New Evolution of Humans Video on YouTube

The origin of mammals from cynodonts is universally accepted.
The origin of humans from primates is universally accepted among paleontologists, not among religious conservatives. Perhaps this short video can help fact check a few misconceptions.

Figure 1. Human evolution video on YouTube. Cllick to view.

Figure 1. Human evolution video on YouTube. Cllick to view.

Here you’ll see the origin of humans,
and all their many body parts, in a new light. We start with fishy tetrapods, just hitting the beachheads 365 million years ago (mya). By 340 mya the first reptiles were already diversifying. Our lineage goes on from there in a stepwise progression with novel traits appearing with each successive taxon every few million years in the fossil record.

The record is becoming more and more complete.
Using the closest known sister taxa to the actual lineage we can document a gradual accumulation of human traits, both bones and soft tissues, as well as likely behaviors based on phylogenetic bracketing. Here the human lineage runs through the reptilomorphs and seymouriamorphs, the basal reptiles, the synapsids, the therapsids, the cynodonts, the mammals, primates, anthropoids and hominids, only some of which ultimately evolved to become human.

Feel free to pause the video
at any point if scenes change before you finish reading a frame.

Look for other YouTube videos
that document the origin of pterosaurs, dinosaurs and turtles in a similar fashion.

More details and reference materials
can be found at ReptileEvolution.com

Want more?
For the story of human evolution going back through raw chemicals, cells, worms and fish (along with all of the above taxa), read “From the Beginning, the Story of Human Evolution” by David Peters (Little Brown, 1991), a copy of which can be found as a pdf online at www.davidpetersstudio.com/books.htm

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The origin of feathers and hair (part 1: skin and scales)

Three clades
developed extra dermal hair-like structures: mammals, dinosaurs (reaching an acme in birds) and pterosaurs. Traditional thinking holds that reptile scales evolved early, along with the origin of the amniotic membrane. Both of these were viewed as adaptations to a non-aquatic, (i.e. ‘dry’) environment. Unfortunately there’s very little evidence for scales in the earliest reptiles (see below). They appear to have lived in a moist coal forest leaf litter environment throughout the Carboniferous.

Basal amniotes
Dhouailly 2009 reports: “The common ancestor of amniotes may have presented both a glandular and a ‘granulated integument’, i.e. an epidermis adorned with a variety of alpha-keratinized bumps, and thus may have presented similarities with the integument of common day terrestrial amphibians. Whereas the glandular quality of the integument was retained and diversified in the mammalian lineage, it was almost completely lost in the sauropsid lineage (non-mammalian amniotes). When the amniote ancestors started to live exclusively on land in the late Carboniferous, they derived from a group of basal
amphibiotic tetrapods, and it is plausible that they evolved a skin barrier similar to that of modern toads to prevent desiccation”

Two dermal proteins
are key to discussions on reptile skin: alpa-keratins and beta-keratins.

Alpha-keratins
Dhouailly 2009 reports: “In all living vertebrates, at least from trout to human, specific types of alpha-keratins characterize the epidermis and corneal epithelium showing a strong homology in the different lineages.In all amniotes, the last supra-basal layers of the epidermis are cornified, meaning they are formed of dead cells filled entirely with alpha-keratin filaments coated with specific amorphous proteins and lipids, providing a barrier to water loss.”

Beta-keratins
Dhouailly 2009 reports: “Only the sauropsids (birds and reptiles) possess an additional capacity for beta-keratin synthesis, an entirely different type of intermediate filament, which appears to result from a phylogenetic innovation that occurred after that of the alpha-keratins.”

Perhaps a correction here: In the large reptile tree there is no clade “Sauropsida.” Rather synapsids are more derived than the basal reptiles that ultimately evolved into the other amniotes. So, if beta-keratins had a single origin, mammals and perhaps their closest ancestors lost the capacity to produce beta-keratins. Phylogenetic bracketing indicates this could have happened at any node between Protorothyris and Megazostrodon.

Scales
When did scales arise? And are lizard scales homologous with those of turtles, crocs, birds, pangolins and opossum tails? Unfortunately fossils of skin and scales are rare.

Carroll and Baird 1972
traced long interwoven ventral ‘scales’ for the basal lepidsosauromorph, Cephalerpeton,  similar to those found in anamniotes like Gephyrostregus watsoni. Carroll and Baird also report, “The skin impressions along the forelimb [of Cephalerpepton] have a slightly pebbly texture—rougher than the limb bones but smoother than the broken surface of the matrix. There is no evidence of discrete scales. An indication of epidermal scales would be expected in this type of preservation, if they were present in the animal.epidermal scales can only be recorded as impressions and this type of preservation is rare and apparently not reported in other Paleozoic reptiles.”

As you’ll recall, reptiles divide at the start into two lineages, the Lepidosauromorpha and the Archosauromorpha.

Lepidosauromorphs 
The most primitive appearance of dermal tissue in the lepidosaurorph line occurs with the scutes of pareiasaurs, Sclerosaurus and basal turtles. These include a bony base. At some point turtles developed scales that covered the face and limbs, but when is not known. My guess is as far back as Stephanospondylus because it was a large and tasty herbivore.

Otherwise nothing on scales appears until  Xianglong, a gliding basal lepidosaurifom (not a squamate). Li et al. 2007 report, “The entire body including the skull is covered with small granular scales, which show little size variation.” Perhaps noteworthy, this is the node at which some short-legged, ground-dwelling flattened owenettids evolved to became large-limbed and arboreal, exposed to the dry air above the damp leaf litter.

Perhaps more misunderstood, those wing spars are actually ossified dermal extensions, as in a sister taxon, Coelurosauravus, not extended ribs, as we carefully considered earlier here and here.

Figure 1. Xianglong, a basal lepidosauriform with dermal extensions, not ribs, with which it used to glide.

Figure 1. Xianglong, a basal lepidosauriform with dermal extensions, not ribs, with which it used to glide.

Then there’s Sphenodon, an extant basal lepidosaur with a variety of large and small scales, some were overlapping and others were not. Basalmost sphenodontids, like Pleurosaurus, were trending toward an aquatic niche. Sphenodon is a burrowing and foraging reptile. the best clue to basal sphenodontid squamation comes from a tritosaur sister, Tijubina (see below).

Of course, all living lizards (squamates) have scales.
and they shed their skin in whole or in patches during ontogeny.

The tritosaur lepidosaurs are a special case,
The basal tritosaur, Tijubina, preserves rhomboid scales on the neck, large rhomboid scales on the trunk and annulated ones on the ventral side of the entire caudal region. Not far removed from Sphenodon with regard to squamation.

By contrast, a more derived tritosaur, Huehuecuetzpalli preserves tiny disassociated calcified granular scales over its dorsal neural arches. A more derived tritosaur, Macrocnemus (Renesto and Avanzini 2002), had a scale covering in the sacral and proximal caudal region.

Now things get more than interesting…
The scales of Cosesaurus (Ellenberger and DeVillalta 1974, Fig. 2) were about the size of the matrix particles in its mold, so they have not been described. However, Cosesaurus had extra dermal tissues in the form of a gular sac, a dorsal frill, fibers streaming from the posterior arm, uropatagia trailing the hind limbs and long hairs emanating from the tail. A larger sister, Kyrgyzsaurus had scales and similar extra dermal ornaments. Sharovipteryx shares these traits and accentuates the uropatagia. Longisquama shares these also but accentuates the dorsal plumes. The latter two taxa also have pycnofibers (hairs) at least surrounding the cervical series. Their sisters, the pterosaurs, accentuate the trailing arm fibers, which become fiber-embedded foldable wings. Pterosaur ‘hair’ reaches its acme in Jeholopterus, which may have used its ‘hair ball’ as a barrier to insects likewise attracted bloody patches of dinosaur skin. In certain basal pterosaurs the tail hairs coalesce to become tail vanes.

Figure 2. The basal fenestrasaur precursors of pterosaurs, including Cosesaurus, Sharovipteryx, Kyrgyzsaurus, Longisquama and a basal pterosaur.

Figure 2. The basal fenestrasaur precursors of pterosaurs, including Cosesaurus, Sharovipteryx, Kyrgyzsaurus, Longisquama and a basal pterosaur.

It is clear in fenestrasaurs that extra dermal membranes were secondary sexual traits, decorations that enhanced their chances for mating. Hairs ultimately became barriers or acted as insulation. Arm fibers ultimately became wings.

Archosauromorphs
Like the basal lepidosauromorph, Cephalerpeton, basal archosauromorphs like Eldeceeon  had ossified belly scales in V-shaped patterns, but not coalesced to form gastralia.

According to Carrool and Baird (1972) in Brouffia, “many ventral scales are present in the blocks. They are quite broad, rather than being narrowly wheat-shaped, as has been considered typical in early reptiles. A faint impression of dorsal scales is evident also, but these are too insubstantial to illustrate.”

Pelycosaurs lacked scales. They were naked. So were basal therapsids as far as the fossil record goes. Estemmenosuchus (Chudinov 1970), an herbivorous therapsid, preserves no scales, hair or hair follicles*. However, the preserved skin was well supplied with glands.

Since all living basal mammals (Fig. 3) are richly endowed with fur, that trait probably extends to the first tiny egg-laying mammals, denizens of the leaf litter. In tiny animals, so in contact with the substrate, the leaf litter and water, hair appears to have developed not only to insulate its little warm-blooded body, but also to act as a barrier to all dermal contact with the environment. Insects, like fleas, had to lose their wings to burrow past the hair to get to the skin.

Figure 2. This is Amphitherium a basal mammal.

Figure 3. This is Amphitherium a basal mammal.

In basal diapsids, the sisters of basal synapsids no dermal material has been found.

Plesiosaurs and ichthyosaurs were naked, so pachylpleurosaurs, thalattosaurs and mesosaurs were likely naked as well. A rare exceptions, the thalattosaur Vancleavea, was covered with large bony scales. Hupehsuchids had short bony plates over the neural spine tips.

For protorosaurs or proterosuchids no dermal scales have been reported.  Dorsal armor developed as large plates in the likely piscivore Doswellia, and to a less degree in Champsosaurus, Diandongosuchus, and then again to a greater degree in parasuchids, proterochampsids and chanaresuchids.

For euarchosauriformes a line of dorsal scutes also appeared on the dorsal midline of Euparkeria and many descendant taxa (except finbacks and poposaurs). The herbivorous Aeotosaurs,  Revueltosaurus and Simosuchus independently expanded their armor in similar ways. So did the carnivorous extant alligators and crocodiles and their ancestors. However basal bipedal and near-bipedal croc taxa, like Gracilisuchus do not preserve scales, other than their dorsal scutes. These may have enhanced the strength of the backbone. Otherwise, basal bipedal crocs were likely not heavily scaled, and neither were the oceanic swimmers, like Metriorhynchus.

That brings us to dinosaurs.
Kaplan (2013) reports “the overwhelming majority had scales or armor.” We’ll cover dinosaur scales and dinosaur feathers in more detail in part 3: feathers.

References
Kaplan M 2013. Feathers were the exemption rather than the rule for dinosaurs. Nature News. doi:10.1038/nature.2013.14379
Renesto S and Avanzini M 2002. Skin remains in a juvenile Macrocnemus bassanii Nopsca (Reptilia, Prolacertiformes) from the Middle Triassic of Northern Italy. Jahrbuch Geologie und Paläontologie, Abhandlung 224(1):31-48.
Carroll RL and Baird D 1972. Carboniferous Stem-Reptiles of the Family Romeriidae. Bulletin of the Museum of Comparative Zoology 143(5):321-363. online pdf
Bennett AF and Ruben JA 1986. The metabolic thermoregulatory status of therapsids. In The Ecology and Biology of Mammal-like reptiles (Hottom, Roth and Roth eds) 207-218. Smithsonian Institution Press, Washington DC
Chudinov PK 1970. Skin covering of therapsids [in Russian] In: Data on the evolution of terrestrial vertebrates (Flerov ed.) pp.45-50 Moscow: Nauka.
Dhouailly D 2009. A new scenario for the evolutionary origin of hair, feather, and avian scales. Journal of Anatomy 214:587-606.
Lecuona A and Desojo, JB 2011. Hind limb osteology of Gracilisuchus stipanicicorum(Archosauria: Pseudosuchia). Earth and Environmental Science Transactions of the Royal Society of Edinburgh 102 (2): 105–128.
Persons WC4 and Currie PF 2015. Bristles before down: A new perspective on the functional origin of feathers.Evolution (advance online publication)
DOI: 10.1111/evo.12634
http://onlinelibrary.wiley.com/doi/10.1111/evo.12634/abstract

* too bad I did not know this when I painted Estemmenosuchus with scales for the cover of a book.

Minor changes to the large reptile tree

Adding a few taxa to the large reptile tree generally causes a reassessment of past scorings that stand out as autapomorphies. Some of these represent earlier mistakes. When the mistakes are corrected the tree can shift the nesting of taxa. Some taxa are only one or two steps away from a minor shift anyway, especially the incomplete taxa. So this can happen. No major tree topologies have changed, however.

Turfanosuchus
Previously nested outside of the Archosauria, Turfanosuchus now nests at the base of the Dinosauriformes along with the PVL 4597 specimen attributed to Gracilisuchus, Trialestes and Herrerasaurus, which drops out of the Theropoda.

Batrachotomus and Saurosuchus
Now nest together. No biggie.

Saurosphargidae
The nesting of the referred specimen of Brazilosaurus at the base of the Thalattosauria somehow shifted Largocephalosaurus and Sinosaurosphargis back to the base of the Sauropterygia (placodonts + plesiosaurs). These two are so different from their sisters, yet this nesting is only held in place by a few steps. And it’s still entirely possible that the dermal armors of saurosphargids and placodonts were derived independently.

Protodiapsids
The list of protodiapsids have arranged themselves into three distinct clades, shortening the phylogenetic distance between the basal synapsid Archaeothyris and basal diapsids like Tangasaurus (Enaliosauria) and Thadeosaurus (Younginids and Archosauriformes).

Cephalerpeton
The basal reptile Cephalerpeton now nests basal to only the new Lepidosauromorpha. This makes the Reptilia truly diphyletic following the tiny Gephyrostegus specimen. Cephalerpeton shares more traits with those early captorhinomorph herbivores than the more insectivorous and lizardy Brouffia, at the base of the new Archosauromorpha.

Milleretta RC14 and Bolosaurids
Bolosaurids now nest separate from the caseids and the higher Lepidosauromorpha.

Odontochelys, still not a turtle
Odontochelys nests outside of the clade that produced Proganochelys, so developed its turtle-like traits by convergence based on the current list of characters and taxa. Another putative turtle ancestor, Eunotosaurus nests closer to caseids.

Tritosaurs up to 18+ taxa
Not bad for a totally new clade… Not counting all the pterosaurs, drepanosaurs, macrocnemids, etc. the Tritosauria now number 18 in the large reptile tree. Let’s put some more of these former oddballs and former enigmas into lepidosaur trees to confirm or deny this topology.

It just takes a little effort and a sense of wonder. And take off those blinders!

Watson’s (1957) View of the Reptilia

Long before computers,
paleontologists used their wits and lists of traits to tie taxa together in evolutionary sequences. Some nestings and match-ups were easy. Others were… not so easy.

Watson 1957 (Fig. 1) produced his version of the reptile family tree produced without the benefit of computers and matrices. In those days, if relationships were unknown they were unlinked in the graphics. Rarely is the entire gamut of the Reptilia presented, so here we have an early version of the large reptile tree.

Figure 1. Click to enlarge. Watson 1957, his view of the reptile family tree overprinted with yellow for the new lepidosauromorpha and with blue for the new archosauromorpha from the large reptile tree.

Figure 1. Click to enlarge. Watson 1957, his view of the reptile family tree overprinted with yellow for the new lepidosauromorpha and with blue for the new archosauromorpha from the large reptile tree. Notably, except for a few easily moved clades, this is not that far from the diphyletic tree recovered at reptileevolution.com.

Some changes since 1957
In the large reptile captorhinids, caseids, pterosaurs, Milleretta and Saurosternon moves to the new Lepidosauromorpha. Hovasaurus, Tangasaurus and thalattosaurs move to the new Archosauromorpha. These changes are noted by the overlying colors. Still, all in all, not too far off the mark!!!

Some things did not change since 1957
Tanytrachelos, Tanystropheus and Macrocnemus nested in Watson’s tree (Fig.1) at the base of the lepidosaurs distinct from the protorosaurs. That shows some insight. Turtles also nested with the lepidosaurs. Protorosaurs and younginids nest in Watson’s tree at the base of the “Thecodontia” now considered the Archosauriformes, as they do in the large reptile tree. Watson assumed these groups all descended from the Millerosauria. The large reptile tree confirms this relationship, with the exception of the lepidosauromorph, Milleretta, which does not nest with the protodiapsid archosauromorphs Milleropsis and Millerosaurus, but is closer to caseids and turtles and lots of other rarely reported taxa.

From then til now
Nowadays we know the origin of reptiles goes back a little further than the Late Carboniferous. Furthermore, we can connect all the leaves on the reptile family tree without the missing links and with complete resolution.

Earlier a similar chronology of fossil reptiles using a computer-generated phylogram mated to a time chart was presented. It gives a fuller picture of Watson’s tree.

Missed this earlier milestone a few days ago: We’ve passed 800 posts here.

References
Watson DMS 1957. On Millerosaurus and the Early History of the Sauropsid Reptiles. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 240: 673: 325-400.

Reptile Phylogram Updated

As promised, updates arrive, but not always promptly.

Here is an updated phylogram of the large reptile tree placed against a time scale. Due to the large number of taxa (340+) it is quite impossible to read this unless you download the PDF file. Then there’s no limit to its magnification.

A phylogram differs from a cladogram in showing the amount of change between taxa by the length of the horizontal bars. Longer bars indicate greater morphological change.

Figure 1. The new phlogram of the Reptilia and its outgroups. Click for pdf file. Even at this scale the diphyletic nature of the Reptilia is readily apparent, as is the great flowering of reptiles in the Permian and Triassic.

Figure 1. The new phlogram of the Reptilia and its outgroups. Click for pdf file. Even at this scale the diphyletic nature of the Reptilia is readily apparent, as is the great flowering of reptiles in the Permian and Triassic.

Some key features

1. Sometime during the Carboniferous (Mississippian + Pennsylvanian) reptiles had their origin and their original split, but not much happened or is known about them from that remote time. Reptiles remain in the minority (it was the age of Amphibians) and no great radiations occurred then.

2. The Permian was a time of great radiation for both the Archosauromorph and Lepidosauromorph lines. Among the former, synapsids paralleled proto-diapsids and early diapsids. Among the latter large diadectomorphs and pareiasaurs dominated.

3. During the PermoTriassic extinction event only a few lineages made it through.

Among the new Lepidosauromorphs the turtles (Proganochelys) and the lepidosaurs (Paliguana, Lacertulus) survived.

Among the new Archosauromorpha three main lines survived. Certain Permian synapsids evolved to become Triassic protomammals and Jurassic mammals. Dicnynodonts also made it through.

Permian enaliosaurs like Claudiosaurus and Stereosternum gave rise to a large marine radiation in the Triassic.

Permian younginoids, like Thadeosaurus and Protorosaurus, gave rise to a large terrestrial radiation in the Triassic.

4. Many of the Triassic lepidosauromorphs did not change much into the Jurassic, Cretaceous and later eras.

By contrast, most of the Triassic archosaurmorphs became extinct or evolved into other taxa during later eras.

5. There are a few chronological oddballs, like Lotosaurus, a taxon claimed to come from Early Triassic sediments, but this seems at odds with the evolution of its purported temporal contemporaries and phylogenetic sisters.

Basal Lepidosauromorpha – the story told with skulls

Sometimes it just helps
to see a bunch of taxa together to get an appreciation for the evolution of one to another to another and another. Well, here are the members of one branch of the basal reptiles, the early plant-eaters, the new Lepidosauromorpha, all taken from the large reptile tree (recently slightly revised).

Click to enlarge. These skulls are arranged phylogenetically according to the results recovered from the large reptile tree.

Figure 1. Click to enlarge. These skulls are arranged phylogenetically according to the results recovered from the large reptile tree.

Contrary to conventional thinking,
the Diadectomorpha and Chroniosuchia are nested here within the Reptilia rather than within the pre-amniotes. Contrary to conventional thinking, the Caseasauria are nested here within the Millerettidae, rather than the Synapsida. These, and other new relationships were determined by adding taxa and thereby expanding the gamut of opportunities for every taxon to nest most parsimoniously – where the changes between taxa are minimized echoing the actual tree of reptile evolution.

Central to these discussions
Romeria primus (Fig. 1 in pink) – is at the base of the millerettids that begat the bolosaurids, acleitorhinids (not related to Lanthanosuchus btw), and the caseasauria, which now has new basal members, Feeserpeton and Australothyris. Romeria primus was largely ignored in prior studies. Now, perhaps, its importance will no longer be overlooked.

Orobates (Fig. 1 in yellow) – is leading the way toward Tseajaia and Tetraceratops, Limnoscelis, Procolophon, the lineage of Diadectes, Chelonia beginning with Stephanospondylus, and not finally the Pareiasauria. Orobates, likewise needs to rise in importance and needs to be added to several more focused phylogenetic analyses.

Saurorictus, Macroleter and the lanthanosuchids, Romeriscus and Lanthosuchus.

Figure 2. Click to enlarge. Saurorictus, Macroleter and the lanthanosuchids, Romeriscus and Lanthosuchus.

I say not finally because the next clade includes Saurorictus and Nyctiphruretus (Fig. 2) and the remainder of the new Lepidosauromorpha, including lanthanosuchids (Fig. 2), owenettids and the Lepidosauriformes.

No strange bedfellows here.
All taxa demonstrated gradual transitions from one to another. With this new phylogeny and tree topology the taxa that may or may not be someday discovered can more accurately be predicted based on phylogenetic bracketing. Hopefully more discoveries will help find the sisters of Orobates that will help define the base of this new, hitherto unknown clade.

Not amphibians!
Hopefully readers will glean the important fact that limnoscelids, chroniosuchids and diadectids are not amphibians (pre-amniotes), which represents conventional thinking. No, they’re nested deep within the Reptilia, far from Gephyrostegus and its ancestors and their kin.

Eudibamus is notably absent
Because Eudibamus is not a bolosaurid. It is a basal diapsid close to Petrolacosaurus. Strong foot homologies and long suite of other traits nest it there, not with heavy, plant-eating bolosaurids.

As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.

Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.

Testing Hill 2005

N.  Brocklehurst wrote,
“I think your repeated assertion that palaeontologists don’t test the relationships you suggest is a bit…well its just not true. Admittedly some havn’t been tested e.g. Tetraceratops (never tested outside synapsids), but a great many have. As just one example Hill (2005) uses a (mostly) genus-level taxon list which covers 80 taxa from almost all the major groups in Amniota with charater list almost 3 times the size of yours to show that Caseids do not go with Milleretids and Bolosaurids, Rhynchosaurs do not go with Rhynchocephalians, Ophiacodontids are not the sister to Therapsids, Synapsids do not go with Archosaurs, Captorhinids do not go with Lepidosaurs, Mesosaurids do not go with marine reptiles…I could go on.”

This is a topic worthy of a post. Coincidentally and several years ago I had studied Hill (2005) and submitted a manuscript describing its faults. It was rejected.

What Hill (2005) was looking for and how he did it
Hill (2005) sought to determine the phylogenetic position of turtles within the Amniota by increasing taxonomic sampling and including integumentary characters, like scutes on glyptodons and sauropods. Strange, mixing such taxa, only because they had scutes. But it was published, so hats off to Hill.

As in all supermatrices, no effort was made by Hill to cull the data or study the taxa. The data was presented ‘as is.’ Hill (2005) reported, “The morphological data set assembled here represents the largest yet compiled for Amniota.” He concluded with, “Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.”

I tested Hill (2005) back in 2006 (long before ReptileEvolution.com) in a three-step process.

1. Taking Hill (2005) as is. 
Hill 2005 created a supermatrix by combining published data and new data based on osteology and histology of the integument. Some strange pairings resulted (Fig. 1). Bulky Diadectomorpha nested as sisters to lithe marine Mesosauridae and as sister taxa to the Synapsida. None of these look very much alike. Round-faced Acleistorhinus nested with flat-faced Lanthanosuchus. Short-faced Trilophosaurus nested with long-faced Choristodera (Champsosaurus). The so-called ‘rib’ gliders nested with marine Sauropterygia. Turtles nest with Sphenodon and both are the sister taxa to Archosauria (dinos + crocs + parasuchia + aetosaurs). Parasuchians nest within aetosaurs. Aetosaurs nest within crocodylomorphs, derived from Protosuchus. Other than these misfits, the rest ain’t too bad. And we can’t blame Hill for this because, true to the method, he was just pulling together published trees (but without casting a critical eye on the data).

To one of Neil Brocklehurst points, note the sphenacodonts and basal therapsids are suprageneric in Hill (2005), so there was the opportunity for some cherry-picking of traits and key taxa. Stenocybus. a key taxon, was not included.

Hill 2005. See text for details.

Figure 1. Hill 2005. See text for details. Suprageneric taxa are marked by black squares.

2. Hill 2005 revision #1
A thorough examination of Hill’s data matrix revealed that hundreds of blank matrix boxes could be scored. Hundreds of others could be more accurately rescored, sometimes with additional character states to more accurately reflect characters. Since this was a supertree compilation, such a critical eye was not part of Hill’s process or method. I don’t like to let things slide.

Taxa that were difficult to access and contributed to excess polytomies using Hill’s scoring, such as Coahomasuchus, the titanosaur sauropods, Glyptosaurinae, Akanthosuchus, Goniopholis, Simosuchus and Mahajangasuchus were deleted. None of these taxa are basal to their respective clades.

Characters that were difficult to determine (foramina, braincase, notochordal opening) were left as Hill’s predecessors had scored them.

The resulting cladogram (Fig. 2) shows more appropriate tree topology with most clades in a more reasonable (more parsimonious) order (sister taxa look more alike overall and in detail), but pareiasaurs and turtles still nest here between lizards and Crurotarsi, which appears untenable.

 Hill (2005) revised.

Figure 2. Hill (2005) revised by the addition of more character scores. Note the topology changes.

3. Hill 2005 revision #2
The addition of a just few taxa (in red) to Hill (2005) revision #1 (Fig. 3) recovers a tree topology very much like the large reptile tree, including the major dichotomy at the base of the Reptilia (a hypothesis totally unknown to Hill in 2005). This underscores the importance of a wide gamut in a taxon list when exploring untested relationships. Here turtles nest with pareiasaurs, Procolophon and other lepidosauromorphs. Casea nests with Millerettidae, far from the Synapsida. Kuehneosaurus nests with similarly-shaped arboreal Lepidosauriformes. Synapsids and mesosaurs nest with sauropterygians and archosauriforms.

Adding taxa to the revision of Hill (2005).

Figure 3. Adding taxa to the revision of Hill (2005). Still not perfect, but a lot better.

It’s worthy to note that
the large reptile tree does not include any glyptodonts, derived crocodylomorphs or very many ornamented lizards. Instead the large reptile tree used more basal taxa to establish a wider gamut of relationships, leaving the above-mentioned highly derived taxa for other more focused studies.

It is also worthy to note that
even with so few taxa, and largely using Hill’s characters, the reptile tree dichotomy was recovered.

To Neil’s point about the Hill (2005) 3x larger character list
Once again: It’s the taxon list (not the number of characters) that needs to expand to figure out the amniote tree topology. As an example, see what just a few extra taxa can do to a tree? (Fig. 3). Any number of characters over 150 tends to flatten out the results from 95% consistency to 98% to 98.5% to 99.1%, never quite reaching, but very closely approaching 100%. On the other hand, every additional taxon provides an additional opportunity for any already included taxon to find a more parimonious partner somewhere on the tree. The larger the list, the better.

Assertion?
No. I tested that sucker. This is evidence.

As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.

Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.

References
Hill RV 2005. Integration of Morphological Data Sets for Phylogenetic Analysis of Amniota: The Importance of Integumentary Characters and Increased Taxonomic Sampling. Systematic Biology 54(4):530–547.