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Shark Proteins Contradict the Standard Phylogeny of Vertebrates

white shark.jpg

Last year I discussed a paper in Nature that found that immunoglobulin proteins were distributed among vertebrates in a manner that doesn't match the standard phylogeny. According to the distribution of these genes, tetrapods (four-limbed vertebrates like humans and frogs) are closer to teleosts (ray-finned fishes like goldfish) than they are to the lungfish or coelacanth, which are typically thought to be our closest relatives among fish. Now, a new study in BMC Genomics, "Characterization of the heart transcriptome of the white shark (Carcharodon carcharias)," has found more genomic evidence that contradicts the standard vertebrate phylogeny. According to an article at Science Daily:

Cornell researchers have discovered that many of the endangered great white shark's proteins involved in an array of different functions -- including metabolism -- match humans more closely than they do zebrafish, the quintessential fish model.
It's not the first time scientists have found this, either. As the paper itself notes: "Similarities between another chondrichthyian [the vertebrate class that includes sharks] and humans were also apparent in the genome sequence comparisons of Venkatesh et al., in which the elephant shark (a chimaera; subclass Euchondrocephali) surprisingly shared a higher degree of gene synteny and more conserved non-coding elements (CNEs) with humans than with either the zebrafish or puffer fish (Fugu rubripes)."

So why is this data "surprising"? As we saw in my piece earlier this year, sharks (which are cartilaginous fish) are equally distant from ray-finned fish (which include zebrafish) as they are from humans (which are tetrapods):

(Simplified phylogeny of Figure 1 in Amemiya et al., "The African coelacanth genome provides insights into tetrapod evolution," Nature, Vol. 496:311-316 (April 18, 2013).)

Accordingly, you'd expect shark genomes to be equally distant from the proteins of both ray-finned fish and mammals. You certainly wouldn't expect shark genes to be more similar to mammals than to ray-finned fish. This finding is even more surprising to evolutionists given that the lifestyle of sharks is far more similar to ray-finned fish than it is to mammals, as the researchers acknowledge:

"We were very surprised to find, that for many categories of proteins, sharks share more similarities with humans than zebrafish," Stanhope said. "Although sharks and bony fishes are not closely related, they are nonetheless both fish ... while mammals have very different anatomies and physiologies. Nevertheless, our findings open the possibility that some aspects of white shark metabolism, as well as other aspects of its overall biochemistry, might be more similar to that of a mammal than to that of a bony fish."
Or as they say in another piece:
Contrary to expectations, the researchers found that the proportion of white shark gene products associated with metabolism had fewer differences from humans than zebrafish (a bony fish) -- an unexpected result given that bony fishes are evolutionarily much more closely related to sharks.

Indeed, more broadly speaking, the researchers were also surprised to find that other aspects of the white shark heart transcriptome, including molecular functions as well as the cellular locations of these functions, also showed greater similarity to human than zebrafish. Like many first looks at complex scientific questions, the unexpected results of this study raises more questions than provides answers.
No wonder one of the Science Daily stories calls these data "unexpected findings." Most likely nobody would have predicted these results. But no one was more surprised than evolutionary scientists, who think rigidly in terms of a nested hierarchy and common ancestry. Once again, Darwinian expectations have been upset by the revelations of the genetic data

Can Common Descent Be Falsified?

While we're on the subject of shark proteins and vertebrate phylogeny, I thought I'd mention a post by our friend PZ Myers over at Panda's Thumb from last spring. He took note of my piece about how immunoglobulin proteins contradict the standard vertebrate phylogeny, and wrote a typically PZ response. He stated that one way to explain this odd distribution is if the genes for IgW were present in the ancestor of all jawed vertebrates, but were then lost in teleosts and tetrapods. PZ assumed I hadn't thought of this, and assured readers that the purported mistake demonstrated my "outright stupidity and dishonesty." But Myers apparently missed that I had pointed out the same thing in my article multiple times. For example, twice I quoted the Nature paper which stated:

immunoglobulin genes that are found only in lungfish and cartilaginous fish ... are believed to have originated in the ancestor of jawed vertebrates but subsequently lost in teleosts and tetrapods.
In my own words, I then noted that "Perhaps the loss of IgW in tetrapods isn't very hard to explain -- maybe IgW was lost in the early stages of the line that branched off other sarcopterygians and led to tetrapods," and perhaps the genes for IgW were also lost in whatever early lineages of teleosts existed at that time. So I fully recognized how evolutionary scientists would likely try to explain this quirky evidence.

PZ misrepresented what I wrote by wrongly claiming I failed to recognize how evolutionary biologists deal with data that doesn't fit a treelike pattern. He again misrepresented me by claiming that I had said because of this contrary data "evolution is proven wrong."

Of course I never claimed that if a single gene contradicts the standard phylogeny, then this means "evolution is proven wrong." In fact, I said nothing of the kind, and multiple times I discussed how evolutionary biologists would try to explain away this contrary data.

The big problem here for common descent isn't that it is falsified by this data. The big problem is that the way evolutionary biologists treat common descent, it really can't be disproved. By inventing more evolutionary steps at will (e.g., either convergent gains or losses of traits), you can force almost any dataset, no matter how inherently un-treelike, into a treelike pattern. As I explained:

This highly unparsimonous evolutionary story is the only way (and the way the Nature paper chooses) to explain why teleosts and tetrapods lack IgW, but lungfish and coelacanths don't. A more straightforward and plausible account of vertebrate relationships would suggest a phylogeny (Figure C) that's quite incompatible with the standard vertebrate phylogeny.

No wonder the New York Times decided not to mention this inconvenient data point that has emerged from the coeolocanth genome: it suggests the coelacanth is NOT "more closely related to people than to other fish," and that "we are" -- yes, big surprise -- NOT "sarcopterygian fish."

Under Darwinian thinking, so long as you're free and easy and unconstrained about invoking convergent gain or loss of genes (or invoking other mechanisms like horizontal gene transfer, etc., etc.), there's almost no dataset that can contradict common descent. Every time you find that one trait predicts one phylogeny, and another trait predicts a conflicting phylogeny, you can effect a reconciliation by invoking at will more evolutionary steps of convergent loss or gain of traits, or invoking a host of other ad hoc explanations. In a worst case scenario, if genes were distributed in the most un-treelike manner imaginable, I suppose you could take all the known genes present in the most recent presumed common ancestor of that group, and then simply invoke losses of genes to reconcile the observed distribution with a tree.

In the immediate term, the trick might seem to salvage common ancestry. Superficially, it gives the impression of resolving a damaging conundrum. However, just below that superficial level, it serves as an unwitting reminder that the raw data is not distributed in a treelike manner, as Darwinian theory expects. This is a nagging problem we see over and over again in phylogenetic studies. Though this or that one or two (or three...) little instances of invoking convergent gain or loss of genes isn't necessarily devastating to common descent, what is a problem is that this sort of thinking goes on all the time in phylogenetics. We find not just here, but over and over and over, making the data appear treelike requires endless massaging. That PZ misrepresented my arguments and called me names isn't news; PZ's insults and obfuscations notwithstanding, these large-scale problems in the methodology in itself call common ancestry into serious question.

Massage it all you like. The data, consistently, does not fit a treelike pattern.

Photo: White Shark/Wikicommons.