I have one hour to analyze in detail a new article about a bird. Can I do it? The answer, yes I did!

When the New Yorker publishes a piece about pure science, as it does in this article about a South American bird, I always suspect there’s a hidden agenda. That’s because the magazine isn’t really pro-science. As I quoted a respected colleague in an earlier post:

The New Yorker is fine with science that either serves a literary purpose (doctors’ portraits of interesting patients) or a political purpose (environmental writing with its implicit critique of modern technology and capitalism). But the subtext of most of its coverage (there are exceptions) is that scientists are just a self-interested tribe with their own narrative and no claim to finding the truth, and that science must concede the supremacy of literary culture when it comes to anything human, and never try to submit human affairs to quantification or consilience with biology. Because the magazine is undoubtedly sophisticated in its writing and editing they don’t flaunt their postmodernism or their literary-intellectual proprietariness, but once you notice it you can make sense of a lot of their material.

. . . Obviously there are exceptions – Atul Gawande is consistently superb – but as soon as you notice it, their guild war on behalf of cultural critics and literary intellectuals against scientists, technologists, and analytic scholars becomes apparent.

I think a lot of that is true, so what’s the reason we get a rather confusing article about the evolutionary history of a South American bird? Well, I don’t know the author’s brief or motivation (Ben Crair is a freelance writer), but judging from the title and the content, this is an article in the “Darwin-was-wrong” genre—in this case mentioning Darwin and the tree of life as being somehow overturned by the ancestry of the hoatzin bird. It isn’t, of course, but in trying to make his case the author produces a farrago of confusion that will not only befuddle the layperson, but also confused both Matthew and me. Click to read (it’s free):

Let’s meet the subject, first. The hoatzin (Opisthocomus hoazin) is one of the world’s weirdest birds in appearance and habits. Here’s its South American range:

Below: a video of what it looks like and the very weird climbing behavior of the chicks, who have retained ancestral claws on its wings (they lose them as adults). When predators attack, the clawed chicks, whose nests are built over water, simply drop into the drink, swim to shore, and use their claws to climb back to the nest.

Here’s a video that makes the climbing behavior more obvious:

The front claws, which made people think the bird is primitive, is not the only weird thing about it (and no, it’s not the only species with claws, just one that uses them for such a bizarre reason). This excerpt is from an article by Elizabeth Deatrick on Sketch, a feature of the Audubon Society.

Hoatzins are the only birds in the world that eat nothing but leaves, which, compared to seeds and fruit, aren’t very nutritious, and are hard to digest. So to accommodate this diet, the Hoatzin has evolved a multi-chambered digestive tract with lots of little “stomachs,” where the leaves can sit for a while and be digested by friendly bacteria. During the digestion process, the bacteria release methane that the bird then belches out, producing an olfactory aura that’s landed the Hoatzin a less-than-flattering nicknamed: the stinkbird. So much for fitting in.

It’s also called the “skunkbird.”

So we have some interesting facts. But what intrigues Crair is that when you try to place the hoatzin on the family tree of birds, it’s very hard. Its structure and morphology aren’t useful, because it diverged from other birds so long ago (it may occupy a long, old branch of its own). So people turn to DNA, which, if you use enough of it, should, via inspecting similarities and differences, tell you what species the hoatzin is most closely related to.  But because it’s so long diverged, that’s been problematic too. Various analyses, depending on which parts of the DNA you look at, have suggested that it’s most closely related to turacos, or maybe to cuckoos, or maybe to rails, or maybe, as this article suggests, to the ancestor of cranes and shorebirds. The problem is that the DNA is so long diverged from that of other bird species that, depending on what part of the DNA you look at and which bird species you use for comparison, you get different answers.

But this is not your typical bird, and we can usually place a bird near its closest relatives if we use a lot of DNA. That kind of analysis sometimes yields surprising results: one I like to mention is that peregrine falcons are more closely related to parrots than to other birds of prey (“raptors”) like hawks, ospreys, and eagles. That’s based on a lot of DNA, and that is the correct placement of falcons on the bird evolutionary tree.

Of course the hoatzkin kind of difficulty does not invalidate the idea of a “branching tree of life”, for we are using a phylogeny of genes (one branching scheme) to determine the phylogeny of species (or populations), which can be a different branching scheme. And if you look at some animals and some genes, you’ll find that the family tree of genes, whose own evolutionary history branches when they mutate, does not match the phylogeny of the species themselves: the evolutionary history of the organisms that contain the genes.

These discrepancies between the “tree” of some genes and of the organisms that contain them have several causes.

The first is what we call “incomplete lineage sorting”. Let me explain. Suppose that an ancestral species has two mutant forms of a gene or DNA segment. Let us call them A, and B. Let us then suppose that the ancestor branches in such a way that it produces species X, Y and Z, and the branch that eventually splits to produce Y and Z comes off separately from the branch that leads to X. Now assume that each of these ancestors has all the A and B mutants, but then species Z loses the A form via genetic drift, while species X and Y lose the B form.  This happens, for genes can change their frequencies by random processes not involving natural selection (“genetic drift”).

The history of the species themselves shows that Y and Z are more closely related to each other than either is to X, since they share a more recent common ancestor. But if you look at the one gene that had the two forms A and B, you’ll see that species X and Y are more closely related than either is to Z in terms of that gene, for they both have form A, while Z has form B. In other words, a tree for this gene shows an evolutionary history different from that of the tree for the species themselves. And if you look at another gene, which drifts independently, you may find that species X and Z are more closely related to each other than either is to species Y.

Since there are a gazillion genes to look at, it’s not unlikely that you would find such discrepancies. The genes can show three different evolutionary histories while there is only one for the species themselves, based on which populations evolved into new species. Gene trees and species trees can be discordant.

The way to solve this, of course, is to use lots and lots of genes, for together they should show a preponderance of phylogenies that match the tree of species themselves, since genes (with two exceptions mentioned below) stay within the borders of species. (The definition of “biological species” involves barriers to gene exchange.)

And, in general, that’s what we find. When we sequence whole genomes of species, like humans, chimps, and gorillas, we find what we knew from other data: humans and chimps (I lump bonobos with chimps) are more closely related to each other than either is to the gorilla, which is the more distant ancestor or “outgroup”. And all four of these species are yet more distantly related to the orangutan.  The more genes we use, the closer we get to reconstructing the true evolutionary history of the species themselves.  

Since the hoatzin is so long removed from other species of birds, it’s evolved nearly independently for nearly sixty million years, and so, depending on which species and which genes you look at, you could find that the hoatzin has genetic similarities that are discrepant if you use different comparison groups. There is no species closely enough related to the hoatzin to allow us to show a general similarity between its genes and that “sister” species. Ergo we don’t know the closest relative of the hoatzin. And we may never know.

I haven’t done a great job explaining this, but perhaps you’ll understand. Still, author Crair doesn’t try to explain this at all, referring in one sentence to incomplete lineage sorting as a “kind of genetic scrambling.” The key, though, is to understand that the evolutionary history of individual genes or segments of the genome is not the same thing as the evolutionary history of the populations of organisms that contained those genes—the species themselves.

The other factors that causes discrepancies between gene trees and species trees are hybridization, which can transfer genes between species that aren’t all that closely related, or horizontal gene transfer (“HGT”) via vectors like viruses. Both of these transfer bits of DNA into species that don’t reflect their evolutionary history, and trying to suss out species’ history from such wide gene exchange is confusing. That, too, could have been a problem with placing the hoatzin, but I doubt it.

Here’s one example from humans. Because of ancient hybridization between Homo sapiens and Neanderthals—I won’t get into the issue of whether they’re different species, though I don’t think they are—if you looked at the right gene in me, Jerry, and compared just that one gene to other gene forms in my species and to the Neanderthal genome, you might find that “for gene X Jerry is more closely related to Neanderthals than to his fellow H. sapiens.” And that would be true. Most of us probably carry a different set of gene bits from Neanderthals, and if you wanted to make a tree using just those bit, you’d find out that every one of us is more Neanderthal than sapiens. But of course this is only for the bits of genome that we’ve inherited after ancient hybridization between Neanderthals and our own ancestors. If you look at whole genome analysis, you’ll see that this small discrepancy washes out and you get the correct answer: all of us are more closely related to each other than to Neanderthals.

It is these issues that allow the author to conclude that the idea of Darwin’s branching evolutionary tree may be way overrated. Here’s how he states it:

The tree is so ingrained in evolutionary biology that scientists encourage “tree thinking.” By learning to think in terms of trees, students can avoid the common fallacy of reading evolution as a ladder in which simpler organisms become more complex, as in the famous image “The Ascent of Man,” which shows a knuckle-walking ape evolving into an upright human. For all its pedagogical value, however, the tree also embeds subtle assumptions about evolution. The tree tends to downplay the genetic variation within species, which can obscure the fact that common ancestors are actually diverse populations that can pass on different versions of a gene to different descendants. It tells a story of endless partition and diversification, with branches that diverge and never reticulate.

Now doesn’t that imply that the idea of evolutionary trees is dubious? In fact, the idea of trees for species, which is the way Darwin meant it to be construed, is doing fine; it just doesn’t always comport with trees for some genes within a species. Tree thinking is well and good and isn’t likely to go away.

And yet. . . and yet Crair admits this in one place:

The outlines of animal evolution still look a lot like a tree in many places, which is why scientists continue to spend so much time developing and debating different branches. But, if tree thinking taught biologists that everything is connected, genes are suggesting that the connections can run even deeper than a tree can capture. To gain a more complete picture—and to answer questions like how such an unusual mix of traits came together in the hoatzin—scientists may need to think outside the tree.

If Crair was careful to distinguish between species trees on the one hand and gene trees on the other, he wouldn’t have to create these apparent “discrepancies”. We’ve known about this issue for years; in fact, I wrote about it in my book Speciation with Allen Orr, and that came out in 2004. (See the Appendix.)

I don’t know if sloppy editing exacerbated the confusions in this article, or whether the author didn’t clarify them (I think he understood them). In the end, we’re simply left with these facts:

a. The hoatzin is a damn weird bird.
b. We haven’t been able to deduce its closest bird relatives.
c. There are evolutionary/genetic reasons for this difficulty.

But that wouldn’t make as click-worthy an article as the one that the New Yorker published—to wit:

a. The hoatzin is a damn weird bird.
b. We haven’t been able to deduce its closest bird relatives.
c. Therefore there must be something wrong with Darwin’s idea of a “tree of life”.

“a” and “b” are what you should remember, and also remember about why the hoatzin smells bad and the weird claws its chicks use to climb up trees.

Now it’s time to feed the ducks!