On Thursday, October 27, 2022 at 9:21:21 AM UTC-4, John Harshman wrote:
> On 10/27/22 5:55 AM, Peter Nyikos wrote:
> > On Wednesday, October 26, 2022 at 4:30:33 PM UTC-4, John Harshman wrote:
> >> On 10/26/22 12:57 PM, Peter Nyikos wrote:
> >>> On Friday, October 21, 2022 at 10:14:35 PM UTC-4, John Harshman wrote:
> >>>> On 10/21/22 1:36 PM, Peter Nyikos wrote:
> >
> >>>>>>>>> "Among modern birds, Parahesperornis is thought to be most closely related to the group that includes ducks and chickens (Galloanserae)."
> >>>>>>>>>
> >>>>>>>>> This made no sense to me. The modern birds (Neornithes) form a clade whose sister group
> >>>>>>>>> is not even the hesperornids: the sister group is represented by the late Cretaceous *Limenavis."
> >>>>>>>
> >>>>>>>> Makes no sense to me either.
> >>>>>>>
> >>>>>>> My fragmentary reading on this makes me suspect that this is another "rotation of tree"
> >>>>>>> misconception. Because the first split seems to be between Galloanserae and
> >>>>>>> all other birds, the smaller of the two clades is given star billing for closeness of relationship.
> >>>>>
> >>>>>> The first split is between Palaeognathae and all other birds. What you have is the second split.
> >>>>>
> >>>>> Based on molecular evidence and phylogenetic methods (MP? ML? other Bayesian?).
> >>>>> But there is plenty of room for convergence when splits go that far back in time,
> >>>>> and plenty of loss of information when we do not have molecular information
> >>>>> for lithornithids.
> >>>
> >>>> It's based on both molecular and morphological evidence,
> >>>
> >>> Combined? or separate? Could you provide a reference where only the morphological is used?
> >
> >> Separately, as a rule. Here's one:
> >>
https://repository.si.edu/handle/10088/21644
> >
> > Thanks, I'll look into it on the weekend.
I got a huge surprise: the authors' research supported the claim
that lithornids are outside the crown group! This would not only
give you an eighth group of birds that survived the K-P disaster,
but it would upend the generally accepted belief that only Neornithine
birds survived it.
> >
> >>>> and your complaints about molecular phylogenetics are not well-informed.
> >>>
> >>> You are trying to read my mind as to how well informed I am. I am not
> >>> giving all my information by any means.
> >
> >> Can we agree that I am likely to be better informed on this subject than
> >> you are? After all, I've published on this very subject:
> >>
> >> Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K.,
> >> Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D.,
> >> Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan
> >> S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of
> >> flight in ratite birds. Proceedings of the National Academy of Sciences
> >> 2008; 105:13462-12467.
> >
> > Research and scholarship are utterly different talents. Isn't that obvious to you?
> It isn't. I think they're both necessary components of any scientific
> paper.
You were comparing yourself to me, so talk about papers misses the point.
Isaak Asimov was the scientific scholar *par excellence*; IMHO his prodigious
output of expository papers [later anthologized] ranging over all the sciences
was more impressive than the science fiction for which he is better known.
On the other hand, his research record was below par even for a place
like Boston University School of Medicine:
"In December 1957, Asimov was dismissed from his teaching post, with effect from June 30, 1958, because he had stopped doing research. After a struggle which lasted for two years, he kept his title,[57] he gave the opening lecture each year for a biochemistry class,[58] and on October 18, 1979, the university honored his writing by promoting him to full professor of biochemistry.[59]"
In contrast, although Stephen Jay Gould was also an excellent scholar and expositor,
he wrote on less diverse areas of science, but he also had some major research accomplishments.
> And I think that paper is very good evidence that paleognaths are
> monophyletic.
I forget--does it make tinamous basal?
> >>>> I assure you that this particular split is exceedingly well supported and can't
> >>>> be accounted for by convergence.
> >>>
> >>> That last clause needs support. For one thing, it depends on what kind of neognaths
> >>> were included in the analysis, and the ratio of ratites to tinamous. We'd need a
> >>> non-volant large neognath to balance against each large ratite, and a small
> >>> non-volant neognath to balance against each kiwi. Also to be fair, all extant
> >>> volant neognaths need to be as weak fliers as tinamous used.
> >
> >> Why is "non-volant" relevant to molecular data? Why is size relevant to
> >> molecular data?
I let this slide at first, but your skepticism here is highly counter-intuitive.
Being active flyers promotes many alleles at the expense of others no matter
how near or far two groups of birds are from each other phylogenetically.
The same is true of size: remember Haldane's classic, "On Being the Right Size"?
> > Why switch to molecular studies? You cannot reasonably evaluate convergence
> > vs. synapomorphy while ignoring the fossil record. Isn't that obvious to you?
> We are discussing whether paleognaths are a monophyletic sister group to
> neognaths or are a polyphyletic assemblage united by convergence only.
> That's not a question of character evolution but of tree shape.
Aren't you confusing cause and effect? Whether two characters are
considered to be "the same" or only convergent is an integral part
of setting up the matrix, which in turn determines the tree, no?
A related phenomenon: the frame shift hypothesis causes cladists
to score the 2-3-4 arrangement of birds to be "the same"
as the 1-2-3 arrangement of theropods, in setting up the matrix.
> In the latter case, however, convergence is an inevitable consequence, while in
> the former, it's still possible but less likely.
Again putting the cart before the horse, ISTM.
>
> And analysis of living taxa only is not useless, though fossils can
> certainly help. Still, if the claim is that the paleognathous palate is
> convergently derived as a consequence of flightlessness,
Who would make such a claim, with tinamous in the background?
Only someone ignorant of them, it seems from what you say next:
> > it's difficult to explain why tinamous have it, even without consideration of Lithornis.
The only claim I made was that some researchers believe the paleognathous
palate of extant birds to be the result of neoteny, to which flightlessnes is
of questionable relevance.
> >>> As for lithornis used, a fossil neognath that is used needs to have approximately
> >>> the same number of characters preserved.
> >>>
> >>> And it's cheating to list penguins as non-volant: they "fly" thru the water with
> >>> their wings as almost their only source of propulsion.
> >
> >> It seems a pointless exercise regardless of whether penguins are excluded.
> >
> > Unless it is done, we will never know whether one or more neognaths
> > would be transferred to the palaeognath clade by it, with convergence
> > overruling synapomorphy in those cases.
Or vice versa, a paleognath being transferred to the neognath clade.
The talk in your reply shifted to molecular analyses, so I'd like to postpone
replying to that part until Friday.
Peter Nyikos
Professor, Dept. of Mathematics
University of So. Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos