Dauber Ant-Bees and Mutant Ninja Turtles

In a 2013 study, some biologists purported to finally have "a single well-resolved and strongly supported tree, robust to multiple methods of phylogenetic inference. Apoidea (spheciform wasps and bees) and ants are sister groups, a novel finding that contradicts earlier views that ants are closer to ectoparasitoid wasps. [emphases mine]"  As with so many phylogenetic studies seeking to marry modern genomics with paleontology and morphology, the work involves crafting a best fit for contradictory indications from various genes--which means that many genes must be sampled.  As explained in a NY Times article:

[Ward] and his colleagues then sequenced more than 300 genes from one species of ant and 10 species of bees and wasps, each representing a different major lineage. In the end, they produced a database far larger than in previous studies.  . . . The scientists then used computers to search for an evolutionary tree that best accounted for their genetic data [i.e. that exhibited the fewest contradictions and anomalies]. Their research clearly pointed to mud dauber wasps and bees as the closest cousins to ants.

Mud dauber wasps! Well, how do you like that?!  Well, this new tree needs a new story.

The new study suggests that mud dauber wasps may offer clues to the evolution of ant societies. The female mud daubers don’t just lay an egg on the ground and fly away. Instead, they first create a mud cylinder in which to house the egg[.] . . .
Dr. Ward doesn’t think it’s a coincidence that the new study reveals bees as having evolved from mud-dauber-like ancestors as well. Bees have also evolved complex societies, in which workers fly off to find pollen and nectar to feed their hives. It may be that only a certain kind of wasp could give rise to either kind of highly social insect.
Dr. Boomsma agreed with this idea. “Colony life with altruistic helpers could only evolve after nests and parental care had evolved first,” he said.

It seems so obvious in retrospect.  Dr. Boomsma sounds like Dr. Pangloss in Eldridge and Gould's "Spandrels" essay.  It may well be that it takes very particular wasp adaptations for complex behavior to emerge.  It may well be that it takes very particular adaptations in any clade.  But if it was never obvious that mud dauber behavior held the key, there must be a reason why it could seem so obvious now, when there wasn't a deep biological principle leading us specifically to mud dauber wasps.

Turtle and Wasp

Scientists instead looked to presumably more remotely related wasps that were much more social.   But eusociality is a paraphyletic phenomenon in Hymenoptera.  Ants and bees seem to be very closely related genetically, and it seems likely that much of their shared genomic information enables their shared social complexity.  The more social vespids have been the usual suspects. "Ants and bees are surprisingly more genetically related to each other than they are to social wasps such as yellow jackets and paper wasps, a team of University of California, Davis, scientists has discovered [emphasis mine]," as another article put it, and consequently the "fossil ant" Cariridris bipetiolata can now be reinterpreted as an ancestral sphecid wasp with putative mud dauber behaviors.  Nothing evolves as fast as evolutionary history.

"That's not a boyd, that's a toytle! Isn't it, Moytle?"

According to Nick Crawford (as reported by Science Daily) "Turtles have been an enigmatic vertebrate group for a long time and morphological studies placed them as either most closely related to the ancestral reptiles, that diverged early in the reptile evolutionary tree, or as closer to lizards, snakes, and tuataras." The same article summed up the history of the turtles evolving story with

Paleontological and morphological studies place turtles as either evolving from the ancestor of all reptiles [branching off very early] or as evolving from the ancestor of snakes, lizards, and tuataras [branching off after the dino-croco-avian (i.e.archosaurian) ancestors have branched off]. Conflictingly, genetic studies place turtles as evolving from the ancestor of crocodilians and birds. [emphasis mine]

So, just by looking at the bones, and not the DNA, turtles appeared to be something very different from what they were inside. Everything up until at least the 1990s pointed to a very, very different lineage that DNA evidence would suggest.  In fact, originally they weren't even thought to be diapsids.  According to the Wikipedia summary, "it was later suggested the anapsid-like turtle skull may be due to reversion rather than to anapsid descent. More recent morphological phylogenetic studies with this in mind placed turtles firmly within diapsids, slightly closer to Squamata [snakes & lizards] than to Archosauria [dino-croco-avians]."

With the advent cladistics and molecular studies, while turtles look primitive, in terms of their genetic information they were believed much more dinosaurian than they look.  Still, some molecular studies were combined with morphological studies to argue for anapsid groupings in "Molecules, morphology, and the monophyly of diapsid reptiles" (2001) by M.S.Y. Lee.

But on 7/26/2011,  Science Daily had announced that microRNAs confirmed the morphological assessment in favor of snakes and lizards:

For decades, paleontologists and molecular biologists have disagreed about whether turtles are more closely related to birds and crocodiles or to lizards. Now scientists have developed a new technique using microRNAs for classifying animals, and the secret is out. Turtles are closer kin to lizards than crocodiles. . . . [T]wo scientists from the Mount Desert Island Biological Laboratory [and other collaborators]. . . have developed a new technique using microRNAs for classifying animals, and the secret is out. Turtles are closer kin to lizards than crocodiles.

So, microRNAs, being stable indicators of group evolution according to the researchers, show that previous studies need to be evaluated. ". . . [W]e had the evidence we needed to say that turtles are a sister group to lizards and not crocodiles."  MicroRNA says that turtles speak Parseltongue.

Not much more than a year before, "a morphological study [in spite of genetics?] conducted by Lyson et al. (2010) recovered them as anapsids most closely related to Eunotosaurus"!

A study reported by Science Daily reported on 5/23/2012 "challenge[d] previous anatomical and paleontological assessments," but judging by the 2011 study, it challenged some previous genetic assessments as well.  So why does the microRNA differ so pointedly from studies based upon a genome-wide DNA inference based on "1145 ultraconserved elements (UCEs) and their variable flanking DNA"?  These later studies, of course, use Bayesian methods (or similar likelihood methods) to determine, based on the selected data, what phylogenetic tree cause the fewest problems.   

Science Daily announced on 11/24/14 that "[s]cientists [at Boston University anyway] place turtles in the newly named group 'Archelosauria' with their closest relatives: birds, crocodiles, and dinosaurs."

Research results, appearing in Molecular Phylogenetics and Evolution, describe how a new genetic sequencing technique called Ultra Conserved Elements (UCE) reveal turtles' closest relatives across the animal kingdom. The new genetic tree uses an enormous amount of data to refute the notion that turtles are most closely related to lizards and snakes.  

What a persistent notion.  But then, we were sure for a long time based on paleontology and morphology, what the tree looked like, even though we really didn't know, it turned out... several times.  These evolutionary ninjas repeatedly have eluded capture until recently (we presume).

Parham notes that studying turtle fossils -- particularly the physical features of their bones -- hasn't always painted an accurate evolutionary picture of turtle relationships across continents and through time. "The turtle tree of life based on fossil turtle anatomy didn't match up with the timing of their appearance in the fossil record, as well as their geography," Parham says. "But the tree of life generated at the Academy's CCG is consistent with time and space patterns we've gathered from the fossil record. These new testing techniques help reconcile the information from DNA and fossils, making us confident that we've found the right tree." [emphasis mine]

So now that there is a lot of data to choose from, it is possible to choose the data and the inference weights to come up with a tree that more closely matches the fossil record.  What a relief!  Like its archosaur cousins the crocodilians, the chelonian seems to be a somewhat devolved critter.  With its devolved anapsid skull and its (convergently!) ankylosaurian body form, it's practically the platypus of the diapsids!    

Lobe-finned Fish, Amphibians, and Devolutionary Processes

So earlier this week I was thinking about von Baerian development and considering a specifically non-recapitulatory view of The Vertebrate Embryo and was thinking, "Could the majority of fish be considered more specialized in terms of the general vertebrate pattern, with the more amphibian-like fish being the archetype rather than the specialization.

Lo and behold, I came across something in Stuart Kauffman's work that evidence seems to have been mounting that the swim bladder came from the lung, not the other way around!  It would be even more intriguing if the archetype for fish were something even more like an amphibian, say a sarcopterygian like Tiktaalik, rather than the more numerous actinopterygians.  The actinopterygians depict for us how (bony) fish are different from other vertebrates.

Now, is it possible that we could learn things about vertebrate development thinking this way much more efficiently than we could with this quasi-Haeckelian recapitulatory progressivism?

The story as I knew it was that fish somehow developed a swim bladder around the time they replaced cartilage with bone.  Since utility is the mother and father of invention in the Darwinian world, the usefulness of swim bladders for pelagic swimming was sufficient to explain their existence.
 
If it turns out that lungs were adaptation preceding tetrapods by ages, well then that too is just what one expects in Darwinland.

It's important to remember that evolutionary logic means never having to say you're sorry.

. . . in 2009, just three years ago . . . the purported fact that 95 percent of the human genome "might as well not be there" was an embarrassment "for creationists," whom in typical Darwinian fashion Dawkins conveniently conflates with intelligent-design advocates. Junk DNA is just what a Darwinist would expect, in other words. Cut to 2012, and now the evident fact that "junk DNA" isn't junk at all but is instead vital for life has become "exactly what a Darwinist would hope for," namely, "to find usefulness in the living world." That is, heads you lose, tails I win. . . . suspiciously convenient self-contradiction. Ah well, as we knew already, being a Darwinist means never having to say "I was wrong." 

But it's not a self-contradiction. With Evolution-Did-It , whatever direction the evidence points is just what Dr. Pangloss would expect, because evolution as a theoretical framework can accommodate almost anything.

Even if the upward trends of progressive (teleological) evolution makes more sense for the historical framework that the evolutionary research program has pursued, what value might there be in more devolutionary hypotheses being assumed.  (Devolution is not nearly as satisfying and validating to Darwinism as complexity-building evolution.)  The alligator is a reptile that is considered the pinnacle of reptilian evolution nor a transition animal but a sort of devolved representative of warm-blooded archosaurs.  Ceolocanths are believed to be derived from sarcopterygians.  The TTSS1 pump might be better thought of as having devolved from the flagellum.  The mimivirus might best thought of as having devolved from a cellular creature.  Maybe Tiktaalik, like the alligator is a throwback, an amphibian that thinks its a fish.  Cynodonts might be better understood as a devolution from monotremes.

The evolutionary relationships of the fossil [for the eutriconodont mammal Yanoconodon] suggest that either the "modern" middle ear evolved twice, independently or that it evolved and was then lost [i.e devolution] in at least one ancient lineage.

Or maybe some are mosaics because phylic boundaries, as we know them, are a trend, not a rule (otherwise, how would either mosaics or missing links be possible?).  Now, Archaeopteryx is no longer the missing link it pretended to be in our textbooks.  It is, for now, more like the coelocanth or alligator.  It is a mosaic that represents the diversity of archosaurs (though not as radically as ceratopsids which had apparently "recapitulated" and rediscovered their four-footed roots.  And if quadruped representatives of the archosaurs were there all along, like the elusive coelocanths, they simply flew under the paleontological radar and avoided the fossil record as many group likely have.

All this puts me in mind of this structuralist (and narrative-agnostic) formulation by Dr. Richard Sternberg:

The approach I am taking to this problem is a variant of structural realism, by which I mean that biological phenomena are manifestations of logico-mathematical structures. This perspective is orthogonal to the origins debate, if you will, because all historical actualities are understood to be space-time instances of pre-existing non-temporal possibilities. Within this context one can accept all that is empirically valid in evolutionary biology, while not axiomatically dismissing the position that structures as well as their “real” instantiations have an intelligent cause.