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John Harshman
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 Posted: Fri Jun 27, 2008 7:09 am Post subject: New phylogeny of birds |
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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.
Montaņo. 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.) |
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metspitzer
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| Posted: Fri Jun 27, 2008 8:46 am Post subject: Re: New phylogeny of birds |
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On Thu, 26 Jun 2008 19:09:44 -0700, John Harshman
<jharshman.diespamdie@pacbell.net> wrote:
| Quote: |
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.
> |
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William Morse
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| Posted: Fri Jun 27, 2008 9:13 am Post subject: Re: New phylogeny of birds |
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John Harshman wrote:
| Quote: |
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.
Montaņo. 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.)
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 |
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John Harshman
Guest
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| Posted: Fri Jun 27, 2008 10:35 am Post subject: Re: New phylogeny of birds |
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William Morse wrote:
| Quote: |
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.
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. Montaņo. 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.)
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)?
|
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.
| Quote: |
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.
| Quote: |
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. |
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Ernest Major
Guest
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| Posted: Fri Jun 27, 2008 11:00 am Post subject: Re: New phylogeny of birds |
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In message <SNZ8k.125$%b.21@trndny02>, William Morse
<wdNOSPAmorse@verizonOSPAM.net> writes
| Quote: |
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.
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. Montaņo. 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.)
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.
|
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.
--
Alias Ernest Major |
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John Harshman
Guest
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| Posted: Sat Jun 28, 2008 5:45 am Post subject: Re: New phylogeny of birds |
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Bob Casanova wrote:
| Quote: |
On Thu, 26 Jun 2008 19:09:44 -0700, the following appeared
in talk.origins, posted by John Harshman
jharshman.diespamdie@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_?
|
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. |
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Bob Casanova
Guest
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| Posted: Mon Jun 30, 2008 5:49 am Post subject: Re: New phylogeny of birds |
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On Sat, 28 Jun 2008 15:21:58 -0400, the following appeared
in talk.origins, posted by Augray <augray@sympatico.ca>:
| Quote: |
On Sat, 28 Jun 2008 12:06:40 -0700, Bob Casanova <nospam@buzz.off
wrote in <lo2d64legepphrv4g9ei1v6j1tg53r1grs@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.
|
OK; that's what I thought. Thanks!
--
Bob C.
"Evidence confirming an observation is
evidence that the observation is wrong."
- McNameless |
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William Morse
Guest
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| Posted: Tue Jul 01, 2008 7:24 am Post subject: Re: New phylogeny of birds |
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Cory Albrecht wrote:
| Quote: |
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.
|
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 |
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Cory Albrecht
Guest
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| Posted: Wed Jul 02, 2008 11:01 am Post subject: Re: New phylogeny of birds |
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Augray wrote:
| Quote: |
On Tue, 01 Jul 2008 12:07:07 -0400, Cory Albrecht
coryalbrecht@hotmail.com> wrote in
aa1qj5xo3s.ln2@xanadu.fenris.cjb.net> :
John Harshman wrote:
Cory Albrecht wrote:
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.
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.
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. :-(
What? You're in Toronto, right?
|
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. |
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John Harshman
Guest
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| Posted: Sat Jul 05, 2008 9:12 am Post subject: Re: New phylogeny of birds |
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Cory Albrecht wrote:
| Quote: |
Augray wrote:
On Tue, 01 Jul 2008 12:07:07 -0400, Cory Albrecht
coryalbrecht@hotmail.com> wrote in
aa1qj5xo3s.ln2@xanadu.fenris.cjb.net> :
John Harshman wrote:
Cory Albrecht wrote:
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.
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.
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. 
What? You're in Toronto, right?
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.
I could send you a pdf, if you like. |
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