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Tuesday, November 03, 2015

Molecular evidence supports the evolution of the major animal phyla

For those of you who are interested in the evolution of the major animal phyla, let me introduce you to the topic.

See the little red circle on the phylogenetic tree on the right? That's what we're talking about.

Most of the major animal phyla are first observed as primitive fossils in the Cambrian about 540 million years ago. The fossils cluster around dates that only span a few million years (about 10 million years). This is the Cambrian Explosion (see little red circle).

There's considerable debate among evolutionary biologists about what caused this relatively rapid appearance of diverse and disparate large fossils. Intelligent Design Creationist, Stephen Meyer decided that such a debate casts serious doubt on evolution as an explanation for the history of life so he wrote a book called Darwin's Doubt.

Meyer thinks he has a much more reasonable explanation. He believes that a supernatural being visited the Earth about 540 million years ago and noticed that it was teeming with life—lots of plants, algae, fungi, protozoa, and bacteria. The god(s) thought there should be some bigger creatures called "animals" so he/she/it/they built a few and let them loose to reproduce and evolve.

None of them look anything like modern animals. Check out the YouTube video below. I'm not going to defend anything said in that video, I just want everyone to understand that the first representatives of the major phyla don't look anything like modern species.

Most biologists don't agree with Meyer's explanation (surprise!). Instead, they look for real evidence to inform them of what happened at this point in the history of life.1 One of the ways they do this is to construct phylogenetic trees from sequence data. This should be a test of whether all these species popped into existence at once or whether they have an evolutionary history.

Molecular phylogenies should also reveal whether the various phyla are related to each other or whether they were all poofed into existence independently within a few days, or weeks, or years, as Stephen Meyer suggests.2

Now you'd think that the molecular data would feature prominently in Darwin's Doubt because it contradicts his story about gods and their propensity to build weird animals. Well if you think that then you don't understand Intelligent Design Creationists. They are remarkably agile at ignoring scientific evidence they don't like.

Meyer dismisses all molecular phylogenies for the following reasons ...
  1. There are no fossils to support the earliest branches in the molecular phylogenies.
  2. There are many different molecular trees and they don't all agree with each other in terms of branching order and timing.
  3. Evolutionary biologists cherry-pick the data by only picking molecules that give reasonable trees.
  4. The trees rely on questionable assumptions; namely, that the molecular clock ticks at a constant rate and that there is a universal tree.
  5. The molecules being compared must be homologous but this is what is being tested so the argument is circular.
His conclusion is ....
Comparative genetic analyses do not establish a single deep-divergence point, and thus do not compensate for the lack of fossil evidence for key Cambrian ancestors—such as the ur-bilateran or the ur-metazoan ancestor. The results of different studies diverge too dramatically to be conclusive, or even meaningful; the methods of inferring divergence points are fraught with subjectivity; and the whole enterprise depends on a question-begging logic. Many leading Cambrian paleontologists, and even some leading evolutionary biologists, now express skepticism about both the results and the significance of deep-divergence studies.
Some of his points are partially valid and they deserve further discussion—discussion, by the way, that you won't find in Darwin's Doubt or in the sequel that tries to respond (unsuccessfully) to other criticism (Debating Darwin's Doubt).

So, a couple of years ago I took a bit of time off to deal with Stephen Meyer's misconceptions and confusion about molecular phylogeny.
The main point here is that the absolute dating of divergence times is very difficult but it doesn't alter the fact that no molecular phylogeny even hints at a sudden creation and every single one of them indicates a "slow fuse" dating back well before the Cambrian Explosion.

Furthermore, the trees all show that the major animal phyla are related by common descent.

Now there's a new paper by dos Reis et al. (2015) looking at this phylogeny. Their tree is shown below. Here's the abstract of the paper ...
The timing of divergences among metazoan lineages is integral to understanding the processes of animal evolution, placing the biological events of species divergences into the correct geological timeframe. Recent fossil discoveries and molecular clock dating studies have suggested a divergence of bilaterian phyla >100 million years before the Cambrian, when the first definite crown-bilaterian fossils occur. Most previous molecular clock dating studies, however, have suffered from limited data and biases in methodologies, and virtually all have failed to acknowledge the large uncertainties associated with the fossil record of early animals, leading to inconsistent estimates among studies. Here we use an unprecedented amount of molecular data, combined with four fossil calibration strategies (reflecting disparate and controversial interpretations of the metazoan fossil record) to obtain Bayesian estimates of metazoan divergence times. Our results indicate that the uncertain nature of ancient fossils and violations of the molecular clock impose a limit on the precision that can be achieved in estimates of ancient molecular timescales. For example, although we can assert that crown Metazoa originated during the Cryogenian (with most crown-bilaterian phyla diversifying during the Ediacaran), it is not possible with current data to pinpoint the divergence events with sufficient accuracy to test for correlations between geological and biological events in the history of animals. Although a Cryogenian origin of crown Metazoa agrees with current geological interpretations, the divergence dates of the bilaterians remain controversial. Thus, attempts to build evolutionary narratives of early animal evolution based on molecular clock timescales appear to be premature.
This is a remarkable paper. The authors discuss all of the potential problems associated with constructing phylogenetic trees with deep divergences. They test all the hypotheses they can think of and they frankly admit that assigning accurate dates to common ancestors is very difficult. They even conclude that there are problems with the molecular clock in this analysis.

In other words, they deal openly and scientifically with every objection that Stephen Meyer raised in his book. That's not at all like the behavior of Intelligent Design Creationists who are nevertheless convinced that they are ones being scientific.

dos Reis et al. (2015) publish their best tree noting the limitations.

Here's what they say about this data.
The results of our study—which integrates fossil and molecular evidence to establish an evolutionary timescale—suggest that the Cambrian explosion is a phenomenon of fossilization, while biological diversity was established in the Neoproterozoic. Integrating all of the sources of uncertainty that we explore (Figure 6, Table 1) allows us to conclude that crown Metazoa originated 833–650 Ma, fully within the Cryogenian, while the component clades of crown Eumetazoa (746–626 Ma), crown Bilateria (688–596) Ma, crown Deuterostomia (662–587 Ma), and crown Protostomia (653–578 Ma) all diverged within a Cryogenian to early- or mid-Ediacaran interval.

The results of our analyses leads us to reject the hypothesis that metazoans, eumetazoans, bilaterians, protostomes, deuterostomes, ecdysozoans, lophotrochozoans, or, for that matter, any of the component phylum-level total groups, originated in the Cambrian.
This is bad news for Stephen Meyer and the Intelligent Design creationists. They have to respond to this excellent paper that challenges all of their objections. What dos Reis et al. are saying is that, in spite of all the limitations, if you look at the big picture it clearly shows that the major animal phyla did not emerge all at once in the Cambrian explosion.

What are the ID proponents going to do? I suggest that they have two options ...
  1. They could admit that the molecular data provides convincing evidence that the major animal phyla evolved from earlier species that predate the Cambrian explosion by millions of years and concede that this scientific result casts serious doubt on the argument that gods created the animals over a short period of time.
  2. They could say the work shows that scientists are wrong and extract quotes from all the bits of the paper showing scientists behaving like proper skeptical scientists. They could say we told you so, blah, blah, blah.
Before I give you the link to their post, take a minute and decide what you think they'll do. Vote now.

Here's the post by some anonymous blogger at Evolution News & Views (sic): "Molecular Clock" Can't Save Darwin from the Cambrian Explosion. Read it to see if your prediction pans out.

Evolution News & Views (sic) doesn't allow comments in order to keep their flock from seeing any objections to their posts. That doesn't stop us from discussing their post on Sandwalk.

1. Most creationists, on the other hand, tend to go with what their parents told them about the creator.

2. Meyer's a little sketchy on the details.

dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, Maximilian J., Donoghue, Philip C. J., and Yang, Z. Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Current Biology. [doi: 10.1016/j.cub.2015.09.066]


  1. It sounds like the EN&V objection basically amounts to: Because the results have error bars, they can't be trusted.

    1. I was about to post exactly that.

      It's like saying rulers are useless and cannot be used at all because they only measure down to milimetre scales.

    2. Contrast it with Usher's precise dating: "The first day of creation began at 6:00 pm (presumably UTC), Saturday, October 22, 4004 BC". Now that is science -- no error bars!

  2. There is no evidence whatsoever as to what the cause (s) and the mechanism of the Cambrian explosion could be. The Cambrian explosion is a very fitting name because Darwinists know very well that they can't and would not be able to explain the non-gradual and rapid appearance of the many new body plans, without any intermediates, by any Darwinian or other evolutionary fairy tails. So, they had no choice but to give it an explosive name to give it some credibility because they are clueless and the obvious is unacceptable for those people. They would rather die than accept the obvious against their preset beliefs.
    Well, all I can say is too bad suckers.....

    1. The paper highlighted in the post is Open Acess. There's no excuse for not reading it...

    2. Thanks for giving us a taste of the usual standard of creationist argumentation, J-Mac. Your satire was perhaps just a little too broad, but it's not wholly unlike the stupid things creationists say.

    3. "There is no evidence whatsoever as to what the cause (s) and the mechanism of the Cambrian explosion could be."

      Posts like these are why we think the ID community has a greater than average representation of the small section of religious people who are also subnormally mentally endowed.

      Seriously. He posted that drivel as a response to a paper that contains what he says does not exist and cannot be known. It takes a "special" kind of person to do that.

    4. Larry, I take exception to a couple of sentences in your post:

      The fossils cluster around dates that only span a few million years (about 10 million years).

      I'd say more like 30 million, from the first tracks, burrows, and body fossils around 550ma to the first appearance of trilobites and the Chengjiang fauna at around 520ma, by which time things had clearly settled down, as the younger Burgess fauna looks almost the same. Now just how much the Chengxiang fauna predates the Chengjiang is open to question, but at least some of the small shellies that correspond to Chengjiang taxa do not predate the Chengjiang, which suggests that they originated around that time. One could also argue about which originations count as parts of the explosion. But I don't think you could reasonably get it down to 10ma.

      I think I agree with the authors that the fossil explosion is to some degree a taphonomic artifact, but it also seems to be a document of the rise of mineralized skeletons.

      The other quibble is about this sentence fragment:

      lots of plants, algae, fungi, protozoa, and bacteria

      Plants? There's no fossil record of plants before the Late Ordovician at best.

      I was able to correctly predict the EN&V response; but of course the title kind of gave it away.

    5. John,

      I deliberately said 10 million to avoid the kind of quibbling that you engaged in. If I said 30 million I was pretty certain that the IDiots would focus on that trivial part of my post and turn it into World War III.

      It never occurred to me that an evolution supporter would do that.

      You are correct about plants. I thought there were bryophytes in the Cambrian but it seems that this is controversial with the majority of plant evolutionary biologists now saying that the first bryophytes are less than 488 million years old.

      I sincerely hope that your reference to "sentence fragment" is not meant as another quibble—this time about grammar.

    6. I only meant that the part I quibbled about was a fragment.

      OK, so "10 million" was a lowball in order to get buy-in from IDiots? Bet that won't work. Meyer, at least, doesn't really care how long the Cambrian explosion is supposed to be, as he thinks no amount of time would be sufficient; any significant evolution, of life, or of his position, is impossible. The Cambrian thing is just a hook to get you into the book, which is really about Doug Axe showing that evolution can't happen. But that wouldn't have been as sexy.

    7. I think I agree with the authors that the fossil explosion is to some degree a taphonomic artifact, but it also seems to be a document of the rise of mineralized skeletons.

      John, what is the distinction underlying the "but" between these two clauses (since mineralized skeletons presumably are better candidates for fossilization)?

    8. I would distinguish a purely taphonomic artifact, in which changes in the conditions of preservation create changes in preservational bias in the absence of evolutionary change, from biases resulting from real evolutionary events. If a taxon evolves greater preservability, and that is reflected in fossils, that isn't an artifact but a faithful recording. But if the conditions for Burgess-type preservation didn't happen before the Chengjiang, then the simultaneous appearance of so many soft-bodied forms is a pure artifact and tells us little about evolution.

    9. Just 'cause you've made me curious now, what, if you know and can outline without going to too much trouble, are "the conditions for Burgess-type preservation"?

    10. There's quite a literature on that and I don't know that I can summarize it quickly. I can offer an entry or two into the literature, though. Nick Butterfield has published a lot on it.

      Butterfield N.J. Exceptional fossil preservation and the Cambrian explosion. Integrative and Comparative Biology 2003; 43:166-177.

      Butterfield N.J. Secular distribution of Burgess-Shale-type preservation. Lethaia 1995; 28:1-13.

    11. It's summarised here:

    12. Hey, that's not bad. This is the most relevant bit: "Burgess Shale type deposits occur either on the continental slope or in a sedimentary basin. They are known in sediments deposited at all water depths during the Precambrian (Riphean stage onwards), with a notable gap in the last 150 million years of the Proterozoic." But that's actually the last 150 million years of the Proterozoic and the first 20+ million years of the Paleozoic.

  3. J rants:
    "There is no evidence whatsoever as to what the cause (s) and the mechanism of the Cambrian explosion could be."

    What you're actually saying is that there's no evidence for god(s) or designer(s).

    Because if you had actually read the piece above, you would've discovered the molecular evidence combined with fossil evidence regarding the Cambrium explosion.

    Thus you went for option 2, more blah blah. Your rant clearly shows who's the sucker around here, doesn't it J?

  4. The creationist response is entirely predictable. It's been the exact same since well before Behe's "I haven't read them, but even if I had, they wouldn't be enough for me" comment in the Kitzmiller case.

    I'm just posting to say thankfully the article is open access.

  5. Thank you Laurence, this is an excellent post :-)

  6. Isn't it wonderful how many of the best science papers describe our level of *un*certainty really well? That seems to be what the ID folks are scared of and one of the things they believe (utterly erroneously) is a weakness in science - describing how things actually are, rather than creating a universal "explanation" by wishing it were true. Of course the other half of the time, like J-Mac, they do the projection thing and accuse science of making a universal explanation of evolutionary theory by wishing it were true, ignoring (as J-Mac assiduously does) the very real and valuable research being done.