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From: jillery <69jpil69@gmail.com>
Newsgroups: talk.origins
Subject: Re: Science has a news article up about "living fossils"
Date: Mon, 18 Mar 2024 08:48:35 -0400
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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:
>>=20
>>> 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-fo=
ssils
>>>>>>>>>
>>>>>>>>> Open access article:
>>>>>>>>> =
https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae02=
8/7615529?login=3Dfalse
>>>>>>>>>
>>>>>>>>> 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.=C2=A0 The changes in their DNA accumulate =
so slowly
>>>>>>>>> that two lineages separated for over 100 million years can =
still
>>>>>>>>> form fertile hybrids.=C2=A0 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.=C2=A0 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).=C2=A0 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-iv=
anov/
>>>>> 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.
>>=20
>>=20
>> 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.
>>=20
>> 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=20
>it's just random. In fact mitochondria in most taxa have lost most of=20
>their crucial genes, and I don't see much difference between the ones=20
>they've lost and the ones they've kept. How is cytochrome c different=20
>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=20
>interact, i.e. more or less any pair of chromosomes? I see no reason to=20
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