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.

• Darwin's Doubt: A Synopsis
• Darwin's Doubt: The Genes Tell the Story?
• The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes
• Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates
• Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates
• Stephen Meyer Says That Constant Mutation Rates Are a "Questionable Assumption"
• Stephen Meyer Says that "Homology" Is a Problem in Molecular Evolution

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.

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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]