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

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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

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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

--- SoupGate-Win32 v1.05
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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

--- SoupGate-Win32 v1.05
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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

--- SoupGate-Win32 v1.05
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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

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