New phylogeny of birds

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John Harshman

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Jun 26, 2008, 10:09:44 PM6/26/08
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This has just been published (it's been up on the Science web site for
the past hour or two, if you have access):

Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M.
J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J.
Huddleston, B. D. Marks, K. J. Miglia, W. A. Moore, F. H. Sheldon, D. W.
Steadman, C. C. Witt, and T. Yuri. 2008. A phylogenomic study of birds
reveals their evolutionary history. Science 320:1763-1768.

Which has already been announced in another thread, but I would like to
correct a few misapprehensions that have already become common in the
press. (Yes, I'm a media whore, and I've been googling ever since the
paper was published.)

1. It's been stated as a surprising discovery of ours that grebes and
flamingos are closest relatives. Weird as it is, this result was
discovered several years ago. We merely confirm it in case there were
still doubters. The real credit goes to Marcel van Tuinen, in van
Tuinen, M., D. B. Butvill, J. A. W. Kirsch, and S. B. Hedges. 2001.
Convergence and divergence in the evolution of aquatic birds. Proc. R.
Soc. Lond. B 268? 269?:1345-1350.

2. Similarly, some reports have claimed that it's a big surprise that a
couple of weird tropical birds, kagu and sunbittern, are related. This
too has been around for years, and was most convincingly shown by Peter
Houde, in Houde, P., A. Cooper, E. Leslie, A. E. Strand, and G. A.
Montaño. 1997. Phylogeny and evolution of 12S rDNA in Gruiformes (Aves).
Pages 121-158 in Avian molecular evolution and systematics (D. P.
Mindell, ed.). Academic Press, San Diego; though Joel Cracraft had come
up with it 20 years earlier.

3. Finally, it's been claimed that our phylogeny shows that tinamous,
flying relatives of the flightless ratites, must have gained flight
independently of other birds. It's much simpler to suppose that various
groups of ratites lost flight independently, a much less shocking
conclusion. (By the way, we have a paper coming out next month in PNAS
that will look into this in detail.)

metspitzer

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Jun 26, 2008, 11:46:25 PM6/26/08
to
On Thu, 26 Jun 2008 19:09:44 -0700, John Harshman
<jharshman....@pacbell.net> wrote:

>
>Which has already been announced in another thread, but I would like to
>correct a few misapprehensions that have already become common in the
>press. (Yes, I'm a media whore, and I've been googling ever since the
>paper was published.)

You should try using Google alerts. Google alerts email you daily of
any search topics you enter. Pretty handy.
>

William Morse

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Jun 27, 2008, 12:13:38 AM6/27/08
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Independent loss of flight would seem to be the default explanation,
given the frequency of its occurrence in island species. Is there a
possibility of tinamous regaining flight (as opposed to separately
evolving it)? My recollection is that regaining of a lost ability, while
extraordinarily rare, had been found among the insects, although I have
forgotten the details. You probably discuss this in your paper, so
perhaps I should just wait for it.

Yours,

Bill Morse

John Harshman

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Jun 27, 2008, 1:35:01 AM6/27/08
to

That would be the second most probable hypothesis. Andrzej Elzanowski
claims (though not yet in print) that he can see a number of tinamou
characters that suggest a regain of flight.

> My recollection is that regaining of a lost ability, while
> extraordinarily rare, had been found among the insects, although I have
> forgotten the details.

"Found" is perhaps too strong. It's been claimed, in stick insects. This
is the reference you're thinking of: Whiting, M. F., S. Bradler, and T.
Maxwell. 2003. Loss and recovery of wings in stick insects. Nature
421:264-267.

> You probably discuss this in your paper, so
> perhaps I should just wait for it.

Actually, we don't discuss that particular question at length. We just
say more or less what you do: there are hundreds of known losses of
flight in birds, and so far no known regainings of flight, suggesting
that the odds are with multiple losses. But Andrzej hasn't published
yet, so we couldn't see what he had to say.

Ernest Major

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Jun 27, 2008, 5:04:35 AM6/27/08
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In message <SNZ8k.125$%b.21@trndny02>, William Morse
<wdNOSP...@verizonOSPAM.net> writes

There was a paper which claimed that the most parsimonious explanation
of the distribution of flight among, IIRC, stick insects, had flight
regained several times. However, it assumed that gain and lose of flight
are equally probable events; remove that dubious assumption, and the
case for some lineages regaining flight is unconvincing.
>
>Yours,
>
>Bill Morse
>

--
Alias Ernest Major

Augray

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Jun 27, 2008, 8:31:10 AM6/27/08
to
On Thu, 26 Jun 2008 19:09:44 -0700, John Harshman
<jharshman....@pacbell.net> wrote in
<JZX8k.9916$xZ....@nlpi070.nbdc.sbc.com> :

>This has just been published (it's been up on the Science web site for
>the past hour or two, if you have access):
>
>Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M.
>J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J.
>Huddleston, B. D. Marks, K. J. Miglia, W. A. Moore, F. H. Sheldon, D. W.
>Steadman, C. C. Witt, and T. Yuri. 2008. A phylogenomic study of birds
>reveals their evolutionary history. Science 320:1763-1768.

Interestingly, there doesn't seem to be strong support for Metaves or
Coronaves.

John Harshman

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Jun 27, 2008, 10:53:43 AM6/27/08
to
Yes, and what support there is comes from the same gene used by Fain &
Houde. So 18 more loci have added nothing to that story. Still, there's
no real contradiction either. As so often, we need more data.

William Morse

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Jun 27, 2008, 6:32:42 PM6/27/08
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Thanks for the reference. For some reason I had been thinking
dragonflies and so wasn't having any luck with a quick search.

Yours,

Bill Morse

Bob Casanova

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Jun 27, 2008, 7:22:16 PM6/27/08
to
On Thu, 26 Jun 2008 19:09:44 -0700, the following appeared
in talk.origins, posted by John Harshman
<jharshman....@pacbell.net>:

<snip>

>3. Finally, it's been claimed that our phylogeny shows that tinamous,
>flying relatives of the flightless ratites, must have gained flight
>independently of other birds. It's much simpler to suppose that various
>groups of ratites lost flight independently, a much less shocking
>conclusion. (By the way, we have a paper coming out next month in PNAS
>that will look into this in detail.)

John, I'm a bit confused about this. Aren't all modern
birds, flying or flightless, supposedly descended from
flying ancestors, meaning that all have wings, whether
functional or atrophied? If so, wouldn't it be relatively
simple for flightless birds, which already have wings, to
have those wings selected for increased usability in a
changed environment, as happened to the finches' beaks in
(strangely enough) _The Beak of the Finch_?
--

Bob C.

"Evidence confirming an observation is
evidence that the observation is wrong."
- McNameless

John Harshman

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Jun 27, 2008, 8:45:02 PM6/27/08
to

I wouldn't think so, actually. The wings of flightless birds don't
function as wings. They have no flight feathers. There's really a lot
such a bird would have to reinvent. I don't say it couldn't happen, but
I don't think it's the way to bet either.

Bob Casanova

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Jun 28, 2008, 3:06:40 PM6/28/08
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On Fri, 27 Jun 2008 17:45:02 -0700, the following appeared

OK, that makes sense (and I thought that most flightless
birds *did* have flight feathers, even if reduced in size;
if that's incorrect it's fairly strong evidence for your
position). Was I correct that all birds are descended from
flying birds so far as we know?

Augray

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Jun 28, 2008, 3:21:58 PM6/28/08
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On Sat, 28 Jun 2008 12:06:40 -0700, Bob Casanova <nos...@buzz.off>
wrote in <lo2d64legepphrv4g...@4ax.com> :

[big snip]

>Was I correct that all birds are descended from
>flying birds so far as we know?

Yes, although early in the last century not everyone believed that to
be the case.

John Vreeland

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Jun 29, 2008, 11:34:50 AM6/29/08
to
On Thu, 26 Jun 2008 19:09:44 -0700, John Harshman
<jharshman....@pacbell.net> wrote:

>This has just been published (it's been up on the Science web site for
>the past hour or two, if you have access):
>
>

"New phylogenies? Feh! You're just rearranging the deck chairs on
the Titanic."

Sorry. Couldn't resist.
Three creation scientists can have an intelligent conversation, if two of them are sock puppets.
---John Vreeland
__

Bob Casanova

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Jun 29, 2008, 8:49:00 PM6/29/08
to
On Sat, 28 Jun 2008 15:21:58 -0400, the following appeared
in talk.origins, posted by Augray <aug...@sympatico.ca>:

OK; that's what I thought. Thanks!

Cory Albrecht

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Jun 30, 2008, 4:53:30 PM6/30/08
to
John Harshman wrote:
> This has just been published (it's been up on the Science web site for
> the past hour or two, if you have access):
>
> Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M.
> J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J.
> Huddleston, B. D. Marks, K. J. Miglia, W. A. Moore, F. H. Sheldon, D. W.
> Steadman, C. C. Witt, and T. Yuri. 2008. A phylogenomic study of birds
> reveals their evolutionary history. Science 320:1763-1768.

It's a shame that publications like Science and Nature are so freaking
expensive.

Wouldn't they make more money for the publishers is they were cheap
enough so that mere science-philes like myself could afford them. I
think that would dramatically increase the number of subscribers.

John Harshman

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Jun 30, 2008, 5:29:58 PM6/30/08
to

Doesn't your local library subscribe? Where I live (San Jose), I could
get a PDF just by going to the main city/university (they're combined)
library. I suspect that a lot more journals are going to go to open
content eventually, but neither should you hold your breath.

Bob Casanova

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Jun 30, 2008, 5:40:52 PM6/30/08
to
On Mon, 30 Jun 2008 16:53:30 -0400, the following appeared
in talk.origins, posted by Cory Albrecht
<coryal...@hotmail.com>:

I believe that's what general-circulation science magazines
like Scientific American are supposed to be for; Science and
Nature are intended for professionals. (IMHO, and YMMV)

William Morse

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Jun 30, 2008, 10:24:20 PM6/30/08
to

Expensive compared to what? My subscription to Science cost me $144 this
year. That's about three months of cable TV if we actually had a normal
subscription rather than the minimum.

Yours,

Bill Morse

Gene Poole

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Jul 1, 2008, 10:02:08 AM7/1/08
to


_Science_ is fairly inexpensive for full-time students. When I went
from full-time to part-time and let my subscription lapse, they called
to ask why. I told them I was only part-time now and couldn't afford
the "Professional" rate, but they pretty much told me they'd look the
other way if I re-subscribed.

They have an online-only subscription too that I believe is not too
expensive (<$100/yr). I find that I don't do too much with the paper
issues but stack them in my closet. I should probably switch to the
online-only version in keeping with "green" sensibilities.

Cory Albrecht

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Jul 1, 2008, 12:07:07 PM7/1/08
to

No. None of the public libraries in my region get proper peer-reviewed
journals of the likes of Science, Nature, etc... The two local
universities only have Science and Nature in pieces with many issues not
showing up in the online catalogs. :-(

Cory Albrecht

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Jul 1, 2008, 12:20:13 PM7/1/08
to

Scientific American Digital, for example, is US$40 for an entire year.
In print it is US$25. To get Science in print form here in Canada it is
US$211, for digital it is US$103.

Even if I bought SciAm from the newsstand every month, I doubt I;d be
spending $211 on it.

Cory Albrecht

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Jul 1, 2008, 12:10:26 PM7/1/08
to

And they could still keep up the high standards of submission and
editorial review even with them being accessible/affordable to us
plebes. Would the increased revenue from a larger circulation not offset
the deceased revenue of a lower subscription price?

Augray

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Jul 1, 2008, 3:45:48 PM7/1/08
to
On Tue, 01 Jul 2008 12:07:07 -0400, Cory Albrecht
<coryal...@hotmail.com> wrote in
<aa1qj5x...@xanadu.fenris.cjb.net> :

What? You're in Toronto, right?

Bob Casanova

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Jul 1, 2008, 7:11:10 PM7/1/08
to
On Tue, 01 Jul 2008 12:10:26 -0400, the following appeared

Possibly, although I'd question whether there are enough
laymen with enough interest in the details, rather than a
good overview and synopses, to make up the difference. I'd
have to assume that they'll do whatever is necessary
(without degrading the content) to maximize income.

Cory Albrecht

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Jul 2, 2008, 2:33:24 AM7/2/08
to

Cambridge, actually. The combined online catalog for Laurier, UWloo and
UGuelph doesn't show that issue of Science with the new bird phylogenies.

Also, It's a 2hr ride on public transit for me to get from the south end
of Cambridge, where I live, to the university district in Waterloo. I
need more than a "maybe it will be there" before I go hop on a bus just
to read & photocopy an article.

Augray

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Jul 2, 2008, 5:02:16 PM7/2/08
to
On Wed, 02 Jul 2008 02:33:24 -0400, Cory Albrecht
<coryal...@hotmail.com> wrote in
<l2krj5x...@xanadu.fenris.cjb.net> :

Okay. Somewhere, somehow, I got the impression that you were in
Toronto. Obviously, that was wrong.


>The combined online catalog for Laurier, UWloo and
>UGuelph doesn't show that issue of Science with the new bird phylogenies.
>
>Also, It's a 2hr ride on public transit for me to get from the south end
>of Cambridge, where I live, to the university district in Waterloo. I
>need more than a "maybe it will be there" before I go hop on a bus just
>to read & photocopy an article.

I can't argue that.

John Harshman

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Jul 5, 2008, 12:12:39 AM7/5/08
to
I could send you a pdf, if you like.

Cory Albrecht

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Jul 5, 2008, 10:10:36 AM7/5/08
to
John Harshman wrote, On 05/07/08 12:12 AM:

> Cory Albrecht wrote:
> I could send you a pdf, if you like.

Please, I would greatly appreciate it.

The Last Conformist

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Jul 7, 2008, 5:29:05 PM7/7/08
to
On Jul 5, 6:12 am, John Harshman <jharshman.diespam...@pacbell.net>
wrote:

> Cory Albrecht wrote:
> > Augray wrote:
> >> On Tue, 01 Jul 2008 12:07:07 -0400, Cory Albrecht
> >> <coryalbre...@hotmail.com> wrote in
> >> <aa1qj5xo3s....@xanadu.fenris.cjb.net> :

I'd love to have one too.

Augray

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Jul 29, 2008, 11:07:22 AM7/29/08
to
On Thu, 26 Jun 2008 19:09:44 -0700, John Harshman
<jharshman....@pacbell.net> wrote in
<JZX8k.9916$xZ....@nlpi070.nbdc.sbc.com> :

>This has just been published (it's been up on the Science web site for
>the past hour or two, if you have access):
>
>Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M.
>J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J.
>Huddleston, B. D. Marks, K. J. Miglia, W. A. Moore, F. H. Sheldon, D. W.
>Steadman, C. C. Witt, and T. Yuri. 2008. A phylogenomic study of birds
>reveals their evolutionary history. Science 320:1763-1768.
>

>Which has already been announced in another thread, but I would like to
>correct a few misapprehensions that have already become common in the
>press. (Yes, I'm a media whore, and I've been googling ever since the
>paper was published.)
>
>1. It's been stated as a surprising discovery of ours that grebes and
>flamingos are closest relatives. Weird as it is, this result was
>discovered several years ago. We merely confirm it in case there were
>still doubters. The real credit goes to Marcel van Tuinen, in van
>Tuinen, M., D. B. Butvill, J. A. W. Kirsch, and S. B. Hedges. 2001.
>Convergence and divergence in the evolution of aquatic birds. Proc. R.
>Soc. Lond. B 268? 269?:1345-1350.
>
>2. Similarly, some reports have claimed that it's a big surprise that a
>couple of weird tropical birds, kagu and sunbittern, are related. This
>too has been around for years, and was most convincingly shown by Peter
>Houde, in Houde, P., A. Cooper, E. Leslie, A. E. Strand, and G. A.
>Montaño. 1997. Phylogeny and evolution of 12S rDNA in Gruiformes (Aves).
>Pages 121-158 in Avian molecular evolution and systematics (D. P.
>Mindell, ed.). Academic Press, San Diego; though Joel Cracraft had come
>up with it 20 years earlier.
>

>3. Finally, it's been claimed that our phylogeny shows that tinamous,
>flying relatives of the flightless ratites, must have gained flight
>independently of other birds. It's much simpler to suppose that various
>groups of ratites lost flight independently, a much less shocking
>conclusion. (By the way, we have a paper coming out next month in PNAS
>that will look into this in detail.)

So, is there any way to estimate how many lineages survived the KT
extinction from this paper?

John Harshman

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Jul 29, 2008, 11:23:09 AM7/29/08
to
Augray wrote:
> On Thu, 26 Jun 2008 19:09:44 -0700, John Harshman
> <jharshman....@pacbell.net> wrote in
> <JZX8k.9916$xZ....@nlpi070.nbdc.sbc.com> :
>
>> This has just been published (it's been up on the Science web site for
>> the past hour or two, if you have access):
>>
>> Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M.
>> J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J.
>> Huddleston, B. D. Marks, K. J. Miglia, W. A. Moore, F. H. Sheldon, D. W.
>> Steadman, C. C. Witt, and T. Yuri. 2008. A phylogenomic study of birds
>> reveals their evolutionary history. Science 320:1763-1768.

[snip]

> So, is there any way to estimate how many lineages survived the KT
> extinction from this paper?

Sure, if you take the tree and use fossil calibration points to turn it
into a measure of absolute time. This is not a simple process, and
different choices of calibration can give you quite different answers.
And we have not yet done such a thing. However, something of the sort
was done a while ago using a much smaller set of data, for which the
same caveats apply. Ericson, P. G. P., C. L. Anderson, T. Britton, A.
Elzanowski, U. S. Johansson, M. Källersjö, J. I. Ohlson, T. J. Parsons,
D. Zuccon, and G. Mayr. 2006. Diversification of Neoaves: Integration of
molecular sequence data and fossils. Biology Letters 2:543-547. I forget
the details, but a conservative estimate would be "quite a few".

Now if you believe in Cretaceous presbyornithids, there's a simpler
answer that doesn't require so much phylogenetic or temporal detail, and
that's "at least 8" (paleognaths, gastornithids, galliforms, anhimids,
anseranatids, presbyornithids, anatids, neoavians).

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