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 > >______________________________________________________________________ > >Ohio-birds mailing list, a service of the Ohio Ornithological Society. >Our thanks to Miami University for hosting this mailing list. >Additional discussions can be found in our forums, at >www.ohiobirds.org/forum/. > >You can join or leave the list, or change your options, at: >http://listserv.muohio.edu/scripts/wa.exe?LIST=OHIO-BIRDS >Send questions or comments about the list to: [log in to unmask] ______________________________________________________________________ Ohio-birds mailing list, a service of the Ohio Ornithological Society. Our thanks to Miami University for hosting this mailing list. 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