3/12/24 6:44 AM, John Harshman wrote:
>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>> On 11/03/2024 23:28, John Harshman wrote:
>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>
>>>>> Open access article:
>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>
>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>> that two lineages separated for over 100 million years can still
>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>>> and can still form fertile hybrids, but the claim is that these fish
>>>>> evolve orders of magnitude more slowly than mammals.
>>>>>
>>>>> The Science news article claims that mammals accumulate 0.02
>>>>> mutations per site per million years, while these fish averaged only
>>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>>> they looked at for this study these fish evolve much more slowly
>>>>> than mammals.
>>>>>
>>>>> The news article notes that other "living fossils" such as
>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>
>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>> evolution, they really should be looking at junk sequences rather
>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>> introns aren't alignable, well, that kills the theory right there.
>>>>
>>>
>>> Tree species thought to be separated by tens of millions of years are
>>> known to hybridise. For example Platanus orientalis and Platanus
>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>> of Tilia I suspect that multiple rounds of introgression has served to
>>> limit the amount of divergence between species. However Tilia does
>>> appear as a short branch in cladograms, supporting the hypothesis that
>>> forest trees have a lower rate of evolution.
>>>
>> Then again, ducks that are thought to be separated by tens of millions
>> of years are also known to hybridize, and their rate of evolution isn't
>> particularly slow.
>>
>All sorts of seemingly long-separated species (both plant and animal)
>are observed. What determines whether the hybrid offspring are fertile,
>infertile or sterile? I found an article on Big Think
>https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
>describing an unsuccessful attempt to produce a "humanzee". Fortunately
>it didn't work. The chromosome count is different in humans and
>chimpanzee, but does this imply that it's essentially impossible?

My understanding is, the limiting factor is the compatibility of mtDNA
with nuclear DNA. As species evolve, mtDNA mutates faster than
nuclear DNA, but they still need to maintain compatibility with each
other. Organisms where the two are poorly compatible fail to thive or
even to survive. Over time, isolated populations can evolve mtDNA
that are no longer compatible with nuclear DNA from other populations.
ISTM infertility between isolated populations would be a natural
though not necessarily inevitable consequence of having two separate
DNA pools.

*********************************
Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial
and nuclear genomes during oogenesis results in ovarian failure and
embryonic lethality. Development. 2017 Jul 1;144(13):2490-2503. doi:
10.1242/dev.151951. Epub 2017 Jun 2. PMID: 28576772; PMCID:
PMC5536873.
**********************************

--
To know less than we don't know is the nature of most knowledge

On 3/12/24 10:59 PM, jillery wrote:
> On Tue, 12 Mar 2024 09:04:22 -0700, erik simpson
> <eastside.erik@gmail.com> wrote:
>
>> On 3/12/24 6:44 AM, John Harshman wrote:
>>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>>> On 11/03/2024 23:28, John Harshman wrote:
>>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>>
>>>>>> Open access article:
>>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>>
>>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>>> that two lineages separated for over 100 million years can still
>>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>>>> and can still form fertile hybrids, but the claim is that these fish
>>>>>> evolve orders of magnitude more slowly than mammals.
>>>>>>
>>>>>> The Science news article claims that mammals accumulate 0.02
>>>>>> mutations per site per million years, while these fish averaged only
>>>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>>>> they looked at for this study these fish evolve much more slowly
>>>>>> than mammals.
>>>>>>
>>>>>> The news article notes that other "living fossils" such as
>>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>>
>>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>>> evolution, they really should be looking at junk sequences rather
>>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>>> introns aren't alignable, well, that kills the theory right there.
>>>>>
>>>>
>>>> Tree species thought to be separated by tens of millions of years are
>>>> known to hybridise. For example Platanus orientalis and Platanus
>>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>>> of Tilia I suspect that multiple rounds of introgression has served to
>>>> limit the amount of divergence between species. However Tilia does
>>>> appear as a short branch in cladograms, supporting the hypothesis that
>>>> forest trees have a lower rate of evolution.
>>>>
>>> Then again, ducks that are thought to be separated by tens of millions
>>> of years are also known to hybridize, and their rate of evolution isn't
>>> particularly slow.
>>>
>> All sorts of seemingly long-separated species (both plant and animal)
>> are observed. What determines whether the hybrid offspring are fertile,
>> infertile or sterile? I found an article on Big Think
>> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
>> describing an unsuccessful attempt to produce a "humanzee". Fortunately
>> it didn't work. The chromosome count is different in humans and
>> chimpanzee, but does this imply that it's essentially impossible?
>
>
> My understanding is, the limiting factor is the compatibility of mtDNA
> with nuclear DNA. As species evolve, mtDNA mutates faster than
> nuclear DNA, but they still need to maintain compatibility with each
> other. Organisms where the two are poorly compatible fail to thive or
> even to survive. Over time, isolated populations can evolve mtDNA
> that are no longer compatible with nuclear DNA from other populations.
> ISTM infertility between isolated populations would be a natural
> though not necessarily inevitable consequence of having two separate
> DNA pools.
>
> *********************************
> Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial
> and nuclear genomes during oogenesis results in ovarian failure and
> embryonic lethality. Development. 2017 Jul 1;144(13):2490-2503. doi:
> 10.1242/dev.151951. Epub 2017 Jun 2. PMID: 28576772; PMCID:
> PMC5536873.
> **********************************

That's one of several possible reasons for incompatibility. Some others
have already been mentioned.

On Wed, 13 Mar 2024 06:28:17 -0700, John Harshman
<john.harshman@gmail.com> wrote:

>On 3/12/24 10:59 PM, jillery wrote:
>> On Tue, 12 Mar 2024 09:04:22 -0700, erik simpson
>> <eastside.erik@gmail.com> wrote:
>>
>>> On 3/12/24 6:44 AM, John Harshman wrote:
>>>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>>>> On 11/03/2024 23:28, John Harshman wrote:
>>>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>>>
>>>>>>> Open access article:
>>>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>>>
>>>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>>>> that two lineages separated for over 100 million years can still
>>>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>>>>> and can still form fertile hybrids, but the claim is that these fish
>>>>>>> evolve orders of magnitude more slowly than mammals.
>>>>>>>
>>>>>>> The Science news article claims that mammals accumulate 0.02
>>>>>>> mutations per site per million years, while these fish averaged only
>>>>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>>>>> they looked at for this study these fish evolve much more slowly
>>>>>>> than mammals.
>>>>>>>
>>>>>>> The news article notes that other "living fossils" such as
>>>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>>>
>>>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>>>> evolution, they really should be looking at junk sequences rather
>>>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>>>> introns aren't alignable, well, that kills the theory right there.
>>>>>>
>>>>>
>>>>> Tree species thought to be separated by tens of millions of years are
>>>>> known to hybridise. For example Platanus orientalis and Platanus
>>>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>>>> of Tilia I suspect that multiple rounds of introgression has served to
>>>>> limit the amount of divergence between species. However Tilia does
>>>>> appear as a short branch in cladograms, supporting the hypothesis that
>>>>> forest trees have a lower rate of evolution.
>>>>>
>>>> Then again, ducks that are thought to be separated by tens of millions
>>>> of years are also known to hybridize, and their rate of evolution isn't
>>>> particularly slow.
>>>>
>>> All sorts of seemingly long-separated species (both plant and animal)
>>> are observed. What determines whether the hybrid offspring are fertile,
>>> infertile or sterile? I found an article on Big Think
>>> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
>>> describing an unsuccessful attempt to produce a "humanzee". Fortunately
>>> it didn't work. The chromosome count is different in humans and
>>> chimpanzee, but does this imply that it's essentially impossible?
>>
>>
>> My understanding is, the limiting factor is the compatibility of mtDNA
>> with nuclear DNA. As species evolve, mtDNA mutates faster than
>> nuclear DNA, but they still need to maintain compatibility with each
>> other. Organisms where the two are poorly compatible fail to thive or
>> even to survive. Over time, isolated populations can evolve mtDNA
>> that are no longer compatible with nuclear DNA from other populations.
>> ISTM infertility between isolated populations would be a natural
>> though not necessarily inevitable consequence of having two separate
>> DNA pools.
>>
>> *********************************
>> Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial
>> and nuclear genomes during oogenesis results in ovarian failure and
>> embryonic lethality. Development. 2017 Jul 1;144(13):2490-2503. doi:
>> 10.1242/dev.151951. Epub 2017 Jun 2. PMID: 28576772; PMCID:
>> PMC5536873.
>> **********************************
>
>That's one of several possible reasons for incompatibility. Some others
>have already been mentioned.

My understanding is there are likely several causes for genetic
incompatibilities. My impression is chromosome count is among the
least of them. As long as the important genes line up during meiosis,
it doesn't really matter if the chromosomes are in multiple pieces.
That's why for example the chromosome 2 fusion wasn't as big a problem
for our ancestors as some claim.

OTOH mtDNA/nuclear DNA incompatibility is an insurmountable problem.
Since the original endosymbiosis billions of years ago, mitochondria
have transferred much of their DNA into the nucleus, in order to speed
their duplication, while keeping for themselves most crucial genes,
for example to regulate ATP synthesis.

Having two separate pools of DNA with different mutation rates
necessarily means that from time to time some gamete fusions will
combine two incompatible pools. Breeding long-isolated populations
makes that even more likely. And once two populations are
biologically isolated, for any reason, they necessarily evolve
independently of each other.

--
To know less than we don't know is the nature of most knowledge

On 3/15/24 12:45 AM, jillery wrote:
> On Wed, 13 Mar 2024 06:28:17 -0700, John Harshman
> <john.harshman@gmail.com> wrote:
>
>> On 3/12/24 10:59 PM, jillery wrote:
>>> On Tue, 12 Mar 2024 09:04:22 -0700, erik simpson
>>> <eastside.erik@gmail.com> wrote:
>>>
>>>> On 3/12/24 6:44 AM, John Harshman wrote:
>>>>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>>>>> On 11/03/2024 23:28, John Harshman wrote:
>>>>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>>>>
>>>>>>>> Open access article:
>>>>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>>>>
>>>>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>>>>> that two lineages separated for over 100 million years can still
>>>>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>>>>>> and can still form fertile hybrids, but the claim is that these fish
>>>>>>>> evolve orders of magnitude more slowly than mammals.
>>>>>>>>
>>>>>>>> The Science news article claims that mammals accumulate 0.02
>>>>>>>> mutations per site per million years, while these fish averaged only
>>>>>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>>>>>> they looked at for this study these fish evolve much more slowly
>>>>>>>> than mammals.
>>>>>>>>
>>>>>>>> The news article notes that other "living fossils" such as
>>>>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>>>>
>>>>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>>>>> evolution, they really should be looking at junk sequences rather
>>>>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>>>>> introns aren't alignable, well, that kills the theory right there.
>>>>>>>
>>>>>>
>>>>>> Tree species thought to be separated by tens of millions of years are
>>>>>> known to hybridise. For example Platanus orientalis and Platanus
>>>>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>>>>> of Tilia I suspect that multiple rounds of introgression has served to
>>>>>> limit the amount of divergence between species. However Tilia does
>>>>>> appear as a short branch in cladograms, supporting the hypothesis that
>>>>>> forest trees have a lower rate of evolution.
>>>>>>
>>>>> Then again, ducks that are thought to be separated by tens of millions
>>>>> of years are also known to hybridize, and their rate of evolution isn't
>>>>> particularly slow.
>>>>>
>>>> All sorts of seemingly long-separated species (both plant and animal)
>>>> are observed. What determines whether the hybrid offspring are fertile,
>>>> infertile or sterile? I found an article on Big Think
>>>> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
>>>> describing an unsuccessful attempt to produce a "humanzee". Fortunately
>>>> it didn't work. The chromosome count is different in humans and
>>>> chimpanzee, but does this imply that it's essentially impossible?
>>>
>>>
>>> My understanding is, the limiting factor is the compatibility of mtDNA
>>> with nuclear DNA. As species evolve, mtDNA mutates faster than
>>> nuclear DNA, but they still need to maintain compatibility with each
>>> other. Organisms where the two are poorly compatible fail to thive or
>>> even to survive. Over time, isolated populations can evolve mtDNA
>>> that are no longer compatible with nuclear DNA from other populations.
>>> ISTM infertility between isolated populations would be a natural
>>> though not necessarily inevitable consequence of having two separate
>>> DNA pools.
>>>
>>> *********************************
>>> Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial
>>> and nuclear genomes during oogenesis results in ovarian failure and
>>> embryonic lethality. Development. 2017 Jul 1;144(13):2490-2503. doi:
>>> 10.1242/dev.151951. Epub 2017 Jun 2. PMID: 28576772; PMCID:
>>> PMC5536873.
>>> **********************************
>>
>> That's one of several possible reasons for incompatibility. Some others
>> have already been mentioned.
>
>
> My understanding is there are likely several causes for genetic
> incompatibilities. My impression is chromosome count is among the
> least of them. As long as the important genes line up during meiosis,
> it doesn't really matter if the chromosomes are in multiple pieces.
> That's why for example the chromosome 2 fusion wasn't as big a problem
> for our ancestors as some claim.
>
> OTOH mtDNA/nuclear DNA incompatibility is an insurmountable problem.
> Since the original endosymbiosis billions of years ago, mitochondria
> have transferred much of their DNA into the nucleus, in order to speed
> their duplication, while keeping for themselves most crucial genes,
> for example to regulate ATP synthesis.

That makes it sound like a purposeful or adaptive process, but maybe
it's just random. In fact mitochondria in most taxa have lost most of
their crucial genes, and I don't see much difference between the ones
they've lost and the ones they've kept. How is cytochrome c different
from cytochrome b, for example?

> Having two separate pools of DNA with different mutation rates
> necessarily means that from time to time some gamete fusions will
> combine two incompatible pools. Breeding long-isolated populations
> makes that even more likely. And once two populations are
> biologically isolated, for any reason, they necessarily evolve
> independently of each other.

Would that not be true for any pair of chromosomes whose products must
interact, i.e. more or less any pair of chromosomes? I see no reason to
elevate that particular reason for genetic isolation over several others.

On Sun, 17 Mar 2024 07:46:53 -0700, John Harshman
<john.harshman@gmail.com> wrote:

>On 3/15/24 12:45 AM, jillery wrote:
>> On Wed, 13 Mar 2024 06:28:17 -0700, John Harshman
>> <john.harshman@gmail.com> wrote:
>>
>>> On 3/12/24 10:59 PM, jillery wrote:
>>>> On Tue, 12 Mar 2024 09:04:22 -0700, erik simpson
>>>> <eastside.erik@gmail.com> wrote:
>>>>
>>>>> On 3/12/24 6:44 AM, John Harshman wrote:
>>>>>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>>>>>> On 11/03/2024 23:28, John Harshman wrote:
>>>>>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>>>>>
>>>>>>>>> Open access article:
>>>>>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>>>>>
>>>>>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>>>>>> that two lineages separated for over 100 million years can still
>>>>>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>>>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>>>>>>> and can still form fertile hybrids, but the claim is that these fish
>>>>>>>>> evolve orders of magnitude more slowly than mammals.
>>>>>>>>>
>>>>>>>>> The Science news article claims that mammals accumulate 0.02
>>>>>>>>> mutations per site per million years, while these fish averaged only
>>>>>>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>>>>>>> they looked at for this study these fish evolve much more slowly
>>>>>>>>> than mammals.
>>>>>>>>>
>>>>>>>>> The news article notes that other "living fossils" such as
>>>>>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>>>>>
>>>>>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>>>>>> evolution, they really should be looking at junk sequences rather
>>>>>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>>>>>> introns aren't alignable, well, that kills the theory right there.
>>>>>>>>
>>>>>>>
>>>>>>> Tree species thought to be separated by tens of millions of years are
>>>>>>> known to hybridise. For example Platanus orientalis and Platanus
>>>>>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>>>>>> of Tilia I suspect that multiple rounds of introgression has served to
>>>>>>> limit the amount of divergence between species. However Tilia does
>>>>>>> appear as a short branch in cladograms, supporting the hypothesis that
>>>>>>> forest trees have a lower rate of evolution.
>>>>>>>
>>>>>> Then again, ducks that are thought to be separated by tens of millions
>>>>>> of years are also known to hybridize, and their rate of evolution isn't
>>>>>> particularly slow.
>>>>>>
>>>>> All sorts of seemingly long-separated species (both plant and animal)
>>>>> are observed. What determines whether the hybrid offspring are fertile,
>>>>> infertile or sterile? I found an article on Big Think
>>>>> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
>>>>> describing an unsuccessful attempt to produce a "humanzee". Fortunately
>>>>> it didn't work. The chromosome count is different in humans and
>>>>> chimpanzee, but does this imply that it's essentially impossible?
>>>>
>>>>
>>>> My understanding is, the limiting factor is the compatibility of mtDNA
>>>> with nuclear DNA. As species evolve, mtDNA mutates faster than
>>>> nuclear DNA, but they still need to maintain compatibility with each
>>>> other. Organisms where the two are poorly compatible fail to thive or
>>>> even to survive. Over time, isolated populations can evolve mtDNA
>>>> that are no longer compatible with nuclear DNA from other populations.
>>>> ISTM infertility between isolated populations would be a natural
>>>> though not necessarily inevitable consequence of having two separate
>>>> DNA pools.
>>>>
>>>> *********************************
>>>> Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial
>>>> and nuclear genomes during oogenesis results in ovarian failure and
>>>> embryonic lethality. Development. 2017 Jul 1;144(13):2490-2503. doi:
>>>> 10.1242/dev.151951. Epub 2017 Jun 2. PMID: 28576772; PMCID:
>>>> PMC5536873.
>>>> **********************************
>>>
>>> That's one of several possible reasons for incompatibility. Some others
>>> have already been mentioned.
>>
>>
>> My understanding is there are likely several causes for genetic
>> incompatibilities. My impression is chromosome count is among the
>> least of them. As long as the important genes line up during meiosis,
>> it doesn't really matter if the chromosomes are in multiple pieces.
>> That's why for example the chromosome 2 fusion wasn't as big a problem
>> for our ancestors as some claim.
>>
>> OTOH mtDNA/nuclear DNA incompatibility is an insurmountable problem.
>> Since the original endosymbiosis billions of years ago, mitochondria
>> have transferred much of their DNA into the nucleus, in order to speed
>> their duplication, while keeping for themselves most crucial genes,
>> for example to regulate ATP synthesis.
>
>That makes it sound like a purposeful or adaptive process, but maybe
>it's just random. In fact mitochondria in most taxa have lost most of
>their crucial genes, and I don't see much difference between the ones
>they've lost and the ones they've kept. How is cytochrome c different
>from cytochrome b, for example?

The process of reducing mtDNA wasn't purposeful, in the sense of
having foresight. It was adaptive aka evolutionary, in the sense that
mitochondria which lost genes necessary to regulate ATP synthesis
would significantly compromise the metabolism of the host organism to
which they were a part, and so would be less likely to increase in the
organisms' population. OTOH mitochondria which kept genes that were
duplicated in nuclear DNA would duplicate themselves more slowly, and
so their host organisms would be less adaptive.

I'm not familiar enough with mitochondrial respiration to have an
informed opinion as to which genes qualify as "crucial". My
understanding is cyt c is involved in the electron transport chain
while cyt b and other cytochromes are not.

>> Having two separate pools of DNA with different mutation rates
>> necessarily means that from time to time some gamete fusions will
>> combine two incompatible pools. Breeding long-isolated populations
>> makes that even more likely. And once two populations are
>> biologically isolated, for any reason, they necessarily evolve
>> independently of each other.
>
>Would that not be true for any pair of chromosomes whose products must
>interact, i.e. more or less any pair of chromosomes? I see no reason to
>elevate that particular reason for genetic isolation over several others.

mtDNA is inherited almost exclusively matrilineally, while nuclear DNA
is inherited from both parents. Also nuclear genes are diploid, while
mtDNA are monoploid. My understanding is for these reasons,
maladaptive mtDNA mutations are more likely to be fatal than
maladaptive nuclear DNA mutations.

--
To know less than we don't know is the nature of most knowledge

On 3/18/24 5:48 AM, jillery wrote:
> On Sun, 17 Mar 2024 07:46:53 -0700, John Harshman
> <john.harshman@gmail.com> wrote:
>
>> On 3/15/24 12:45 AM, jillery wrote:
>>> On Wed, 13 Mar 2024 06:28:17 -0700, John Harshman
>>> <john.harshman@gmail.com> wrote:
>>>
>>>> On 3/12/24 10:59 PM, jillery wrote:
>>>>> On Tue, 12 Mar 2024 09:04:22 -0700, erik simpson
>>>>> <eastside.erik@gmail.com> wrote:
>>>>>
>>>>>> On 3/12/24 6:44 AM, John Harshman wrote:
>>>>>>> On 3/12/24 3:50 AM, Ernest Major wrote:
>>>>>>>> On 11/03/2024 23:28, John Harshman wrote:
>>>>>>>>> On 3/11/24 4:17 PM, RonO wrote:
>>>>>>>>>> https://www.science.org/content/article/these-gars-are-ultimate-living-fossils
>>>>>>>>>>
>>>>>>>>>> Open access article:
>>>>>>>>>> https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae028/7615529?login=false
>>>>>>>>>>
>>>>>>>>>> These researchers looked at Gar, but it also applies to sturgeons.
>>>>>>>>>> These two bony fish lineages seem to have a very slow rate of
>>>>>>>>>> molecular evolution.  The changes in their DNA accumulate so slowly
>>>>>>>>>> that two lineages separated for over 100 million years can still
>>>>>>>>>> form fertile hybrids.  3 million years is pushing it for species
>>>>>>>>>> like lions and tigers that can still form hybrids, but the hybrids
>>>>>>>>>> are sterile. Bonobos and chimps are around 3 million years divergent
>>>>>>>>>> and can still form fertile hybrids, but the claim is that these fish
>>>>>>>>>> evolve orders of magnitude more slowly than mammals.
>>>>>>>>>>
>>>>>>>>>> The Science news article claims that mammals accumulate 0.02
>>>>>>>>>> mutations per site per million years, while these fish averaged only
>>>>>>>>>> 0.00009 mutations per million years.  For the 1100 coding exons that
>>>>>>>>>> they looked at for this study these fish evolve much more slowly
>>>>>>>>>> than mammals.
>>>>>>>>>>
>>>>>>>>>> The news article notes that other "living fossils" such as
>>>>>>>>>> coelacanths (0.0005) evolve faster, but slower than amphibians
>>>>>>>>>> (0.007).  It sounds like terrestrial animals evolve faster than fish.
>>>>>>>>>
>>>>>>>>> If it's repair mechanisms they hypothesize as the cause of slow
>>>>>>>>> evolution, they really should be looking at junk sequences rather
>>>>>>>>> than just 4-fold degenerate sites. I suggest introns. And if the
>>>>>>>>> introns aren't alignable, well, that kills the theory right there.
>>>>>>>>>
>>>>>>>>
>>>>>>>> Tree species thought to be separated by tens of millions of years are
>>>>>>>> known to hybridise. For example Platanus orientalis and Platanus
>>>>>>>> occidentalis, and also with Tilia, Quercus and Aesculus. In the case
>>>>>>>> of Tilia I suspect that multiple rounds of introgression has served to
>>>>>>>> limit the amount of divergence between species. However Tilia does
>>>>>>>> appear as a short branch in cladograms, supporting the hypothesis that
>>>>>>>> forest trees have a lower rate of evolution.
>>>>>>>>
>>>>>>> Then again, ducks that are thought to be separated by tens of millions
>>>>>>> of years are also known to hybridize, and their rate of evolution isn't
>>>>>>> particularly slow.
>>>>>>>
>>>>>> All sorts of seemingly long-separated species (both plant and animal)
>>>>>> are observed. What determines whether the hybrid offspring are fertile,
>>>>>> infertile or sterile? I found an article on Big Think
>>>>>> https://bigthink.com/the-past/soviet-human-ape-super-warriors-humanzee-ivanov/
>>>>>> describing an unsuccessful attempt to produce a "humanzee". Fortunately
>>>>>> it didn't work. The chromosome count is different in humans and
>>>>>> chimpanzee, but does this imply that it's essentially impossible?
>>>>>
>>>>>
>>>>> My understanding is, the limiting factor is the compatibility of mtDNA
>>>>> with nuclear DNA. As species evolve, mtDNA mutates faster than
>>>>> nuclear DNA, but they still need to maintain compatibility with each
>>>>> other. Organisms where the two are poorly compatible fail to thive or
>>>>> even to survive. Over time, isolated populations can evolve mtDNA
>>>>> that are no longer compatible with nuclear DNA from other populations.
>>>>> ISTM infertility between isolated populations would be a natural
>>>>> though not necessarily inevitable consequence of having two separate
>>>>> DNA pools.
>>>>>
>>>>> *********************************
>>>>> Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial
>>>>> and nuclear genomes during oogenesis results in ovarian failure and
>>>>> embryonic lethality. Development. 2017 Jul 1;144(13):2490-2503. doi:
>>>>> 10.1242/dev.151951. Epub 2017 Jun 2. PMID: 28576772; PMCID:
>>>>> PMC5536873.
>>>>> **********************************
>>>>
>>>> That's one of several possible reasons for incompatibility. Some others
>>>> have already been mentioned.
>>>
>>>
>>> My understanding is there are likely several causes for genetic
>>> incompatibilities. My impression is chromosome count is among the
>>> least of them. As long as the important genes line up during meiosis,
>>> it doesn't really matter if the chromosomes are in multiple pieces.
>>> That's why for example the chromosome 2 fusion wasn't as big a problem
>>> for our ancestors as some claim.
>>>
>>> OTOH mtDNA/nuclear DNA incompatibility is an insurmountable problem.
>>> Since the original endosymbiosis billions of years ago, mitochondria
>>> have transferred much of their DNA into the nucleus, in order to speed
>>> their duplication, while keeping for themselves most crucial genes,
>>> for example to regulate ATP synthesis.
>>
>> That makes it sound like a purposeful or adaptive process, but maybe
>> it's just random. In fact mitochondria in most taxa have lost most of
>> their crucial genes, and I don't see much difference between the ones
>> they've lost and the ones they've kept. How is cytochrome c different
>>from cytochrome b, for example?
>
>
> The process of reducing mtDNA wasn't purposeful, in the sense of
> having foresight. It was adaptive aka evolutionary, in the sense that
> mitochondria which lost genes necessary to regulate ATP synthesis
> would significantly compromise the metabolism of the host organism to
> which they were a part, and so would be less likely to increase in the
> organisms' population. OTOH mitochondria which kept genes that were
> duplicated in nuclear DNA would duplicate themselves more slowly, and
> so their host organisms would be less adaptive.
>
> I'm not familiar enough with mitochondrial respiration to have an
> informed opinion as to which genes qualify as "crucial". My
> understanding is cyt c is involved in the electron transport chain
> while cyt b and other cytochromes are not.

I'm afraid your understanding is wrong. Cyt b is part of the electron
transport chain. While it's true that most of the genes retained by
animal mitochondria are crucial parts of ATP production, so are many of
the genes lost from the mitochondrial genome after transfer to the
nuclear genome. Many of the proteins involved have to be imported into
the mitochondrion, which doesn't seem at all optimal. This seems more
like constructive neutral evolution than adaptive evolution. Now of
course loss of a crucial gene can only be neutral if it's already been
transferred to the nucleus, but that sort of transfer is quite common.
The usual fate of such transfers ("numts") is to decay over time, but
during the short period when they're functional, the mitochondrial gene
could potentially be lost.

On 18/03/2024 14:23, John Harshman wrote:
>
> I'm afraid your understanding is wrong. Cyt b is part of the electron
> transport chain. While it's true that most of the genes retained by
> animal mitochondria are crucial parts of ATP production, so are many of
> the genes lost from the mitochondrial genome after transfer to the
> nuclear genome. Many of the proteins involved have to be imported into
> the mitochondrion, which doesn't seem at all optimal. This seems more
> like constructive neutral evolution than adaptive evolution. Now of
> course loss of a crucial gene can only be neutral if it's already been
> transferred to the nucleus, but that sort of transfer is quite common.
> The usual fate of such transfers ("numts") is to decay over time, but
> during the short period when they're functional, the mitochondrial gene
> could potentially be lost.

For a mitochondrial gene to be transferred to the nuclear genome, not
only does a copy have to be integrated into the nuclear genome, and
transcribed, but the resulting protein has to be imported into the
mitochrondrion. If I understand correctly that usually (universally?)
requires the acquisition of a mitochondrial targeting sequence.

--
alias Ernest Major

On 3/18/24 8:09 AM, Ernest Major wrote:
> On 18/03/2024 14:23, John Harshman wrote:
>>
>> I'm afraid your understanding is wrong. Cyt b is part of the electron
>> transport chain. While it's true that most of the genes retained by
>> animal mitochondria are crucial parts of ATP production, so are many
>> of the genes lost from the mitochondrial genome after transfer to the
>> nuclear genome. Many of the proteins involved have to be imported into
>> the mitochondrion, which doesn't seem at all optimal. This seems more
>> like constructive neutral evolution than adaptive evolution. Now of
>> course loss of a crucial gene can only be neutral if it's already been
>> transferred to the nucleus, but that sort of transfer is quite common.
>> The usual fate of such transfers ("numts") is to decay over time, but
>> during the short period when they're functional, the mitochondrial
>> gene could potentially be lost.
>
> For a mitochondrial gene to be transferred to the nuclear genome, not
> only does a copy have to be integrated into the nuclear genome, and
> transcribed, but the resulting protein has to be imported into the
> mitochrondrion. If I understand correctly that usually (universally?)
> requires the acquisition of a mitochondrial targeting sequence.
>
Quite so, making it a significantly rarer event. Then we enter a stage
in which there are two versions of the mitochondrial protein, and one of
them is superfluous. Given the much higher mutation rate of the
mitochondrial genome, the mitochondrial gene is much more likely to
suffer a deactivating mutation, after which deletions will chip away at
its sequence, eventually disposing of it entirely.

A quick search finds a review of metazoan mitochondrial genomes, and
there's more variation than I had supposed. The bulk of it is in tRNA
genes, but some of the important protein-coding genes are also missing
in some species. Check out table 2. It even, very surprisingly, appears
that a couple of genes have been added to the mitochondrial genome in a
few of the assayed species.

https://www.nature.com/articles/hdy200862