July 2011-July 2018: Marking 7 years of paleo-heresies.

On July 12, 2011
a new blogpost entitled, “Welcome to The Pterosaur Heresies” first appeared online. It was (and is) meant to be the newsletter for taxon additions to the large reptile tree (LRT, 1255 taxa) at ReptileEvolution.com. More complete explanations and documentation can be provided here than at ReptileEvolution.com.

Starting two days later (July 14, 2011) and for the next three days,
the several hypotheses of pterosaur origins were compared one with another.

About a week later (July 22, 2011)
a completely resolved family of pterosaurs was presented. This was the first one to include several specimens from all well-known genera and the first to include tiny Solnhofen pterosaurs, first listed by Peters 2007. Previously tiny pterosaurs had been ignored based on the false premise that they were juveniles of larger specimens. That is a disproved hypothesis that continues to make the rounds. And we said goodbye to the clade, “Pterodactyloidea” because now 4 clades are recovered that share all of the pterodactyloid-grade traits, while two others share some, but not all of those traits. Have other workers started to include tiny Solnhofen pterosaurs in their analyses? No.

On the last day of that first month (July 31, 2011)
a  phylogenetic analysis of just 235 taxa was presented that recovered a completely resolved and diphyletic Reptilia (= Amniota), with one branch, the new Lepidosauromorpha, containing turtles, pterosaurs and lepidosaurs and their many relatives. The other branch, the new Archosauromorpha, contained mammals, enaliosaurs, archosaurs and their many relatives. An amphibian-like reptile, Gephyrostegus was their last common ancestor.  Today, with more than 1000 additional taxa, the original topology from seven years ago remains unchanged. Have other workers started to include basal amphibian-like reptiles in their analyses? No.

In the seven years since July 2011
hundreds of exciting and heretical discoveries have been recovered. Some of these resolve long-standing problems by simply adding taxa. Others shed new light on topics that were not thought to be problems at all by simply adding taxa. Ironically, several other workers gained worldwide acclaim for ‘discovering’ relationships that were recovered in the LRT and promoted here years earlier. Still other workers continue to criticize the LRT, claiming it should have failed some time ago, but the LRT continues to grow.

Unfortunately,
a propagandistic pall was cast on the LRT, so most workers have ignored the taxon inclusion/exclusion suggestions offered here, leaving their work open to criticism from the ever-growing authority of the LRT.

Whatever the faults of the LRT,
the specimens included here need only be included in more focused analyses using independent character lists to test them. In other words, the faults don’t have to be employed, only the suggested taxa. When that happens, confirmation of the LRT has been the typical result. Why? Because the wide gamut and sheer number of taxa minimize the possibility of taxon exclusion, the number one problem in prior, less inclusive analyses. If you have a tetrapod of unknown affinity, test it here at the LRT.

One unexpected and disappointing discovery:
DNA analysis, the standard for crime-fighting and paternity questions, has not been able to replicate the results of wider trait studies. Rather, DNA studies lose their efficacy over large phylogenetic distances when compared to the trait-oriented LRT. Worse yet for paleontology, DNA cannot be used with most fossils. Unfortunately, many paleontologists still believe in the validity of DNA studies.

Figure 2. Dr. Sean Carroll and Dr. Antonis Rokas

Figure 1. Dr. Sean Carroll and Dr. Antonis Rokas

On that note…
Quoted from EvolutionNews.org, “Finally, a study published in Science in 2005 (Rokas and Carroll 2006) tried to use genes to reconstruct the relationships of the animal phyla, but concluded that “despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” The following year, the same authors published a scientific paper titled, “Bushes in the Tree of Life,” which offered striking conclusions. The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The paper even contends that “the recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”

I was not aware of that 2005 paper
before a few days ago. It needs to be more widely considered.

While other blogs journalistically report on the works of others,
the Pterosaur Heresies scientifically tests the work of others. That’s what sets it apart. That’s what makes it fun, interesting and rewarding. That’s what makes it controversial. Hopefully, that’s why you’re a subscriber. If, instead, you keep waiting for the LRT to crash and burn, well, that should have happened by now, don’t you think?

This July 2018,
seven years after it was started in 2011 with 235 taxa, there are 1000+ more taxa, all gradually blended in a tree topology that has been growing organically and with virtual complete resolution (some taxa known only from mandibles and other scraps are less resolved). Still, critics keep harping on the same perceived shortcomings (too many taxa, too few traits, not enough firsthand observation, lack of expertise)—while not harping on the shortcomings of traditional studies (principally taxon exclusion) that fail to produce gradually blended (= similar) sister taxa. There has always been a double standard at play, not only here, but for new hypotheses in geology, astronomy, physics, and paleontology. It’s universal and has been at work for centuries. It used to be that religious leaders led the charge against new ideas. Now we have PhDs trying to do the same.

Even scientists are not immune from this thing we call ‘human nature.’
Dr. J Ostrom complained about it, too. It’s human nature to follow authority, to go with the majority, and to suppress contra-indicators. Facts sometimes take decades to be widely accepted, and that’s just the way it is. It’s not acceptable, but that’s the way it is.

The beauty of science is
you, yes you can perform your own analysis to confirm or refute any analysis you read about here or anywhere. If I can do it… you can do it.

Thank you for your readership.
If there are subjects/taxa you want me to cover, or issues that need resolution, let me know. I look forward each day to corresponding with each and every one of you.

References
Peters D 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Rokas A and Carroll SB 2006. Bushes in the Tree of Life. PLoS Biology, 4(11): 1899-1904.

refined-fine-tuned-placental-mammal-family-tree/

 

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.