Convergence part 4: “an epic myth”

I promised in part one of this series that I would show why the argument that convergence is a problem for evolution is daft, and I haven’t really done that. What I’ve done so far is show that the argument includes a false premise, namely that evolutionary biologists have only recently become aware that convergence is widespread.

In parts onetwo, and three, I showed that some intelligent design proponents misrepresent the history of biological thought regarding convergence. They have created an alternate history in which biologists from Darwin to Dawkins were barely aware of convergent evolution, and have only in the last few decades been forced to confront it. Whether this is dishonesty or just bad scholarship, I can’t say, but it is a big, stinking pile of wrong.

But I haven’t really engaged their core argument, a fair paraphrase of which is that convergence, the appearance of similar phenotypes in distantly related species, is evidence against (or even falsifies) common descent. For example, Cornelius Hunter says convergence

…violates the evolutionary pattern. Regardless of adaptation versus constraint explanations, and any other mechanisms evolutionists can or will imagine, the basic fact remains: a fundamental evidence and prediction of evolution is falsified. —2017-05-25

[Read more…]

Convergence part 3: “the Darwinists’ lollapalooza”

In parts one and two, I showed that suggestions by some intelligent design advocates that evolutionary biologists have only recently become aware of widespread convergence are false. At least one ID proponent, though, has gone further, suggesting that convergence is a post hoc rationalization invented by ‘Darwinists’ to hide their dirty little secret that common descent is not supported by evidence.

Phylogenetic tree from The Origin of Species

Not the first tree of life. The one figure from The Origin of Species. By Charles Darwin [Public domain], via Wikimedia Commons.

Physicist Lee M. Spetner makes this argument in his book The Evolution Revolution. I don’t own The Evolution Revolution, but Casey Luskin has helpfully, and approvingly, quoted some critical passages:

Convergent evolution is the Darwinists’ lollapalooza. They made it up to keep their phylogenetic tree from falling apart, but they can’t say how convergence happens. — As quoted by Casey Luskin, 2014-10-19

[Read more…]

Convergence part 2: “exceptions to the rule”

In part 1, I argued that some advocates of intelligent design give a misleading picture of the history of evolutionary thought on the topic of convergence. To hear them tell it, convergence, or at least convergence as a widespread phenomenon is a recent discovery, unknown to Darwin and to the architects of the modern synthesis. For example, Günter Bechly says,

One of the most essential doctrines of Darwinian evolution, apart from universal common descent with modification, is the notion that complex similarities indicate homology and are ordered in a congruent nested pattern that facilitates the hierarchical classification of life. When this pattern is disrupted by incongruent evidence, such conflicting evidence is readily explained away as homoplasies with ad hoc explanations like underlying apomorphies (parallelisms), secondary reductions, evolutionary convergences, long branch attraction, and incomplete lineage sorting.

When I studied in the 1980s at the University of Tübingen, where the founder of phylogenetic systematics, Professor Willi Hennig, was teaching a first generation of cladists, we still all thought that such homoplasies are the exceptions to the rule, usually restricted to simple or poorly known characters. Since then the situation has profoundly changed. Homoplasy is now recognized as a ubiquitous phenomenon (e.g., eyes evolved 45 times independently, and bioluminiscence 27 times; hundreds of more examples can be found at Cambridge University’s “Map of Life” website).

I don’t know who gave Dr. Bechly the idea that homoplasies are rare, but I’m pretty sure it wasn’t Willi Hennig. Dr. Bechly was there, and I wasn’t, but I’m going to go out on a limb here anyway and say that Willi Hennig wasn’t even at the University of Tübingen in the 1980s. I can be fairly confident that this is the case, because Willi Hennig died in 1976.

[Read more…]

Convergence part 1: “quite unexpected”

A number of advocates of intelligent design have written variations on the theme that convergence is a problem for evolution. I aim to show why this argument is daft.

First of all, what is convergence? Definitions differ, and I’m not going to get into an extended discussion of the differences. A definition that will serve well enough is Anurag Agrawal’s, “the independent evolution of similar phenotypes.” A phenotype, and this will be important, can refer to a single trait, multiple traits, or the entire set of traits expressed by an organism. Green-eyed is a phenotype. A calico pattern of fur color is a phenotype. All of the traits that make up a particular cat are also a phenotype. A phenotype can describe a trait (or set of traits) of an individual or of a species, so just as being 5’10” tall is a phenotype, so is being bipedal.

Convergence typically refers to the latter kind of phenotype, those that characterize a species. So if, for example, seasonal changes in coat color have independently evolved in a bird, a lagomorph, a mustelid, and a canid, that’s an example of convergence of a single trait.

Zimova 2018 Fig 1

Figure 1 from Zimova et al. 2018. Seasonal coat colour species in their winter (top row) and summer (bottom row) coats. (A) Rock ptarmigan; (B) mountain hare; (C) stoat; (D) Arctic fox. None of these species share a common ancestor with seasonal coat polymorphism; they evolved it convergently. Photos by stock.adobe.com: Pilipenko D, Paul Carpenter, Stephan Morris, Diego Cottino; Mills lab research photo, and Seoyun Choi.

[Read more…]

This awkward condition

I’ve written several times about the process of inversion that occurs during the development of algae in the family Volvocaceae. Today I was going through a paper I’d read (and even written about) before, and I came across a turn of phrase I appreciated regarding inversion:

The fully cleaved embryo contains all of the cells of both types that will be present in an adult but it is inside out with respect to the adult configuration. This awkward condition is quickly corrected by a gastrulation-like inversion process.

The quote is from Benjamin Klein, Daniel Wibberg, and Armin Hallmann’s 2017 paper, “Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri.” Setting aside that animal gastrulation and Volvox inversion may not be as similar as they are often portrayed, I love the description of inside-out colonies as “awkward”. As if they just realized they left the house with their shirt half tucked in and inversion is their way of saying “Excuse me while I get myself sorted out here.”

[Read more…]

Are the multicellular volvocine algae monophyletic?

One of the strengths of the volvocine algae as a model system is that they span a range of sizes and degrees of complexity. Sizes range from tens of microns to a couple of millimeters, cell numbers range from one to 50,000 or so, some species do and some don’t have cellular differentiation, and some do and some don’t undergo inversion during development. This variation makes the volvocine algae ripe for comparative analyses, which I and many others have done. It also allows many of the intermediate steps between unicellular and complex multicellular life to be identified, as David Kirk did in his “twelve-step” paper.

The volvocine algae have clearly taken some of those steps more than once. Cellular differentiation, for example, has evolved at least three times, in the genus Astrephomene, in the so-called Volvox section Volvox (a.k.a. Euvolvox), and in the lineage that includes Pleodorina and the other Volvox species. One thing they seem to have only done once, though, is to evolve multicellularity itself.

There have been dozens of studies addressing the evolutionary relationships among various species of volvocine algae. Most have been from Hisayoshi Nozaki’s lab, though I and many others have weighed in as well. Nearly all of them, at least those that address the topic, agree that the three families that make up the multicellular volvocine algae–the Tetrabaenaceae, Goniaceae, and Volvocaceae–uniquely descend from a common ancestor. In other words, the multicellular volvocine algae are monophyletic.

Three important cladistic terms are used to summarize the evolutionary relationships among a group of species. If all of the members of the group descend from a common ancestor, and nothing else descends from that ancestor, the group is called monophyletic. Mammals, for example, are monophyletic. A monophyletic group is also called a clade. If all group members are descended from a common ancestor, but so are some non-group members, the group is called paraphyletic. Reptiles, for example, are paraphyletic, because there is no clade that includes all reptiles that doesn’t also include birds. The word ‘paraphyletic’ should nearly always be followed by ‘with respect to’: reptiles are paraphyletic with respect to birds.

The bottom of the barrel, in terms of evolutionary relationships, is polyphyly. A group is considered polyphyletic if its members don’t share a recent common ancestor at all, in other words, if they have multiple evolutionary origins. Flying animals are polyphyletic. Algae are polyphyletic. The genus Volvox is polyphyletic. Polyphyletic taxa are the scum of the phylogenetic Earth. Telling a taxonomist that a group she has named is polyphyletic is a deadly insult.

The prevailing view of volvocine evolutionary relationships is that the family Volvocaceae is sister to the Goniaceae (that is, each is the other’s closest relative), and the Tetrabaenaceae are sister to the Volvocaceae + Goniaceae. Two new papers infer relationships among volvocine algae and their unicellular relatives, and one of them challenges the view of multicellular monophyly.

[Read more…]

Peer review isn’t magic

In response to Tom Sheldon’s dire warnings of the dangers of preprints, “Preprints could promote confusion and distortion,” I’ve suggested that what really promotes confusion and distortion is credulous reporters failing to apply basic journalistic standards:

Peer review isn’t a magic wand that guarantees that only solid work gets published, and it isn’t a substitute for skepticism. Reporters have a responsibility to evaluate the evidence in a paper whether it is peer reviewed or not.

A couple of recent examples are relevant. First, the claim by mathematician Michael Atiyah to have proven the Riemann Hypothesis, an immensely important number theory problem related to the distribution of prime numbers. Remember, along with promoting “confusion and distortion,” Sheldon had warned that preprints could rob journalists of “time and breathing space,” pressuring them to rush to sensationalize bad science. Reporting on Atiyah’s claim shows what utter nonsense this is.

[Read more…]

Ulvophyte multicellularity: the sea lettuce genome

Ulva

Sea lettuce (Ulva sp.), Jericho Beach, Vancouver, BC, February 28, 2011.

David Kirk called the Chlorophyte green algae “master colony-formers” because multicellularity has evolved so many times within this class:

Although members of most chlorophycean genera and species are unicellular flagellates, multicellular forms are present in 9 of the 11 chlorophycean orders (Melkonian 1990). Multicellularity is believed to have arisen independently in each of these orders, and in some orders more than once.

In contrast, multicellularity has probably only evolved once or twice in the probable sister group of the Chlorophyceae, the Ulvophyceae. So when numbers like 25 get thrown around for the number of times multicellularity has evolved, something like half of those times were in the green algae.

We know a lot less about how multicellularity evolved in the Ulvophyceae than we do in the volvocine algae within the Chlorophyceae. A big step forward in understanding ulvophyte multicellularity happened last week, though, with the publication of the Ulva mutabilis genome.

[Read more…]