The Perfect Bird Family Tree…

… is certainly still in the future. But we have seen a step in that direction in a new paper, coming out this week in Science. This research applies intensive and extensive genomic analysis to the avian phylogenetic tree. The results are interesting.

ResearchBlogging.orgThis paper is summarized in a number of locations, most notably here on Living the Scientific Life. Here, I will summarize it only very briefly. However, there are two observations I would like to make about this paper and its apparent meaning. One has to do with the nature of science, and the other has to do with the nature of evolution in particular. I’ll argue that we can quantify (almost non-trivially) the number of times science is wrong. I’ll also argue that Stephen Jay Gould was wrong (not totally, but not trivially) about one of his most important assertions (other than his musings about the myth of vaginal orgasms … we’ll talk about that another time).


The paper in question comes out of a project called the Early Bird Assembling the Tree-of_Life Research Project, based at the Field Museum in Chicago. The project is huge, with people assembled from all across the world, collecting piles of data and coming up with a new bird phylogeny.

Check out this description:

… we made more than 26,000 DNA-DNA comparisons among ca. 1700 bird species, representing all of the orders and 168 of the 171 families in Wetmore’s … classification. A new classification was proposed [based on this research] …

source

Those words are NOT about the present paper, but rather, were written by Charles G. Sibley describing the research he did with Alquist prior to 1986. Sibley and Alquist’s DNA bird phylogeny did everything the current paper proports to do, but earlier, and in the context of much less certainty about the relationships among the groups of birds. Sibly and Alquist’s studies were also among the first uses of DNA to build phylogenies of ANY large groups of species and served as the template for much of the work done on other groups through the 1980s and 1990s.

So what about the current paper?

For more than five years, the Early Bird Assembling the Tree-of-Life Research Project, centered at The Field Museum, has been examining DNA from all major living groups of birds. Thus far, scientists have built and analyzed a dataset of more than 32 kilobases of nuclear DNA sequences from 19 different locations on the DNA of each of 169 bird species. The results of this massive research, which is equivalent to a small genome project …

Comparatively, the earlier research (which was more than one paper, of course) seems more intensive and extensive. The work by Sibley and Alquist used ALL of the DNA (sort of … I’m glossing details here) as it was a hybridization rather than sequence comparison technique, and Sibley and Alquist used WAY more species.

So given the intensity of the earlier work, how can this later work actually contribute so much, and virtually re-write bird phylogeny?

Because hybridization techniques produce results that can be garbled … and you can’t really tell when they are garbled as well as you might want to …. for early branches of an ancient phylogeny. So, if you think about bird phylogeny as a book with lots of chapters, and the chapters have paragraphs and such, Sibley and Alquist got the data sorted out within each chapter very nicely, and put all the chapters together in a structure that was reasonable but subject to revision. The present study is the revision. The present study uses techniques that purport to allow resolution of these problem areas of the phylogeny. (Again, I oversimplify, but only a little.)

Certain aspects of the avian phylogeny were confirmed by the present study, but the reason everyone is going gaga over this work is the set of unexpected findings. Some of these have to do with wacky divergences. Hummingbirds

i-d8cc5ca8ab9b422c7078f58dc25e8eec-hummingbird.jpg

evolved from a group characterized by the nightjars

i-7932f888af9c67a36391ac56ed11d9d5-nightjar.jpg

(nighthawks, whip-poor-will, etc.)

That shows that evolution is amazing in how it can produce great diversity. As we knew. But what is more interesting is the new cases of convergence. For instance, Falcons and hawks are in separate groups and do not necessarily share a common ancestor that is hawk-like. Falcons are with the song birds and parrots while hawks are with the some of the owls and the hornbills.

What is the meaning of all of this? In some sense, it is too early to say. This is all very complicated. Think of a phylogeny as a set of hypotheses. A taxon with species defined as its members is a proposal that can be tested with new data or analysis. Well, many of the hypotheses regarding major taxa of birds are damaged by this analysis. Beautiful hypotheses are getting wiped out by complex genomic facts. And each of these hypotheses has an associated group of researchers working with it. Some will be delighted to find out this new information … it will confirm suspicions or clear up questions. Others will not like it. Some will play, some will fight. Either way, there will be dust, and the dust will take time to settle.

But for now, I’d like to propose two items for your consideration, as promised.

First, a way to think about science. Of N attempts to understand or describe a given system (in this case, the system is bird phylogeny) the number of incorrect attempts is either N or N-1, such that it is N until the description is stable. That should be obvious. But the second part of my assertion is never obvious: It is very difficult to tell the difference between the N state and the N-1 state.

I was at a major scientific meeting 20 some years ago when Sibley and Alquist’s research was really dawning on people. They gave a talk that was shortly thereafter embodied in a chapter of a publication on birds, the culmination of the research I cited above. It changed the way we think in a big way (about phylogenies) and in many many small ways (one per species, in a sense). The present paper does not overthrow Sibley and Alquist, but it does provide major and important revisions. The point is, Sibley and Alquist was the big kahuna of bird phylogeny. Sibley and Alquist figured it out. It was obvious that only minor fixing up would be needed.

Apparently not.

Are we at N-1? (Where N is the sum of all those major bird taxonomy/diversity/phylogeny moments from just before Darwin to more recent.) I’m betting not.

The second point I want to make is much more important and utterly contentious. Toss me to the dogs, if you want, but I’m going to say it:

Stephen Jay Gould stated, again and again (I’m sure I’ve seen him mutterting this on the Redline Subway on the way back from Red Sox games….) that if you re-ran the history of evolution, like re-playing a movie, the story would never be the same twice.

This non-sameness seems to be (but is not) critical to the non-teleology of evolution. But I think it is wrong.

I think that if you replayed the evolution movie again and again, starting with the Cambrian Explosion, you would get woodpeckers, humingbirds, and raptors again and again and again and again and again. You might not get birds every time, but you’d get these guilds. They may be in very different places on the phylogenetic tree, but these adaptive syndromes would be represented every time (and others, too, of course).

So it would not be like playing the same movie over and over again, but it would be like staging the same play again and again with different actors and different interpretations. But it would NOT be as different as different movies of the same genre again and again.

No, the history of life, played again and again, would be the same each time at a level somewhere between, say, Lethal Weapon (again and again) or Jaws (again and again) on one hand and multiple iterations of A Midsummer Night’s Dream on the other

Hackett, S.J., Kimball, R.T., Reddy, S., Bowie, R.C., Braun, E.L., Braun, M.J., Chojnowski, J.L., Cox, W.A., Han, K., Harshman, J., Huddleston, C.J., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Yuri, T. (2008). A Phylogenomic Study of Birds Reveals Their Evolutionary History. Science, 320(5884), 1763-1768. DOI: 10.1126/science.1157704

Comments

  1. #1 David Marjanovi?, OM
    June 27, 2008

    Sibley and A[h]lquist’s DNA bird phylogeny

    No, that was not a phylogeny. DNA-DNA hybridization is a phenetic method, not a phylogenetic one. It measures similarity instead of counting shared derived features; it doesn’t even try to tell shared retained features apart from shared derived features and doesn’t even try to distinguish shared ancestry from convergence.

    and virtually re-write bird phylogeny?

    It doesn’t. It confirms many revolutionary findings of molecular analyses published in 2004 and 2006. (This includes swifts & hummingbirds being inside the nightjars & goatsuckers & oilbirds, flamingos and grebes being sister-groups and far apart from storks/herons and loons and cranes/rails, falcons and hawks & eagles being far apart, and much more.) It’s just the first one with an impact factor over 3 or so.

    I think that if you replayed the evolution movie again and again, starting with the Cambrian Explosion, you would get woodpeckers, humingbirds, and raptors again and again and again and again and again. You might not get birds every time, but you’d get these guilds. They may be in very different places on the phylogenetic tree, but these adaptive syndromes would be represented every time (and others, too, of course).

    Even if so, they wouldn’t necessarily be birds, let alone Neornithes. Think of the hummingbirds: the Old World hummingbirds died out in the Oligocene, and since then we’ve had nocturnal hummingbird-sized moths in that niche.

    And I don’t see any connection between this point and the new paper. What have I missed?

  2. #2 Greg Laden
    June 27, 2008

    What have I missed?

    Uffda, Where do I begin?

    David, you are one of the smart people ruined by cladistics. I probably can’t fix that.

    A phylogeny is a tree-like structure modeling the evolutionary relationships among species or other taxonomic groups. There are many ways to do it, and Sibly and Alquist made phylogenies.

    A cladist is a person who addresses phylogeny through a very limited but useuful set of techniques, and who is often incapable of understanding complexity and ambiguity and would prefer that the rest of biology bend, however unnecessarily and uncomfortably, to the cladist’s dogma.

    On your point about virtually re-writing bird phjylogeny. Partly correct. I was originally going to segue into a critique of the hype that this new paper is getting because it is overblown. However, instead I decided to be nice and just made reference to the dust that will be flying. In fact, the phrase “virtually rewrite” does not have much meaning. I think I may go and make some adjustments to the text.

    Your response to my assertion regarding replaying history causes me to tell you to go read it again because I think you are telling me to say what I’m pretty sure I already said. But you are a pedant with a penchant for being vague, so there is probably something you are telling me that I’m not going to get or care too much about.

    The connection between the paper and the post? I can spell it out more clearly for you: Homoplasy should be rare if Gould is absolutely right. The more common it is, the sillier his assertion looks. An equally valid connection: I read something then I wrote something about it.

  3. #3 Rick MacPherson
    June 27, 2008

    greg…
    i’m not gonna toss you to the dogs on this one… i don’t know boo about bird phylogeny, but i am going to add some thoughts on how steve gould’s characterized…

    considering australia’s marsupial fauna alone, it’s easy to see evidence for your argument… in the absence of placental mammals, evolution filled ecological guilds with what was available… and it certainly plays out in marine reef communities where isolated atolls in the indo-pacific are little species factories, churning-out fascinating ecological players to fill available niches… but there’s the hard and soft version of contingency that steve sold… he was percolating various versions into his essays years before codifying it in “wonderful life”… if i’m reading the versions correctly, steve freely admits that there were limits to hardcore contingency and at some point along the history of life, oak trees, hippos, petunias, and homos sapiens were likely (if not inevitable)… get enough morphology and proteins already coded and certain trends play out over time…

    but i don’t think steve, in the very end, was even defending an empirical argument for contingency as a macroevolutionary process so much as he was defending his “view of life” heavily flavored by cultural and literary extrapolation… his entire epilog to “the structure of evolutionary theory” is nothing if not a final attempt to clarify this view… his analogy of a possible replay of life in a world where charles darwin was not born allows that natural selection and evolutionary theory would still develop and win acceptance in the scientific community…. his thought experiment of why should it matter if it were darwin, or wallace, or even great great great grandfather laden is more of an esthetic and philosophical point… his emotional rationale for why we care–the details, the sequence, the story–speaks more to the history and romance of science than the mechanics of evolutionary theory…

    i’d hate for steve’s legacy to be seen as some sort of lock-step, unyielding adherence to contingency at all costs…

    my own sense is i think what steve was really trying to accomplish with his “tape of life” metaphor was not so much hammer home the notion that our present is but one of many possible presents that COULD have happened… the important message i think he was trying to get across (at least in the story he told with the burgess shale fauna) was how could anyone standing on the shores of cambrian sea possibly PREDICT from the phyla scuttling about that we would end up with oak trees, hippos, petunias, and homos sapiens? if there’s anything the man muttered, it was that the history of life only makes sense in hindsight…

  4. #4 Greg Laden
    June 27, 2008

    Your last point is exactly right (well, the rest is too, but I want to focus on that) … It could be said that in retrospect, evolution is totally predictable but actually predicting into the future is somewhat more difficult….

    There is another part of this, tough, that I’ve alluded to above only parenthetically. The degree to which evolutionary ‘history’ is inevitable could put force behind any form of the teleological argument. Personally, I think that Gould over-emphasized contingency as non-predictability for that reason in his popular writings (which was most of his writings by count).

    Besides, I like giving him a hard time. I only knew him a little, interacted a few times, but I never once (over several years with the occasional chance) saw him give another human being credit for having a thought that he (gould) might learn from. For that level of rudeness, I chose to not sanctify him. There must have been some people he did not treat like intellectual dirt (maybe his students?). (I’m speaking here only in academic settings. In more social settings he was a party monkey, of course).

  5. #5 Rick MacPherson
    June 27, 2008

    fair enough, greg…
    i also didn’t mean to suggest sanctifying the man… he was a real prick at times…

    but i did also see him (in academic settings during graduate seminars) show some real hubris… with the late great jack sepkoski, with the late great robert nozick, with the not so late and not so great alan dershowitz, and with the amazing andy knoll…

  6. #6 Greg Laden
    June 27, 2008

    We will perhaps swap Gould-Dershowitz stories….. I’ve got only one but it is fun.

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