Ontology and Phylogeny

I've just read Conrad's 2008 "Phylogeny and Systematics of Squamata (Reptilia) Based on Morphology" and it has frankly left my head spinning.  What bothers me is that although this is the best attempt so far at figuring out squamate relationships, there is a big difference between the phylogeny that he developed and the one that I think is intuitively good.  I'm not saying that I prefer one evolutionary hypothesis over all others in the face of contradictory evidence, I'm saying that the distribution of characters on the tree is different from how I think a good distribution would look.  

For example, several characters that are given as unambiguous synapomorphies of a major group, are also shared with other major groups.  Iguaniamorpha, as far as I can tell is synonymous with Iguania under Conrad's taxonomy and are defined by what I consider to be mostly bad synapomorphies which include obliteration of the notochordal canal by centrum ossification, procoelous vertebrae, premaxilla fusion and possession of a ventromedial process of the pterygoids.  All of these are shared by some major schleroglossan groups!  Just about every lizard is procoelous.  Gekkotans are the only ones that I can think of that have an unossified notochort, and that is probably due to the highly derived, paedomorphic state of the group rather than an ancestral condition, something that should have been apparent from comparison to Sphenodon sp. as the outgroup.  A fused premaxilla turns up allot throughout squamate evolution: iguanians, varanids, mosasaurs, snakes, dibamus, some skinks, some geckos.  

The ventromedial process of the pterygoid is especially problematic because it not only appears in other major groups, particularly the Scincophidia (tax. nov.) and the anguinae, but it is reversed several times back and forth within the Iguania.  The Chamaeleontiformes, which includes the living acrodont iguanians and several fossil taxa is considered one of the major divisions in iguanians in other analyses has one reversal from the 'ancestral' condition and there is yet another reversal from the chamaeleontiform condition in two fossil taxa within that group.  This happens again later in the Scincophidia.  It supposedly united some derived skinks, dibamids, amphisbaenids and snakes, but dibamids don't actually have it.  This isn't the only character that does this, but I'm using it as the example.  

Intuitively, reversals from the ancestral character state shouldn't go back and forth several times in one lineage.  If it does, then there must be a strong functional correlate to it and it is therefore a highly plastic and probably bad character.  Also, characters like this popping up all over the tree would make it very hard to think of the systematics in terms of a dichotemous key.  I realize that a dichotemous key doesn't actually reflect evolutionary relationships, but if you only have one or two characters that unite big groups, it aught to at least be close or show up at some point in the creatures development.  It works for plants, birds, mammals and just about every really major group, so why not lizards?

The analysis has 363 characters and 222 ingroup taxa, so clearly this isn't a problem that is just going to be solved by throwing more characters or more taxa at it.  So what other options are there?  Character weighting or unidirectional characters?  The snakes with legs are my preferred group for this example but other groups could be used.  In the Conrad analysis, snakes fell out with other legless lizards in a clade supported by characters largely relating to enclosure of the braincase and modification of the palate.  That by itself doesn't really pose a problem except that snakes with legs, some of the oldest known fossil snakes, fall out as derived macrostomatans.  They are legged beasts nested deep within an otherwise legless group.  I find it hard to believe that they either re-evolved seemingly vestigial legs or that every other group independently lost them.  Possession of legs is such a big character that it implies that the polarity of other, more fine detail characters, is wrong.  Do you make leg possession a unidirectional character?  Weight it more than other characters?  Both of these seem wrong since the natural polarity of a character should be supported by the other characters in an analysis.  

The problem of convergence in snakes and legless lizards could be huge.  The uropeltine snakes are a very bizarre group, specialized for a very specific mode of life.  If they are a natural group, one would expect them to come out in a fairly basal position due to the sheer number of characters that they have in common with each other compared to any other member of the snakes.  If there is a single charcter that would, say unite them with Cylindrophis and 5 that unite them with each other, then Cylindrophis might be pulled out and stuck with macrostomatans because of plesiomorphies.  Establishing character polarity in a group is important but difficult, even in groups that you are certain are monophyletic.  The basal split between horned lizards (phrynosomatidae) and all other iguanians seems similar.  You have a very bizarre, highly specialized group, of unquestioned monophyly pulled out into a basal position on the phylogenetic tree.  This kind of thing could be what causes all of the character reversals higher up in the tree.

Riddle of the Skinks

I've been officially in grad school now for a few weeks, and it's about time that I actually nailed down what my thesis project is going to be.  Originally I was going to work on Western Australian agamid lizards, but I was informed that there was an easier group to work on: skinks.  The argument was this 'nothing is known about the morphology of australian agamids but next to nothing is known about australian skinks.'  Consequentially, the lizard that I'll be describing in minute detail is a small, sand swimming skink named Eremiascincus.  That is a good start, but what exactly will be the usefulness of describing this species if there is nothing described to compare it to.  Supposedly the goal of this project is to provide a tool for identifying isolated skull fragments in the fossil record.  Knowing the detailed osteology of one lizard basically tells you: okay, it's not that one, it must be one of the other 150 closely related species.

It turns out that the reason that little is known is not for a lack of trying, but rather the fact that the details one must consider are so fine and esoteric that little progress is even possible.  For example, Eremiascincus was erected as a separate genus in 1979 after about 150 in the genus Sphenomorphus, a genus that contained more than 150 species.  None of the diagnostic characters used to erect the genus were osteological.  In fact, what apparently justified making it a separate genus was a the possession of a line of dorsal ridges and either lots of stripes or very few stripes (depending on which species of Eremiascincus one is examining).  Stripiness?!  Seriously!?  The description isn't much help either, listing characters that definitely place it in the Sphenomorphous group of skinks, but are characters that hardly make it unique (quite the opposite really).  

Then there is the diagnosis of the Sphenomorphous group.  It turns out that the genus sphenomorphous is no longer used to refer to any Australian skinks.  All the the Australian sphenomorphine skinks were placed into other genera.  As soon as I find out what they were put into and on what basis, I might have something to go on.   As it is, there is an ok phylogenetic tree available based on molecular data, but I'd really only use that for corroboration of morphological data, or to look at what closely related taxa to describe with Eremiascincus.

Missing You

Last summer, I did some surveying with a woman named Steph. Besides finding fossils, Steph was focused on getting as much area done as possible. She surveyed very, very fast, so that I was sure that she couldn't possibly have been getting everything. I brought this to the attention of our supervisor and was told that she didn't think that Steph was going too fast. Having been either chewed out or brushed off when ever I brought it up, I just dropped the subject. As a consiquence though, in an area that we nick-named Valley of the Birds, we apparently missed what is possibly the most significant bonebed ever found in this particular formation. The way that it was found was that last week my supervisor and the lead paleontologist for the company were out mapping the geology of the area on their own time and litterally stumbled upon it. It's bee described to me as so obvious and extensive that there is no way that we could have missed it if we had actually looked at those rocks. As a result, I feel bad for having let myself be pressured into going faster than I thouht was adequate for the survey and my supervisor feels bad for having not taken my complaints seriously. We're now planning on going back and resurveying areas that were previously done by only Steph and I so that we can correct for her influence over the results.

Long Overdue Update

I'm waiting for my supervisor to finish some office stuff before we go out into the field to extract a large (possibly) brontothere jaw from an extremely large block of sandstone, so I thought that I should take this opportunity to post a long overdue update on what has been going on.

I've been in Vernal, Utah since mid July and will likely be out here until the stat of October, when everyone else takes off and makes it impossible for me to continue working. What I've been doing is what we lovingly call "catch and release paleontology." That is, I'm doing surveys of a very large area on the Ute Tribe Indian Reservation so that when oil wells are put there in the next couple of years, they will know what spots to avoid so as to minimize the impact on this valuable scientific and cultural resource. The bad thing is, and this is the release portion of the name, although we are finding vast quantities of extremely scientifically valuable fossils, that would probably close to double the total collections of fossils from this time period, we are prohibited by the tribe from actually collecting anything on their land. We are allowed to collect fossils from BLM land (hense why I'll be heading out in a few minutes) but our survey of BLM land is restricted to areas where they have already decided to put an oil well. The opinion of the Ute tribe appears to be that they want the fossils saved from destruction by drilling equipment and bulldozers, so that they can be destroyed by the ravages of natural erosion instead.

The most common thing that we find on the reservation is fragmentary turtle remains. There are three or four distinct kinds of turtles here, but only one is readily distinguishable by the texture of its shell. Typically, the turtles are broken by erosion into such small pieces that the texture of the shell is the only thing that we can go by. Other than turtles, we are also finding crocodiles, alligators, tapirs, rhinos, primitive horses, primitive artiodactyls called protoreodonts and leptoreodonts, camels, brontotheres (looks like a rhino but only distantly related) and a variety of microfossils. Most of the animals we find are only fragmentary remains, with jaws and teeth being the most commonly preserved part of a mammal. This is not to say that other parts are not sometimes found as well. In fact, on my first day out in the field, I found the skull of a rhino practically sticking out the side of a cliff.

The number of co-workers that I have has varied widely since I got here as different people arrive and leave as their schedules allow. With two exceptions though, they've all been (at least) moderately attractive young women. The face of paleontology is certainly changing.

Beyond work thought, there hasn't been much going on for me. My Birthday was last month and my parents ordered some really interesting books (Cope's Bible and Este's Phylogeny of the Lizards if you're interested in knowing) and my grandparents sent me checks cumulatively large enough that I can get an air scribe and a stereomicroscope. Tremendous thanks to them if they are reading this! I've also gotten to do some fossil hunting on my own including going out near Bonanza and digging in the Parachute Creek member of the Green River formation. Things that I found there include a large number of fossilized beetles, flies, mosquitos, weavles, leaves and even a small number of exquisite flowers. I also got to go over the mountains to the Bridger Basin (a historically famous area for eocene mammals: Cope and Marsh faught bitterly over naming creatures from that area). The purpose of my brief visit there was to help SWCA's lead paleontologist, Paul Murphy, look for fossils from the upper most Bridger formation, which is also the least fossiliferous, in order to find support for the hypothesis that the upper Bridger is the same age as the Uinta Formation.
I also had a brief and somewhat dissappointing trip to Denver for the Mineral and Fossil show that was out there, but Peter Larson of the Black Hills institute once again beat me to the interesting lizard fossils. I'm fairly confident that he got a new species of mosasaur from Morocco, since it had teeth that were intermediate in form between globidens and a more classic mosasaur dentition.
That pretty much brings everyone up to date. I will have pictures of events so far in an upcoming post and I intend to start posting more regularly.

Paleo News

I haven't updated in a while, so I thouht that I would do the public service of providing links to recent news articles related to paleontology.

The miocene fossil remains of a small land mammal have been found on the south island of New Zealand. This disproves the view that the landmass has been without indiginous mammals since it split from the rest of Gondwanaland during the Cretaceous. This means that there was either a lineage that survived on the island from the original split, or that there was some sort of contact (maybe a land bridge) with other land masses that allowed the imigration of the mammals to the island at some point in the intervening period. The article implies that discovery means that New Zealand's flightless birds such as the kiwi and the kakapo (possibly too cute to live) would have lost their ability to fly in the presence of indiginous mammals. I think that it is possible that the kiwi lost flight in the presence of mammals, but that is because it is part of the paleornithine clade (including ostriches, emus, rheas, moas) that are almost all flightless (tinamous aren't). I suspect that the relative defenselessness of New Zealand birds would have been a novelty that arose in the pleistocene or late pliocene. link

The Joggins fossil cliffs, a deposit that has revealed some of the earliest and most primitive amniote fossils in the world, is going to get a gift shop. The province of Nova Scotia and the Canadian government are puting up $7 million for an interpretive center at the site in hopes of getting it classified as a world heritage site (something that I assumed it already was). I don't really see this as the blessing that others might. On the one hand, it will bring attention to the site and hopefully a means of generating funding for further research on fossils from it. However, it has been my experience that the best way to preserve a site is to keep the general public as far away from it as possible. It isn't as though scientists won't think to explore the cliffs for fossils if it doesn't get advertising or a place on a tourist map. Among people who know vertebrate paleontology, it's already one of the most famous sites in the world. Bringing in the public is just an invitation to loose fossils to day trippers and amature collectors. I'll grant that other fossil based world heritage sites have interpritive centers (the burgess shale comes to mind) but they are usually hard to get to, and as far as I know, haven't really generated new research. link

An insectivorous mammal has been recovered from the lower Cretaceous of Mongolia with a preserved gliding membrane between it's limbs. The discovery, reportedly a member of a newly designated order, represents the earliest airborn mammals, greatly surpassing the earliest bats from the eocene. Several articles also mistakenly report that this mammal predates the birds in it's aerial exploits. Archaeopteryx, from the Kimmeridgian stage of the Jurassic, predates the new mammal by about 30 million years. Furthermore, fossil birds from Lioaoning are about the same age as the gliding mammal. link

In more news from Mongolia, more Tarbosaurus remains have been found in an international effort (including University of Alberta proffessor Phil Currie), thereby bulsturing my claim made nearly a year ago to a fossil dealer in Tucson that for $100,000 I could find my own Tarbosaur. link