More on bird taxonomy; this is pretty long, so delete if not interested...

Steve brings up the point, quoted below, that many of the results cited
in this Science paper are quite different from the Sibley and Alquist
tome from 1990.  This is certainly true, and there are several reasons
for this:

1) Sibley and Alquist used the DNA-DNA hybridization method.  This
whole-genome approach is now mostly discredited, and many of its results
have been discarded, particularly in the realm of bird taxonomy.  There
are several problems with this method including the way that they
incompletely compared all of the birds that they sampled.  There are
also problems in that differences among birds are not additive - the
difference between a chickadee and a nuthatch versus a nuthatch and a
creeper does not tell you what the difference between a chickadee and a
creeper will be.  And hybridizing a chickadee genome in the lab to a
warbler might give you a different DNA-similarity value than hybridizing
a warbler to that same chickadee.  E-mail me if you want more
information on this, as this gets pretty esoteric really quickly...

2) Resolving how the major groups of birds are related to each other is
a persistent problem because the Neoaves (that is, all birds except for
ratites, tinamous, chickenlike birds, and ducks and their relatives)
seem to have diversified very quickly.  This means that a lot of the
current taxonomic Orders of birds first appeared around the same time,
so there was not much time for DNA differences among those groups to
accumulate, and there has been a lot of time for those DNA differences
to be wiped out by more recent evolutionary changes.

The Hackett et al. paper is very important, and it confirms some
important associations (like grebes and flamingos as close relatives, as
well as Kagu and Sunbittern as close relatives), but it is not the final
word on how all birds are related to each other.  They point this out in
their paper; oddballs like Hoatzin are still difficult to pin down.

As scientists collect more and more genetic data, they are finding out
that each gene may be biased in certain ways in certain birds, so no one
gene is adequate for these studies.  By studying 19 genes, they were
able to look out how and why each gene differed and look for consensus
among the genes (the genes occur on 15 different chromosomes and have
wildly differing functions in the birds).  Nineteen genes in one
phylogeny paper is a very large number - previous papers have used just
one to five, typically.

Parrots and falcons as close relatives has been suggested a few times,
and the notion that falcons are not closely related to other day-active
raptors has some momentum (data from other labs has suggested that
falcons and owls are perhaps more closely related).  The truly shocking
result is that the closest living relative to the songbirds is the
parrots.  This is a novel suggestion and one that a lot of people are
finding hard to accept.

How does this relate to Ohio birds?  Only peripherally, but this is the
sort of thing that makes birds hop around to different parts of the
field guide.  Results like this are responsible for moving the loons and
grebes out of the front of the field guides and replacing them with the
gallinaceous (grouse, quail, and such) and ducks, geese, and swans.
More changes will be coming; DNA, morphology, song, and other data are
being collected at a tremendous pace on all aspects of bird taxonomy.

If you are curious what changes are being considered right now for North
and Central America, you can track the proposals under consideration by
the American Ornithologists' Union (AOU):

http://www.aou.org/committees/nacc/proposals/pending.php3

The biggest change under consideration that will affect Ohio birds is a
tanager-cardinal rearrangement, moving Scarlet and Summer Tanagers into
the Cardinal family.  European Starling might become Common Starling.
Nelson's Sharp-tailed Sparrow may become Nelson's Sparrow.

Results of the Science paper by Hackett and others will certainly be
considered by AOU in the near future.

Andy

Steven A. Edinger wrote:
> Dear Fellow "Bird Nerds",
>
>        After reading this and the Re: to it, I grabbed a copy of
> "Phylogeny and
> Classification of Birds: A Study in Molecular Evolution" by Charles G.
> Sibley
> and Jon E. Ahlquist (1990).  The study used DNA-DNA hybridization to
> establish
> phylogenetic trees, which used DNA from the entire genome of the
> species, not
> just a portion of the DNA.  Jon Ahlquist was always very fond of saying,
> "Why
> would you just want to use a few genes when you can use the whole
> genome?"  His
> point being, "Knowing part of the story can be very misleading compared to
> knowing the entire story."  According to the figure included with the
> article
> Bill linked to this new study uses just 19 loci (19 genes).  I do not
> have the
> background needed to answer Jon's question:  Are the findings of this study
> using 19 loci more accurate then the findings of Sibley and Ahlquist using
> DNA-DNA hybridization of the whole genome?
>
>        In Figures 355 and 356 on pages 840 and 841 of Sibley and
> Ahlquist the Parrots
> are "on page 840", as significant distance from the Falcons, Hawks and
> Eagles,
> which are clustered together, "on page 841".  Before there were DNA
> analyses
> there were analyses using the characters of organisms (mostly morphological
> structures) and cladistic methods to evaluate phylogenetic relationships
> based
> on shared, derived characteristics.  To my knowledge none of the
> phylogenetic
> studies based on shared derived characteristics placed Parrots and Falcons
> close together, saying they are closely related.  I know the Sibley and
> Ahlquist findings for the most part confirmed the cladistic analyses that
> preceded them, and that some of the "controversial" finding they had,
> such as
> the idea that New World Vultures are related to Storks, had been
> proposed by
> other before Sibley and Ahlquist, based on analyses of morphological
> characteristics of the two groups.  What also came before DNA studies were
> proteins studies, using the structure of the proteins (a direct product
> of the
> DNA) to study relatedness.  Again, I never heard of a protein study
> suggesting
> a close evolutionary relationship between Parrots and Falcons, and that
> Falcons
> are not clustered with Hawks and Eagles.
>
>        One might ask, "Why should you expect the morphology and the DNA
> to tell the
> same or very nearly the same story?"  Well, the morphology of the
> organisms is
> based on the proteins that are produced in the organism, including (perhaps
> especially!) the regulatory proteins that stimulate, inhibit and time the
> developmental changes in the organism.  Those regulatory proteins attach
> to DNA
> to stimulate (or inhibit) the gene's production of proteins.  The
> structure and
> function of the proteins depends on the DNA they are produced from.
> What these
> results seem to suggest, in part, is that very similar DNA would produce
> very
> similar proteins and that these very similar proteins would then produce
> birds
> with radically different morphologies.  There is something about that
> scenario
> that just plain doesn't make sense!  Another implicit implication is that
> somebody is horribly wrong; Either "you" with the new results or "them"
> with
> the old results.  It is not that often that different data for the same
> study
> subject disagree this sharply!
>
> Best wishes and good birding!
>
> Steve Edinger
>

--
Andy Jones, Ph.D.
William A. and Nancy R. Klamm Endowed Chair of Ornithology
and Head of Department of Ornithology
Cleveland Museum of Natural History
1 Wade Oval Drive, University Circle
Cleveland, OH 44106
http://www.cmnh.org/site/researchandcollections_Ornithology.aspx

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