Re: Why all apes including humans do not have tails

On 2024-04-06 7:37 PM, Arkalen wrote:

On 07/04/2024 00:16, DB Cates wrote:

On 2024-04-06 2:55 AM, Arkalen wrote:

On 05/04/2024 23:07, DB Cates wrote:

On 2024-04-05 3:56 AM, Arkalen wrote:

On 01/03/2024 05:31, DB Cates wrote:

On 2024-02-29 1:17 PM, Bob Casanova wrote:

On Thu, 29 Feb 2024 08:05:05 -0800, the following appeared
in talk.origins, posted by erik simpson
<eastside.erik@gmail.com>:
>

On 2/29/24 3:55 AM, RonO wrote:

On 2/28/2024 5:41 PM, erik simpson wrote:

On 2/28/24 3:21 PM, RonO wrote:

It turns out that the common ancestor that between gibbons and the
great apes had an ALU transposon jump into the intron between exon 6
and exon 7 of the TBXT gene.  There was already an transposon between
exon 5 and exon 6.  Monkeys and apes have the ALU insertion in the
intron between exon 5 and exon 6, but the apes have the second ALU
insertion in the intron between exons 6 and 7.  So it turns out that
apes still have the exon 6 sequence in the TBXT gene, but the two ALU
transposon sequences form a stem loop structure in the RNA transcript
that messes up processing so exon 6 is skipped and exon 5 is stuck to
exon 7 in the final ape mRNA.  So part of what makes us human is due
to a transposon insertion mutation into the TBXT gene.
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The insertion happened in the common ancestor of all extant apes, and
has been retained by the extant ape lineages.
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https://www.nature.com/articles/s41586-024-07095-8
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The article is open access.
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Ron Okimoto
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Another effect of this modification is also "Moreover, mice expressing
the exon-skipped Tbxt isoform develop neural tube defects, a condition
that affects approximately 1 in 1,000 neonates in humans10. Thus,
tail-loss evolution may have been associated with an adaptive cost of
the potential for neural tube defects, which continue to affect human
health today."
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Evidently, the advantages of losing the tail outweigh the disadvantage
of the neural tube defects.
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What were the advantages?
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Some other simian lineages have lost their tails, but what is the
advantage?
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Apes did become brachiators, but other simian lineages did not, and some
simian lineages that adopted a similar lifestyle for supporting
themselves in the trees, actually developed prehensile tails as a fifth
limb for supporting themselves hanging from branches.
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For birds there was a selective advantage in terms of weight, and the
tailbones degenerated and fused into a small nub.  The tail was not
lost, and birds still have a nub that they call a pygostyle that still
supports the muscles that control the tail movements and so the feathers
associated with the tail.
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Ron Okimoto
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I believe the article mentions that bipedalism is speculated to have
made bipedalism easier.
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No causal link there... ;-)

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That could be a just-so story, but mutations
that are adopted and fixed within a population must have advantages that
outweigh potential advantages.
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Indubitably.

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Really? Drift is out?
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I don't know if drift is ever out but is it particularly plausible in the case of tail loss, something that seems really rare in tetrapods? Like, what lineages actually lost their tails - like, really lost, not "reduced" or "replaced by a non-bony appendage that serves a taily function": frogs, apes, manx cats... bears are maybe on their way... who else?
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Well, my reply was not specific to the 'tailless' idea but rather to the
more general statement "mutations that are adopted and fixed within a population must have advantages that outweigh potential advantages." and
the "Indubitably." reply.

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Fair enough, I'd missed that context and I agree it was a reasonable response to that sentence in isolation.
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However, you seem to making the claim that 'rare' fixed mutations are
less likely to be due to drift. It would seem to me that common (over many lineages) fixed mutations, even if not identical but responsible
for very similar morphology, are almost certainly due to selection. Rare
fixed mutations that have not been *demonstrated* to be associated with
enhanced reproductive success are more likely to be due to drift.
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I'm not sure whether by "rare" mutation you mean "rarely found" or "rarely occurs".

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We have a miscommunication. I was referring to *fixed* mutations only, not mutations in general. I don't think there are such things as "rare mutations". There are some biases and special circumstances, but I think it can be stated that mutations occur randomly without too much violation of reality. The total number of mutations extant in a given population depends on mutation rate, genome size, and population size in any cases meaning that every possible mutation happens regularly over time. The *really* bad ones are eliminated early and are never observed. Most are neutral or near neutral and are, at a very low probability, randomly (biased by things like proximity to highly conserved areas) fixed by drift. A significant number are deleterious and are eliminated before fixation by selection and a small number are useful in the extant environment and are positively selected and have a higher rate of fixation.
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So my argument is that any *particular* mutation that becomes fixed in one or a few populations is more likely to be due to drift while one that becomes fixed in many diverse populations is much more likely to be due to selection. This also applies to different mutations that have the same or similar phenotypic effects.
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 I'm not sure I completely follow/agree but I might be being biased by the fact I came into this talking about a phenotypic trait not a mutation and that gets back to how the whole thing started with a misunderstanding anyway, and it might be best to leave it at that.

Sounds like a good idea.

 

In terms of "rarely occurs", such mutations are
definitely much less likely to get fixed by drift than by natural selection, because drift depends almost purely on statistics and those are by definition not in favor of rare occurrences.
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In terms of "rarely found" I don't think I'd say that; in principle both drift and selection can result in rare traits or common ones via different dynamics.
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The reason I think it speaks to drift in this case is *how rare* it is over *how large* a population. Basically the possibilities seem to be:
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- the base rate of occurrence of this mutation is extremely low - much lower than that of mutations causing limb loss for example. It's possible enough that the genetics & developmental pathways of tails in tetrapods make it so but it strikes me as implausible, and the mutation described in the article doesn't look like an unusually unlikely one.
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- the base rate of occurrence of this mutation is higher than the number of time it got fixed suggests, which in turn suggests the mutation is deleterious for almost all tetrapods - either because their tails are universally useful, or because this is a tricky developmental pathway to mess with without negative impacts.
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If the second is true then that leaves two non-mutually-exclusive options for why it got fixed in the few cases it did: it was particularly beneficial in those groups, or it wasn't deleterious for them the way it is for other tetrapods. While the second *does* mean the trait could arise via drift, the fact it's not deleterious for them when it is for *all other tetrapods* is itself an oddity that demands explanation beyond "drift".
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In the three clades I listed (still haven't thought of others, still interested to see if anyone does) tail loss seems pretty clearly selective in frogs and pretty clearly due to drift in Manx cats but that latter case almost "proves the rule" - we have a clear founder effect, a very recent trait in a small population that we can doubt would persist over geologic time, and in a species that humans haven't been provably messing with as blatantly as dogs but still somewhat. I've never heard of a notable bottleneck in early ape evolutionary history but it's possible this isn't the kind of thing there would be much evidence for or against this far out; the other two factors however are definitely out for apes.
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Actually this made me realize another reason to doubt the "base likelihood happens to match up to 3 in all tetrapods" option: the fact frogs went tail-less so much earlier than apes or Manx cats. Like, the base rate is either high enough that the mutation would occur early in tetrapod history in a then-much-lower-and-less-diverse population and be available for selection to work on, OR it's low enough that it would never drift to fixation once in non-amphibian tetrapods until apes. Those are radically different base rates ! It's not impossible to be fair, genetics change and the base rate could have been different in early tetrapods vs amniotes for example. But those are some assumptions we're adding there.
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Not to mention the article suggests tail loss could be associated with neural tube defects, which would definitely make drift much less likely.
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Could you be more explicit here?
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It would make the trait deleterious, and while mildly deleterious traits can fix through drift it's kind of core to the point of natural selection that the probability of this happening drops sharply the more deleterious the trait is (founder effects aside).
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Okay, tell me where I'm wrong here and if I'm not wrong, justify your conclusion.
It seems to me that you are claiming that association with a severely deleterious effect would prevent fixation by drift but selection in the same circumstances would work.
Selection will fix a severely deleterious mutation??

 No, selection will *weed out* a severely deleterious mutation, thus preventing it getting fixed via drift.
 

Okay,  I agree completely with that. But I thought the argument was being applied to a mutation that *was* fixed in the population. Must be my misunderstanding.

 <snip>
 

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Don Cates ("he's a cunning rascal" PN)