Older paper - read it

[satoshi]

https://www.cell.com/current-biology/fulltext/S0960-9822(10)01089-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982210010894%3Fshowall%3Dtrue

[satoshi]

https://www.cell.com/current-biology/fulltext/S0960-9822(09)02073-9

[satoshi]

https://www.cell.com/current-biology/fulltext/S0960-9822(09)02057-0

[satoshi]

On Monday, October 8, 2018 at 7:50:02 PM UTC-6, satoshi wrote:
> https://www.cell.com/current-biology/fulltext/S0960-9822(09)02073-9

evidence of a deity?

[Bob Casanova]

On Mon, 8 Oct 2018 19:03:15 -0700 (PDT), the following
appeared in talk.origins, posted by satoshi
<travellin...@gmail.com>:

>On Monday, October 8, 2018 at 7:50:02 PM UTC-6, satoshi wrote:
>> https://www.cell.com/current-biology/fulltext/S0960-9822(09)02073-9

Yields:

"The page or action you requested has resulted in an error"

>evidence of a deity?

Nope; deities wouldn't be expected to provide broken links.
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Wolffan]

On 09 Oct 2018, Bob Casanova wrote
(in article<4qqprd9h5e5m3sv58...@4ax.com>):

> On Mon, 8 Oct 2018 19:03:15 -0700 (PDT), the following
> appeared in talk.origins, posted by satoshi
> <travellin...@gmail.com>:
>
> > On Monday, October 8, 2018 at 7:50:02 PM UTC-6, satoshi wrote:
> > > https://www.cell.com/current-biology/fulltext/S0960-9822(09)02073-9
>
> Yields:
>
> "The page or action you requested has resulted in an error"
>
> > evidence of a deity?
>
> Nope; deities wouldn't be expected to provide broken links.

The full link ends in %3Dtrue. Satoshi can’t even quote links properly. If
he’s a diety, he’s not up to the level of the turtle in Pratchett’s
_Small Gods_. (No, not Great A’Tun. The small one.)

[satoshi]

works over here

copy paste

Summary

Cases of convergent evolution — where different lineages have evolved similar traits independently — are common and have proven central to our understanding of selection. Yet convincing examples of adaptive convergence at the sequence level are exceptionally rare [1]. The motor protein Prestin is expressed in mammalian outer hair cells (OHCs) and is thought to confer high frequency sensitivity and selectivity in the mammalian auditory system [2]. We previously reported that the Prestin gene has undergone sequence convergence among unrelated lineages of echolocating bat [3]. Here we report that this gene has also undergone convergent amino acid substitutions in echolocating dolphins, which group with echolocating bats in a phylogenetic tree of Prestin. Furthermore, we find evidence that these changes were driven by natural selection.
Main Text

The ability of some bats and all toothed whales to produce sonar pulses and process the returning echoes for prey detection and orientation (echolocation) is a spectacular example of phenotypic convergence in mammals. Echolocation requires exceptionally high frequency hearing and, though echolocating whales and bats generate their calls differently, their cochleae show multiple convergent anatomical features [4]. In particular, the cochlear OHCs in both taxa are shorter and stiffer than in other mammals [4], and this inferred adaptation for processing ultrasound is supported by audiograms that reveal correspondingly higher frequency thresholds [5].
To test whether convergent changes in bat Prestin genes have also occurred in echolocating whales, we sequenced the entire gene in a range of echolocating toothed whales and non-echolocating baleen whales, as well as additional bats (see Table S1 in the Supplemental Data available on-line with this issue). Trees based on nucleotide alignments from this larger dataset strongly supported the accepted species tree topology, albeit with the clustering of echolocating bats reported earlier [3]. However, in trees based on amino acid sequences, constructed using a range of different phylogenetic methods, we found that the echolocating dolphins now formed a well-supported group with echolocating horseshoe and Old World leaf-nosed bats (node posterior probability = 0.99 or 0.94 depending on the analysis), members of which emit Doppler-sensitive signals dominated by a constant frequency (CF) component [6] (Figure 1A). Intriguingly, the addition of the sperm whale, which appears to echolocate at much lower frequencies [7], was seen to decrease support for this convergent signal, leading to the cetaceans and bats both forming monophyletic groups. The extent of sequence convergence between bats and whales was thus not sufficient to unite these clades when non-dolphin odontocetes were included in the analysis.
Figure thumbnail gr1
Figure 1Evidence of sequence convergence in the Prestin gene between dolphins and bats.
Show full caption
View Large Image Figure ViewerDownload Hi-res image Download (PPT)
We assessed the support for phylogenetic convergence between echolocating dolphins and bats by comparing likelihood values at each site on a tree constrained to show monophyly of the bats and of the cetaceans and on our maximum-likelihood amino acid tree. We found that support for the convergent tree was distributed along the entire coding sequence (Figure 1B) and, therefore, was not caused by gene conversion. To assess the statistical support for our results, we generated a null distribution of 100,000 simulated sites that were allowed to evolve randomly on the constrained tree under the best-fitting model of evolution. These results confirmed that the total support for the convergent tree was significantly greater (p < 0.001) than expected under this model.
To identify sites showing unexpected support for convergence, we used the same simulations to calculate the chance of observing site-wise likelihood values higher than we observed at each site, calculating the false discovery rate to correct for multiple testing. This approach identified eight sites showing unexpected support for convergence (q < 0.05; Figure 1B). Comparing amino acid sequences between echolocating whales and bats and their respective reconstructed ancestors revealed additional convergent sites. In total, echolocating whales collectively shared 14 derived amino acids with echolocating bats, including ten with CF bats (see Supplemental Data). Four of these sites (G167S, I384T, A565S and E700D) were unique to CF bats and echolocating whales, though A565S was only seen in the sperm whale. We also found six additional replacements that could also be convergent, but which we could not confirm with certainty because of unresolved ancestral states (see Supplemental Data). The dichotomy between convergent and parallel evolution may be of little relevance [8], but we note that most, but not all, convergent sites were parallel changes from the same ancestral amino acid residue. No significant relationship was found between the rate of amino acid substitution at a site and support for the convergent topology, confirming that long-branch attraction artefacts do not explain the signal we have observed.
To investigate the causes of this convergent signal, we estimated rates of nucleotide substitutions that changed the amino acid (non-synonymous rate) or left no change (synonymous rate) at each site, for different parts of the species tree. The ratio of non-synonymous to synonymous rates (ω) measures the strength of selection at a site, from 0 for strong purifying selection to greater than 1 for positive selection. For sites that have evolved neutrally, we found no relationship between ω and the support for convergence, whereas sites under purifying selection showed a significant negative relationship between ω and support for convergence. However, the ω for sites showing a shift in functional constraint in the echolocating whales correlated significantly with support for convergence (p ∼ 0.018), and, of 33 sites predicted to fall into this category, 31 (94%) had ω values greater than one (Figure 1C, Table S2). Finally, none of these relationships were significant when sites were modelled as varying in ω within the bats showing convergence.
Our results suggest that the observed sequence convergence between dolphins and CF bats in Prestin has been driven by adaptive evolution of the dolphin gene. To date, no specific anatomical parallels have been drawn between these groups, perhaps with the exception of the fine tuning of the cochlear basal membrane in the porpoise (Phocoena) [9]. However, detailed comparisons of OHC length and fine-scale structure in cetaceans and bats are lacking [4], and could provide clues given the high frequency hearing thresholds recorded in dolphins and some CF bats. Regardless, our findings of adaptive sequence convergence between two highly divergent groups that share a complex phenotype is unprecedented, and suggests sequence convergence may be more common than previously suspected.
The editors of Current Biology welcome correspondence on any article in the journal, but reserve the right to reduce the length of any letter to be published. All Correspondence containing data or scientific argument will be refereed. Queries about articles for consideration in this format should be sent by e-mail to cb...@current-biology.com
Acknowledgments

This work was supported by grants awarded by the Key Construction Program of the National “985” Project and “211” Project to S.Z., the Royal Society to S.J.R. and the Research Councils UK to J.A.C. We thank Gang Li for technical advice, Beibei He for support in the laboratory and P. Jepson for samples.
Supplemental Data

Download .pdf (.13 MB) Help with pdf files
Document S1. Supplemental Experimental Procedures, Supplemental References, and Two Tables

[Wolffan]

On 10 Oct 2018, satoshi wrote
(in article<fa89a059-8b0e-4fcc...@googlegroups.com>):

> On Wednesday, October 10, 2018 at 3:50:02 AM UTC-7, Wolffan wrote:
> > On 09 Oct 2018, Bob Casanova wrote
> > (in article<4qqprd9h5e5m3sv58...@4ax.com>):
> >
> > > On Mon, 8 Oct 2018 19:03:15 -0700 (PDT), the following
> > > appeared in talk.origins, posted by satoshi
> > > <travellin...@gmail.com>:
> > >
> > > > On Monday, October 8, 2018 at 7:50:02 PM UTC-6, satoshi wrote:
> > > > > https://www.cell.com/current-biology/fulltext/S0960-9822(09)02073-9
> > >
> > > Yields:
> > >
> > > "The page or action you requested has resulted in an error"
> > >
> > > > evidence of a deity?
> > >
> > > Nope; deities wouldn't be expected to provide broken links.
> >
> > The full link ends in %3Dtrue. Satoshi can’t even quote links properly. If
> > he’s a diety, he’s not up to the level of the turtle in Pratchett’s
> > _Small Gods_. (No, not Great A’Tun. The small one.)
>
> works over here

when you post it, it doesn’t work in most non-Google readers. That’s Yet
Another known bug in Google’s system which will never be fixed. To be
precise, posts from Google don’t wrap properly. This doesn’t matter
(much) with ordinary text, but can and will break links. Especially very long
links. Google users will not see a problem. Virtually everyone else will. You
can’t quote links properly because you use Google Groups.

Pray point out anything about deities.

[Bob Casanova]

On Thu, 11 Oct 2018 07:34:21 -0400, the following appeared
in talk.origins, posted by Wolffan <akwo...@zoho.com>:

>On 10 Oct 2018, satoshi wrote
>(in article<fa89a059-8b0e-4fcc...@googlegroups.com>):
>
>> On Wednesday, October 10, 2018 at 3:50:02 AM UTC-7, Wolffan wrote:
>> > On 09 Oct 2018, Bob Casanova wrote
>> > (in article<4qqprd9h5e5m3sv58...@4ax.com>):
>> >
>> > > On Mon, 8 Oct 2018 19:03:15 -0700 (PDT), the following
>> > > appeared in talk.origins, posted by satoshi
>> > > <travellin...@gmail.com>:
>> > >
>> > > > On Monday, October 8, 2018 at 7:50:02 PM UTC-6, satoshi wrote:
>> > > > > https://www.cell.com/current-biology/fulltext/S0960-9822(09)02073-9
>> > >
>> > > Yields:
>> > >
>> > > "The page or action you requested has resulted in an error"
>> > >
>> > > > evidence of a deity?
>> > >
>> > > Nope; deities wouldn't be expected to provide broken links.
>> >
>> > The full link ends in %3Dtrue. Satoshi can’t even quote links properly. If
>> > he’s a diety, he’s not up to the level of the turtle in Pratchett’s
>> > _Small Gods_. (No, not Great A’Tun. The small one.)
>>
>> works over here
>
>when you post it, it doesn’t work in most non-Google readers. That’s Yet
>Another known bug in Google’s system which will never be fixed. To be
>precise, posts from Google don’t wrap properly. This doesn’t matter
>(much) with ordinary text, but can and will break links. Especially very long
>links. Google users will not see a problem. Virtually everyone else will. You
>can’t quote links properly because you use Google Groups.

Yeah, I just noticed the "orphan"part of the link, the
"(09)02073-9" hanging off the end. I didn't know that was
one of Gurgle's "features", and I'll be on the lookout for
it in future. Thanks!

>> species tree. The ratio of non-synonymous to synonymous rates (?) measures

>> the strength of selection at a site, from 0 for strong purifying selection to
>> greater than 1 for positive selection. For sites that have evolved neutrally,

>> we found no relationship between ? and the support for convergence, whereas

>> sites under purifying selection showed a significant negative relationship

>> between ? and support for convergence. However, the ? for sites showing a

>> shift in functional constraint in the echolocating whales correlated

>> significantly with support for convergence (p ? 0.018), and, of 33 sites
>> predicted to fall into this category, 31 (94%) had ? values greater than one

>> (Figure 1C, Table S2). Finally, none of these relationships were significant

>> when sites were modelled as varying in ? within the bats showing convergence.

As usual, there is nothing there.