Ratite polyphyly
John Harshman
Harshman, J., E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K.
Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D.
Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W.
Steadman, S. J. Steppan, C. C. Witt, and T. Yuri. 2008. Phylogenomic
evidence for multiple losses of flight in ratite birds. Proc. Natl.
Acad. Sci. USA 105:13462-12467.
Abstract: Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are
large, flightless birds that have long fascinated biologists. Their
current distribution on isolated southern land masses is believed to
reflect the breakup of the paleocontinent of Gondwana. The prevailing
view is that ratites are monophyletic, with the flighted tinamous as
their sister group, suggesting a single loss of flight in the common
ancestry of ratites. However, phylogenetic analyses of 20 unlinked
nuclear genes reveal a genome-wide signal that unequivocally places
tinamous within ratites, making ratites polyphyletic and suggesting
multiple losses of flight. Phenomena that can mislead phylogenetic
analyses, including long branch attraction, base compositional bias,
discordance between gene trees and species trees, and sequence alignment
errors, have been eliminated as explanations for this result. The most
plausible hypothesis requires at least three losses of flight and
explains the many morphological and behavioral similarities among
ratites by parallel or convergent evolution. Finally, this phylogeny
demands fundamental reconsideration of proposals that relate ratite
evolution to continental drift.
Augray
<jharshman....@pacbell.net> wrote in
<VxSuk.21250$uE5...@flpi144.ffdc.sbc.com> :
>Some of you may be interested in this:
>
>Harshman, J., E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K.
>Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D.
>Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W.
>Steadman, S. J. Steppan, C. C. Witt, and T. Yuri. 2008. Phylogenomic
>evidence for multiple losses of flight in ratite birds. Proc. Natl.
>Acad. Sci. USA 105:13462-12467.
[snip abstract]
It doesn't seem to be available just yet.
John Harshman
online any time within the next week, and in print the week after that.
John Wilkins
PDF please?
--
John S. Wilkins, Philosophy, University of Queensland
scienceblogs.com/evolvingthoughts
But al be that he was a philosophre,
Yet hadde he but litel gold in cofre
William Morse
Interested but hardly surprised. Flightlessness AFAIK is known to have
evolved several times on islands, so it doesn't seem that hard for it to
have evolved independently among ratites (just to nitpick, kiwis are not
especially large). And convergent evolution is clearly capable of
evolving the types of similarities seen among the ratites, as evidenced
by the anteating mammals. The interesting point will be how the
reconstruction sheds light on the ratite (as a polyphyletic group)
evolution related to continental drift, and how this evidence accords
with that from mammal evolution.
Yours,
Bill Morse
John Harshman
What, you don't subscribe to PNAS? I'll send you one when I get one.
Greg G.
http://www.comics.com/comics/franknernest/archive/franknernest-20080902.html
http://tinyurl.com/65zogp
--
Greg G.
How many Smurfs could a Smurf-stomper stomp, if a Smurf-stomper could
stomp Smurfs?
Cory Albrecht
Me, too, please?
John Wilkins
My university has crippled the internet to the point that it pays me to
do everything I need to online at home. However, the only way I can get
PNAS or other PDFs is through the uni internet because it's all based on
IP numbers. I *can* get it through the uni, but it's so much easier to
type:
"PDF Please?"
John Harshman
Well, it's all about your convenience. As it happens, the paper has just
today been published on line. I'll send you one right now.
John Harshman
r norman
<jharshman....@pacbell.net> wrote:
John W, just ask me. I'll send you papers without all the guff. As
long as you continue denying macroevolution I'll even pull back (ever
so slightly) on the emergence business.
John Harshman
Cory Albrecht
> Cory Albrecht wrote:
>> John Wilkins wrote, On 01/09/08 11:26 PM:
>>
>> Me, too, please?
>>
> Yeah, OK.
Thank you muchly.
If I get the new job for which I have second interview tomorrow morning,
I promise that I shall stop pestering you for PDFs of Nature articles
that you write.
Mostly because I'll have to move to the university district so I won't
have to do a frigging 2 hour commute via public transit every morning. :-P
Then again, bigger salary might mean I can afford a subscription. Does
it make me a science geek if I say I've alway wanted my very own
subscription to nature? :-)
John Harshman
John Wilkins
Thanks. I will blog on it when my brain reboots from tutoring
undergraduates.
> >
> > John W, just ask me. I'll send you papers without all the guff. As
> > long as you continue denying macroevolution I'll even pull back (ever
> > so slightly) on the emergence business.
> >
> You don't understand. Guff is part of the service. Lagniappe, if you will.
I'm going to ignore these McGuffins.
TomS
<5Ckvk.18765$LG4....@nlpi065.nbdc.sbc.com>, John Harshman stated..."
doi:10.1073/pnas.0803242105
--
---Tom S.
"As scarce as truth is, the supply has always been in excess of the demand."
attributed to Josh Billings
Augray
<jharshman....@pacbell.net> wrote in
<VxSuk.21250$uE5...@flpi144.ffdc.sbc.com> :
Here's a whole series of dumb/trivial questions:
Did you look into the possibility of including the Moa and Elephant
Bird in your analysis? (Actually, a more realistic question might be:
for how many seconds did you consider including these taxa?)
The recurring term "the Root of the Avian Tree" makes one think that
you and your co-authors define Aves as the crown group (as opposed to
using "Neornithes" to label that clade). Was this to avoid semantic
confusion? Was there some debate as to what term to use?
Was the final sentence in the conclusion yours?
Are the Brauns related somehow?
And *finally*, there are no "affiliations" referenced by c or e.
Rupert Morrish
Trying to get you to work instead of read t.o.?
Rupert Morrish
[snip]
> Interested but hardly surprised. Flightlessness AFAIK is known to have
> evolved several times on islands, so it doesn't seem that hard for it to
> have evolved independently among ratites (just to nitpick, kiwis are not
> especially large).
Seems to me that a great spotted kiwi would be quite large for a volant
bird, although considerably larger birds certainly do fly.
John Wilkins
I can only read it as a devout wish that I stay at home...
>
> > However, the only way I can get
> > PNAS or other PDFs is through the uni internet because it's all based on
> > IP numbers. I *can* get it through the uni, but it's so much easier to
> > type:
> >
> > "PDF Please?"
John Harshman
There is actually DNA sequence for moas, three complete mt genomes. But
mt data aren't up to the job of sorting out ratite phylogeny. Getting
nuclear sequence out of moas is a difficult job that we didn't
contemplate at all, though I understand that Alan Cooper has succeeded.
Elephant birds are much more difficult to work with than moas, and
there's not even any mt sequence for them.
For what it's worth, if you add the mt sequences to the analysis, moas
come out as sister to tinamous, with no change to the rest of the tree.
That's four origins of flightlessness, if you're counting.
> The recurring term "the Root of the Avian Tree" makes one think that
> you and your co-authors define Aves as the crown group (as opposed to
> using "Neornithes" to label that clade). Was this to avoid semantic
> confusion? Was there some debate as to what term to use?
I personally favor the crown group definition, but "avian" is just a
word for "bird", and our paper took no position on Neornithes vs. Aves.
> Was the final sentence in the conclusion yours?
No. That was Ed's, if I recall.
> Are the Brauns related somehow?
Conceivably, though neither of them knows it. It's a pretty common name
in Germany.
> And *finally*, there are no "affiliations" referenced by c or e.
No affiliations, but there are footnotes. Look in the bottom right
corner of the page.
Cory Albrecht
> Cory Albrecht wrote:
>> Then again, bigger salary might mean I can afford a subscription. Does
>> it make me a science geek if I say I've alway wanted my very own
>> subscription to nature? :-)
> Science and/or PNAS.
So one of those would be a better a better investment for somebody like
me who's not even a duffer?
That reminds me, I should go back to working through Wilkins' basic
concepts list.
You know, it's so much easier for me to look good over in
alt.talk.creationism. Without people like you and the rest of the t.o.
intelligentsia (I'd say names, but I'm afraid I'd miss somebody
deserving of mention) around I can pretend that I'm one of the more
knowledgeable apes. :-)
Ernest Major
<coryal...@hotmail.com> writes
>John Harshman wrote, On 02/09/08 09:59 PM:
>> Cory Albrecht wrote:
>>> Then again, bigger salary might mean I can afford a subscription. Does
>>> it make me a science geek if I say I've alway wanted my very own
>>> subscription to nature? :-)
>
>> Science and/or PNAS.
>
>So one of those would be a better a better investment for somebody like
>me who's not even a duffer?
Some recent papers, and most older papers, on PNAS are available as free
downloads. So Science or Nature would be a better investment, on the
grounds that it gives you access to more additional papers.
Alternatively you could just go to www.doaj.org and follow the links.
>
>That reminds me, I should go back to working through Wilkins' basic
>concepts list.
>
>You know, it's so much easier for me to look good over in
>alt.talk.creationism. Without people like you and the rest of the t.o.
>intelligentsia (I'd say names, but I'm afraid I'd miss somebody
>deserving of mention) around I can pretend that I'm one of the more
>knowledgeable apes. :-)
>
--
Alias Ernest Major
John Harshman
> John Harshman wrote, On 02/09/08 09:59 PM:
>> Cory Albrecht wrote:
>>> Then again, bigger salary might mean I can afford a subscription. Does
>>> it make me a science geek if I say I've alway wanted my very own
>>> subscription to nature? :-)
>
>> Science and/or PNAS.
>
> So one of those would be a better a better investment for somebody like
> me who's not even a duffer?
Not necessarily. It's just that if you wanted to read either of my
recent papers, you'd need one of those journals. They're all quite
expensive, though I haven't priced any of them lately. Way more than I
want to spend.
> That reminds me, I should go back to working through Wilkins' basic
> concepts list.
>
> You know, it's so much easier for me to look good over in
> alt.talk.creationism. Without people like you and the rest of the t.o.
> intelligentsia (I'd say names, but I'm afraid I'd miss somebody
> deserving of mention) around I can pretend that I'm one of the more
> knowledgeable apes. :-)
I'm sure that's one reason why all of us, excepting the creationists of
course, are here.
Cory Albrecht
> Alternatively you could just go to www.doaj.org and follow the links.
Oh, cool! Thank you.
William Morse
> William Morse wrote:
> [snip]
>
>> Interested but hardly surprised. Flightlessness AFAIK is known to have
>> evolved several times on islands, so it doesn't seem that hard for it
>> to have evolved independently among ratites (just to nitpick, kiwis
>> are not especially large).
>
> Seems to me that a great spotted kiwi would be quite large for a volant
> bird, although considerably larger birds certainly do fly.
Good catch. I agree that great spotted kiwis qualify as large birds.
What I should have said is that _some_ kiwis are not especially large.
William Morse
> Cory Albrecht wrote:
>> John Harshman wrote, On 02/09/08 09:59 PM:
>>> Cory Albrecht wrote:
>>>> Then again, bigger salary might mean I can afford a subscription. Does
>>>> it make me a science geek if I say I've alway wanted my very own
>>>> subscription to nature? :-)
>>
>>> Science and/or PNAS.
>>
>> So one of those would be a better a better investment for somebody like
>> me who's not even a duffer?
>
> Not necessarily. It's just that if you wanted to read either of my
> recent papers, you'd need one of those journals. They're all quite
> expensive, though I haven't priced any of them lately. Way more than I
> want to spend.
>
challenged). A little less than we spend on basic cable TV, a good deal
less than we spend on broadband internet, and much less than we would
spend if we wanted full service cable TV. I pay more for the newspaper.
My only regret is that I so often fail to read it.
Yours,
Bill Morse
John Harshman
Ah, but I can't read basic cable at the library. Call me cheap.
r norman
The journal Science is, in my opinion, mostly valuable for the news
and commentary information, not to mention the job ads. The research
reports are so diversified in content and usually so abbreviated (a
requirement of the editorial board) and technical that they are
extremely difficult to read. My students, when required to present
reports on a current research paper, would tend to go for Science or
Nature papers because of their brevity but then discover that it is
actually easier to digest a longer paper in a regular journal than to
figure out just what a Science research note is about without lengthy
introduction and extended discussion sections.
In particular, if you want updates on evolution, that is such a
sparsely covered subject there that you will certainly not get your
money's worth. Science is available in many large city public
libraries, and is always available at college and university
libraries. A trip to one of these once or twice a month will be far
more informative and far less expensive.
John Wilkins
> Rupert Morrish wrote:
> > William Morse wrote:
> > [snip]
> >
> >> Interested but hardly surprised. Flightlessness AFAIK is known to have
> >> evolved several times on islands, so it doesn't seem that hard for it
> >> to have evolved independently among ratites (just to nitpick, kiwis
> >> are not especially large).
> >
> > Seems to me that a great spotted kiwi would be quite large for a volant
> > bird, although considerably larger birds certainly do fly.
I got a real scare the first time I saw one in New Zealand. It was
considerably larger than a turkey.
>
> Good catch. I agree that great spotted kiwis qualify as large birds.
> What I should have said is that _some_ kiwis are not especially large.
>
> >> And convergent evolution is clearly capable of evolving the types of
> >> similarities seen among the ratites, as evidenced by the anteating
> >> mammals. The interesting point will be how the reconstruction sheds
> >> light on the ratite (as a polyphyletic group) evolution related to
> >> continental drift, and how this evidence accords with that from mammal
> >> evolution.
> >>
> >> Yours,
> >>
> >> Bill Morse
> >>
> >
Tiny Bulcher
> William Morse <wdNOSP...@verizonOSPAM.net> wrote:
>
>> Rupert Morrish wrote:
>>> William Morse wrote:
>>> [snip]
>>>
>>>> Interested but hardly surprised. Flightlessness AFAIK is known to
>>>> have evolved several times on islands, so it doesn't seem that
>>>> hard for it to have evolved independently among ratites (just to
>>>> nitpick, kiwis are not especially large).
>>>
>>> Seems to me that a great spotted kiwi would be quite large for a
>>> volant bird, although considerably larger birds certainly do fly.
>
> I got a real scare the first time I saw one in New Zealand. It was
> considerably larger than a turkey.
If you saw one in the wild, I shall have to call you a jammy bastard and
hate you for ever. The number of times I eagerly focused my bins only
see yet another fucking chaffinch ... sometimes I hope there is a hell,
and that the fuckwits who introduced European birds to the world, and NZ
in particular, are in it.