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From: DB Cates <cates_db@hotmail.com>
Newsgroups: talk.origins
Subject: Re: Why all apes including humans do not have tails
Date: Sat, 6 Apr 2024 21:10:53 -0500
Organization: University of Ediacara
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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.
>>>>>>>>>>>
>>>>>>>>>>> The insertion happened in the common ancestor of all extant 
>>>>>>>>>>> apes, and
>>>>>>>>>>> has been retained by the extant ape lineages.
>>>>>>>>>>>
>>>>>>>>>>> https://www.nature.com/articles/s41586-024-07095-8
>>>>>>>>>>>
>>>>>>>>>>> The article is open access.
>>>>>>>>>>>
>>>>>>>>>>> Ron Okimoto
>>>>>>>>>>>
>>>>>>>>>> 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."
>>>>>>>>>>
>>>>>>>>>> Evidently, the advantages of losing the tail outweigh the 
>>>>>>>>>> disadvantage
>>>>>>>>>> of the neural tube defects.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> What were the advantages?
>>>>>>>>>
>>>>>>>>> Some other simian lineages have lost their tails, but what is the
>>>>>>>>> advantage?
>>>>>>>>>
>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>> Ron Okimoto
>>>>>>>>>
>>>>>>>> I believe the article mentions that bipedalism is speculated to 
>>>>>>>> have
>>>>>>>> made bipedalism easier.
>>>>>>>>
>>>>>>> No causal link there... ;-)
>>>>>>>>
>>>>>>>> That could be a just-so story, but mutations
>>>>>>>> that are adopted and fixed within a population must have 
>>>>>>>> advantages that
>>>>>>>> outweigh potential advantages.
>>>>>>>>
>>>>>>> Indubitably.
>>>>>>>>
>>>>>> Really? Drift is out?
>>>>>>
>>>>>
>>>>> 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?
>>>>>
>>>> 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.
>>>
>>> Fair enough, I'd missed that context and I agree it was a reasonable 
>>> response to that sentence in isolation.
>>>
>>>> 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.
>>>>
>>>
>>> I'm not sure whether by "rare" mutation you mean "rarely found" or 
>>> "rarely occurs". 
>>
>> 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.
>>
>> 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.
>>
> 
> 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 
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