As a follow-on to Andy's comments, DNA-DNA hybridization isn't a
comparison of every gene within the genome. A comparison of the
complete avian genome would require a similar effort as the Human
Genome Project for EACH SPECIES compared. Clearly, this is outside
the range of feasibility at present. Perhaps someday it will be
reasonable to make such a comparison but it will still be very
expensive.

Bob Beason

>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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