The evidence for intelligent design just keeps getting stronger. It’s long been known that the Cambrian explosion isn’t the only explosion of organisms in the fossil record. There’s also something of a fish explosion, an angiosperm explosion, and a mammal explosion. Paleontologists have even cited a “bird explosion,” with major bird groups appearing in a short time period. Frank Gill’s 2007 textbook Ornithology observes the “explosive evolution” of major living bird groups, and a paper in Trends in Ecology and Evolution titled “Evolutionary Explosions and the Phylogenetic Fuse” explains:

A literal reading of the fossil record indicates that the early Cambrian (c. 545 million years ago) and early Tertiary (c. 65 million years ago) were characterized by enormously accelerated periods of morphological evolution marking the appearance of the animal phyla, and modern bird and placental mammal orders, respectively.

Now, a massive genetic study published in Science has confirmed the fossil evidence that birds arose explosively. According to an article titled, “Rapid bird evolution after the age of dinosaurs unprecedented“:

His research helped confirm that some of the first lineages of modern birds appeared about 100 million years ago but that almost all of the modern groups of birds diversified in a small window of less than 10 million years, just after the dinosaurs were wiped out by an asteroid.

Another news article calls it a “‘Big Bang’ of bird evolution” and one of the technical papers uses the same language:

Paleobiological and molecular evidence suggests that such “big bang” radiations occurred for neoavian birds (e.g., songbirds, parrots, pigeons, and others) and placental mammals, representing 95% of extant avian and mammalian species, after the Cretaceous to Paleogene (K-Pg) mass extinction event about 66 million years ago (Ma).

The article further cites “an explosive diversification within Neoaves.” So both fossil and genetic evidence suggests diverse organisms arose in an “explosion” or “big bang” that lasted “less than 10 million years.” Sounds familiar. Where have we heard something like this before?

All this came from a study of bird genomes, so how did they come to this conclusion using genetics rather than fossils? It’s because some of the lower branches — read: basic relationships between various major bird groups — were difficult to resolve even when researchers studied whole genomes (a method that tends to obscure conflicts between trees based upon individual genes or gene sets, see below). The technical paper that reports the avian phylogeny explains the inability to resolve these branches. It appeals to “rapid” evolution — that is, where insufficient time elapsed to allow for differences to accumulate in key genetic markers and thereby generate useful phylogenetic signals, allowing scientists to infer evolutionary relationships between bird groups:

Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

They found that the major interorder groups diverged in an even more rapid explosion — in merely 1 to 3 million years:

[O]ur genome-scale analysis supports the hypothesis of a rapid radiation of diverse species occurring within a relatively short period of time (36 lineages within 10 to 15 million years) during the K-Pg transition, with many interordinal divergences in the 1- to 3-million-year range.

So now, difficulties reconstructing early branches of bird phylogeny isn’t evidence against evolution. Rather, it’s evidence for “rapid” evolution.

But there’s a problem, and it’s deeply hidden in their methodology. While the whole-genome technique they used produced a robust tree when it comes to many of the major positions of bird groups, this technique obscures conflicts between individual gene-based trees. And indeed, they found that much data based upon individual genes or genetic segments conflicted with the overall tree:

All estimates of gene trees differ from our candidate species trees. No single intron, exon, or UCE locus from our TENT data set had an estimated topology identical to the ExaML TENT or MP-EST* TENT. … The absence of a single gene tree identical to the avian species tree is consistent with studies in yeast, indicating that phylogenetic studies based on one or several genes, especially for rapid radiations, will probably be insufficient.

Another paper from this genomic study found data that required “independent” (i.e., convergent) genetic evolution in bird sex chromosomes. Another Science article, “Bird genomes give new perches to old friends,” reported difficulties reconstructing the tree:

When the researchers tried to build the new avian family tree, “we were shocked to find we couldn’t get a solid answer,” Jarvis recalls. As the consortium developed more sophisticated bioinformatics tools to analyze the genome data, they discovered that protein-coding genes by themselves were not the most reliable for building good trees. The non-coding regions within or between genes, called introns, gave better answers. And although the group had access to supercomputers, they still had to come up with a way to allocate the analysis to the machines’ many microprocessors. “It took 3 years to iron out the kinks,” Gilbert says. (emphasis added)

The fundamental problem is this: They are finding data that doesn’t fit a treelike pattern. But they aren’t going to reject common ancestry. They’re just going to appeal to ad hoc explanations whenever necessary to explain why the data doesn’t fit a tree. Convergent or “independent” evolution is just one of the mechanisms they invoke. As another one of the papers in the study explains:

there is increasing evidence that loci can have conflicting evolutionary histories (so that their phylogenetic trees are topologically different) because of many biological causes, including incomplete lineage sorting (ILS), a process that is especially common in rapid radiations, characterized by a succession of short branches in the phylogenetic tree, such as is believed to have occurred in the avian and mammalian evolutionary lineages.

Incomplete lineage sorting (ILS) occurs when a gene has multiple alleles, and some alleles are lost (or retained) due to genetic drift or selection in a pattern that doesn’t match the true phylogeny, messing up the phylogenetic signal. The great thing about ILS for evolutionary biologists is that when they find data that doesn’t fit a tree, they can invoke ILS in an ad hoc, after-the-fact, as-needed kind of manner to help explain away that pesky data. The main paper that constructed the phylogeny claims that ILS makes it difficult to resolve many of the early branchings deep in the tree:

Overall, these results reveal considerable ILS during the neoavian radiation and that, even with genome-scale data, ILS may affect the inference of small local relationships in the deep branches of the species tree that have long been more challenging to resolve.

Isn’t that convenient? Just where we want to know deep evolutionary relationships between bird groups, ILS messes them up. Is ILS just another epicycle used to explain why it’s difficult to resolve many evolutionary relationships? Could there be other explanations for why they aren’t finding a clear signal of evolutionary relationships? Could it be that common descent is not the answer?

But this whole-genome technique only ignores non-treelike patterns in the molecular data. It doesn’t do away with convergence among physical traits. In fact, their molecular phylogeny generates massive new instances where convergent evolution (or loss) among the physical traits of major bird groups (such as water birds, birds of prey, and vocal learners) is needed:

The non-monophyly of the birds of prey at the deepest branches of the Australaves and Afroaves radiations suggests that the common ancestor of core landbirds may have been an apex predator, followed by two losses of the raptorial trait. Seriema at the deepest branch of Australaves could be considered to belong to a raptorial taxon because they kill vertebrate prey (94) and are the sole living relatives of the extinct giant “terror birds,” apex predators during the Paleogene. The deepest branches after Accipitriformes and owl among the Afroaves, the mousebirds and cuckoo-roller, have Eocene relatives with raptor-like feet, and the cuckoo-roller specializes on chameleon prey. This suggests that losses of the predatory phenotype were gradual across successive divergences of each of the two core landbird radiations. More broadly, the Columbea and Passerea clades appear to have many ecologically driven convergent traits that have led previous studies to group them into supposed monophyletic taxa. These convergences include the footpropelled diving trait of grebes in Columbea with loons and cormorants in Passerea, the wading-feeding trait of flamingos in Columbea with ibises and egrets in Passerea, and pigeons and sandgrouse in Columbea with shorebirds (killdeer) in Passerea. These long-known trait and morphological alliances suggest that some of the traditional nongenomic trait classifications are based on polyphyletic assemblages.

In other words, this molecular study has separated many groups previously thought to be closely related because of their similar physical traits, as is made very clear from Figure 1 of the paper. As Nature puts it, “the tree of life for birds has been redrawn” by this study. Bird relations are thus quickly becoming a classic case of conflict between molecule-based and morphology-based trees.

The authors of this study don’t appear to give the slightest worry about these conflicts, and simply appeal to convergent evolution for these similar physical characteristics that don’t fit their molecule-based tree. This raises a troubling question: If similar morphology doesn’t indicate inheritance from a common ancestor in these cases, how do we know that similar morphology indicates common ancestry in so many other cases (where physical similarity is still said to indicate inheritance from a common ancestor)? The answer is we don’t know that similarity indicates common ancestry, because convergent evolution undermines the rationale that is used to infer common ancestry in the first place.

One PhD biologist wrote me the following about this:

I just saw a quick blurb about the Science issue on avian genomics and things are very different from what one would have predicted based on taxonomy. Of course evolutionists make their own stories to account for this. I guess convergent evolution occurs all over the place?
Things like this indicate to me a designer is cleverer than evolution at constructing different species. Despite similarities in genomics, the phenotypes of the birds can still be highly variable.

These authors would disagree, of course. That’s because their methodology fundamentally assumes that common ancestry is true and that there is no common design. If you ignore the conflicts between different trees, and appeal to “massive protein-coding sequence convergence and high levels of incomplete lineage sorting,” then you can construct a tree — regardless of the fact that much of the data doesn’t fit a treelike pattern. Indeed, this study reveals other evidence that contradicts the tree of life. More on that in a subsequent post.

Image: By Concerto [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons.