Looking for a furcula in Compsognathus

No furcula has been described in Compsognathus.
So if there is one, it has been hiding. I use DGS to look for possible candidates (Fig. 1).

Figure 1. Forelimbs and pectoral girdle for Compsognathus. A possible tiny furcula is identified here.

Figure 1. Forelimbs and pectoral girdle for Compsognathus. A possible tiny furcula is identified here.

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The premaxilla of Halszkaraptor: shorter than they thought.

Figure 1. Halszkaraptor images from Cau et al. Note the reconstruction with a too long premaxilla (red circle).

Figure 1. Halszkaraptor images from Cau et al. Note the reconstruction with a too long premaxilla (red circle). Short nore: the gastralia shown here evidently were not present in the fossil, but were imagined into place. Halszkaraptor nests with Shuvuuia, which also lacks gastralia. Let me know if either is incorrect. 

Originally described
by Cau et al. 2018 with 11 (x2) premaxillary teeth, Halszkaraptor stands out for having seven too many teeth in the premaxilla compared to all sister candidates. A closer look at the premaxilla reveals a mouth full of teeth, but the premaxilla has only four (x2) teeth. Cau et al. were kind enough to publish several views of the rostrum (Fig. 2).

Figure 1. The premaxilla and maxilla of the troodontid dinosaur Halszkaraptor shows the premaxilla is shorter with fewer teeth than originally described.

Figure 2. The premaxilla and maxilla of the troodontid dinosaur Halszkaraptor shows the premaxilla is shorter with fewer teeth than originally described.

Not alone on the cladogram.
Halszkaraptor is joined by Haplocheirus, which also has a similar short premaxilla (Fig. 3).

Figure 3. Haplocheirus nests close to Halszkaraptor in the LRT and has a similar short premaxilla.

Figure 3. Haplocheirus nests close to Halszkaraptor in the LRT and has a similar short premaxilla.

References
Cau A, et al. 2017. Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs. Nature. doi:10.1038/nature24679

wiki/Halszkaraptor
wiki/Shuvuuia
wikiHaplocheirus

The origin of Lissamphibia (frogs, salamanders, caecilians)

The origin of modern amphibians has been controversial.
A new paper by Pérez-Ben et al. 2018 seeks to clarify the issue. According to Wikpedia, “Currently, the three prevailing theories of lissamphibian origin are:

  1. Monophyletic within the temnospondyli
  2. Monophyletic within lepospondyli
  3. Diphyletic (two separate ancestries) with apodans within the lepospondyls and salamanders and frogs within the temnospondyli.”

From the Pérez-Ben et al. abstract:
Current hypotheses propose that the living amphibians (lissamphibians) originated within a clade of Paleozoic dwarfed dissorophoid temnospondyls. Morphological traits shared by these small dissorophoids have been interpreted as resulting from constraints imposed by the extreme size reduction, but these statements were based only on qualitative observations. Herein, we assess quantitatively morphological changes in the skull previously associated with miniaturization in the lissamphibian stem lineage by comparing evolutionary and ontogenetic allometries in dissorophoids. Our results show that these features are not comparable to the morphological consequences of extreme size reduction as documented in extant miniature amphibians, but instead they resemble immature conditions of larger temnospondyls. We conclude that the truncation of the ancestral ontogeny, and not constraints related to miniaturization, might have been the factor that played a major role in the morphological evolution of small dissorophoids.

The authors appear to be dividing
tiny (miniaturized) frogs from frogs in general (= immature temnospondyls). And that’s a good start.

The second hypothesis (above)
is supported and recovered in the large reptile tree (LRT (1154 taxa, subset in figure 1) in which Lissamphibians are indeed derived from dissorophids, but dissorophids are lepospondyls (yellow-green clade below), which are derived from reptilomorphs and seymouriamorphs (orange clade below), while temnospondyls are much more primitive and diphyletic (pink and blue clades below). The phylogenetic miniaturization occurred much earlier than Lissamphibia, which is a much larger clade if it is still defined by the inclusion of the more distantly related caecilians, deep within the Microsauria.

FIgure 2. Subset of the LRT has a larger gamut of taxa. Here lepospondyls nest together when more basal tetrapods are added to the taxon list than are present in figure 1.

FIgure 2. Subset of the LRT has a larger gamut of taxa. Here lepospondyls nest together when more basal tetrapods are added to the taxon list than are present in figure 1.

Quantitive approaches
have never trumped phylogenetic approaches.

First: Recover the cladogram.
Let it tell you what happened, and when and how. The dissorophids are indeed derived from more primitive temnospondyls, but several intervening transitional clades must be accounted for. 

References
Pérez-Ben CM, Schoch RR and Báez  AM 2018. Miniaturization and morphological evolution in Paleozoic relatives of living amphibians: a quantitative approach
https://doi.org/10.1017/pab.2017.22Published online: 23 January 2018

Caihong: the iridescent Jurassic troodontid

The preservation in situ is spectacular,
(Figs. 1, 2), but probably pales in comparison to the in vivo appearance of early Late Jurassic Caihong juju (PMoL-B00175 (Paleontological Museum of Liaoning, 161 mya), a new troodontid theropod dinosaur, which includes iridescent feathers.

Figure 1. Skull of Caihong from Hu et al. 2018.

Figure 1. Skull of Caihong from Hu et al. 2018. Arrow points to bony lacrimal crest/protuberance. At a screen resolution of 72 dpi this image of a 6cm long skull is about twice life size.

Caihong differs from other theropods

  1. Accessory fenestra posteroventral to promaxillary fenestra
  2. Lacrimal with prominent dorsolaterally oriented crests
  3. Robust dentary with anterior tip dorsoventrally deeper than its midsection
  4. Short ilium (<50% of the femoral length, compared to considerably >50% in other theropods).

Furthermore,
Caihong shows the earliest asymmetrical feathers and proportionally long forearms in the theropod fossil record. But the coracoids remained short discs. So it was not flapping those long feathered arms. It had extensively feathered toes. (Remember, chicken leg scales are former feathers and otherwise birds are naked beneath their feathers.)

About that unique lacrimal crest…
Note that the parietal has taphonomically moved anterior to the frontal. That’s odd, but it sets up another possibility for that elliptical crest bone. Look how it would precisely fit into the space created by the posterior parietal in dorsal view (Fig. 1). More precise, higher resolution data might provide some insight into this possibility.

Figure 2. Caihong overall in situ. This taxon nests better with Buitraptor, not Xiaotingia.

Figure 2. Caihong overall in situ. This taxon nests better with Buitraptor, not Xiaotingia.

Hu et al. nested Caihong
as a basal deinonyychosaur with the coeval Xiaotingia outside of the Troodontidae, but inside of the clade that includes two Solnhofen birds (only Archaeopteryx and Wellnhoferia). Microraptor, Dromaeosaurus and Rahonavis and others. The cladogram nests long-snouted Buitreraptor with Rahonavis and Unenlagia in an unresolved sister clade to the Xiaotingia/Caihong clade. Only a few nodes had Bootstrap scores higher than 50 and the nodes proximal to Caihong are not among them.

By contrast
the large reptile tree (LRT, 1153 taxa) nests long-snouted Caihong with even longer-snouted Buitreraptor in the troodontid clade that includes Anchiornis and Aurornis, basal to more derived troodontids and ‘Later’ Jurassic Solnhofen birds. Rahonavis and Microraptor nest with therizinosaurs and ornitholestids respectively.

Figure 1. Buitreraptor skull with bones and missing bones colorized.

Figure 3. Buitreraptor skull with bones and missing bones colorized. This skull is over 3x the size of Caihong.

Aurornis (Fig. 4) was basal, Caihong was transitional and Buitreraptor was derived in this clade of small troodontids with increasingly longer rostra.

Figure 1. Eosinopteryx and kin, including Xiaotingia, Aurornis and Archaeopteryx (Thermopolis).

Figure 4. Eosinopteryx and kin, including Xiaotingia, Aurornis and Archaeopteryx (Thermopolis).

Caihong may share these ‘unique’ traits
which are damaged in Buitreraptor. 

  1. Accessory fenestra posteroventral to promaxillary fenestra
  2. Lacrimal with prominent dorsolaterally oriented crests
  3. Robust dentary with anterior tip dorsoventrally deeper than its midsection
  4. Short ilium (<50% of the femoral length, compared to considerably >50% in other theropods).

References
Hu et al. (9 co-authors) 2018. A bony-crested Jurassic dinosaur with evidence of iridescent plumage highlights complexity in early par avian evolution. Nature.com/Nature Communications, 12 pp.  DOI: 10.1038/s41467-017-02515-y

Snake evolution: new paper suffers from taxon exclusion

DaSilva et al. 2018
bring us a new perspective on snake evolution that employs molecules, physical traits, embryos, fossils, CT scans… a huge amount of data and labor… perhaps all for nought because they excluded so many pre-snake taxa (Fig. 2). And their results do not produce a gradual accumulation of derived traits (Fig. 1), even when they omit the mosasaur skulls listed at their base of snakes. Here I added that missing mosasaur skull.

Figure 1. Figure 1 from DaSilva et al. 2018 with mosasaur skull added here. Note the complete lack of a gradual accumulation of traits leading to snakes and the very derived snake skull placed at the base of all snakes.

Figure 1. Figure 1 from DaSilva et al. 2018 with mosasaur skull added here. Note the complete lack of a gradual accumulation of traits leading to snakes and the very derived snake skull placed at the base of all snakes. No wonder they omitted adding the mosasaur skull to the parade of pre-snakes. IF you were part of this study and failed to raise your hand at this RED FLAG, then do better next time.

The DaSilva et al. abstract:
“The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.”  Fossorial = burrowing.

The DaSilva et al. Supplementary Data reports:
“To include a large dataset of squamate specimens, including extant, fossil, and embryonic taxa (see details below as well as Fig. 1 (main text) and Supplementary Fig. 1), we used a composite phylogenetic hypothesis based on the most recent molecular as well as combined molecular and morphological studies on squamate evolution.”

As readers know by now,
molecular data fails at large phylogenetic distances. It produces false positives. Even so, their large number of physical traits (691 morphological characters and 46 genes) should have given them a good cladogram… unless they omitted huge swaths of taxa.

Which is what they did (Fig. 2).

Even though they used fossil and embryological data,
their results do not produce a gradual accumulation of traits (Fig. 1). Nor do they employ appropriate outgroup taxa, either for squamates or for snakes (Fig. 2).

Without these key transitional taxa,
the authors have no idea what the basalmost squamates and snakes should look like. Here’s what the large reptile tree (LRT, 1152 taxa) recovered (Fig. 1):

Figure 1. Subset of the LRT focusing on squamates and snakes. Note how many key taxa in the origin of snakes have been omitted by the DaSilva et al. study.

Figure 1. Subset of the LRT focusing on squamates and snakes. Note how many key taxa in the origin of snakes have been omitted by the DaSilva et al. study.

If nothing else,
I hope readers gain a critical and skeptical eye toward published material. Sometimes it’s not what they say, but what they omit that spoils their results.

The LRT is a good base
to begin more focused studies in tetrapod evolution. It covers virtually all the possible candidates so workers can have high confidence that their more focused studies include relevant taxa and exclude irrelevant taxa.

For more information on snake origins
click here and/or here, along with links therein.

References
DaSilva FO et al. (7 co-authors) 2018. The ecological origins of snakes as revealed by skull evolution. Nature.com/Nature Communications (2018)9:376  1–11. DOI: 10.1038/s41467-017-02788-3 pdf

Another overlooked turtle ancestor just got published

Considered
congeneric with Elginia mirabilis (from Late Permian Scotland), the new elginiid comes from Late Permian China (Figs. 1, 2). The authors (Liu and Bever 2018) correctly identified the material in a specific sense, but had no idea what they had in a broader sense, because they only tested Elginia against pareiasaurs.

It’s really part of the genesis of turtles (Fig. 2), and we’re glad to see it!

Once again,
taxon exclusion raises its blind head. We’ve known Elginia was a turtle ancestor since 2014 when that went online. Unfortunately co-author Bever had earlier published on the genesis of turtles, relying on pre-turtle-mimic Eunotosaurus. Both are tested in the large reptile tree (LRT, 1152 taxa) and Eliginia nests with turtles. Eunotosaurus does not. It is more closely related to Acleistorhinus and kin. When Liu and Bever include Meiolania and Niolamia (Fig. 2) in their analyses, then they’ll see how it all plays out.

Elginia wuyongae (Figs. 1, 2) is smaller than Elginia mirabilis, lacks long horns and nests between the big desert pareiasaur, Bunostegos (Fig. 2), and its Scottish namesake at the base of hard shell turtles. Importantly, E. wuyongae preserves a few post-cranial data, including the genesis of the hard-shell turtle carapace…which is incredible news!!!

But you’re hearing that here first.
Jiu and Bever did not understand the importance and so overlooked it.

Figure 1. Elginia wuyongae was just described. It shows the genesis of shell formation in hard shell turtles.

Figure 1. Elginia wuyongae was just described. It shows the genesis of shell formation in hard shell turtles. That tiny last sacral vertebra (near the four dots) suggests a tiny tail was present. 

Lacks a rostrum…
skull is pretty beaten up, parts missing, holes pocket bones, lacks a palate. Squamosal misidentified originally (repaired here). Still, you gotta love it! It has post-cranial clues lacking in other transitional taxa. And it fills a gap!

How can workers not notice the family resemblance? 

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT.

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT. Those other horned pareiasaurs are basal turtles, meiolaniids with substantial carapace and plastron. Both sides of the new Elginia skull are shown. The squamosal is tucked inside the overlapping supratemporal in these transitional taxa. 

The authors do mention the turtle connection, like so:
“…and their long-hypothesized, but now largely rejected, potential as the close relatives
of turtles (Rieppel & deBraga 1996; Lyson et al. 2010; Lee 2013; Lyson et al. 2013; Bever et al. 2015; Schoch & Sues 2015; Laurin & Pi~neiro 2017).” It’s not surprising how many workers think this – because they don’t test the taxa that need to be tested, as they are tested here in the LRT. Remember, a consensus of workers can be wrong.

On that note:
Liu and Bever are still clinging to the invalid clade Parareptilia.

References
Liu J and Bever GS 2018. The tetrapod fauna of the upper Permian Naobaogou formation of China: A new species of Eliginia (Parareptilia, Pareiasauria). Papers in Paleontology 2018: 1-13.

Eutherian phylogeny and niches

Over the past two weeks
I’ve been attracted to poor Bootstrap scores in the large reptile tree (LRT, 1151 taxa, subset Fig. 1) reexamining data and re-scoring where necessary. The result is a tree with improved Bootstrap scores. Herewith, the eutherian (placental) mammal subset of the LRT.

Figure 1. Subset of the LRT focusing on eutherian mammals. Colors refer to niches.

Figure 1. Subset of the LRT focusing on eutherian mammals. Colors refer to niches.

Sharp-eyed readers
will find the one node that is not resolved in this tree. Hint: the specimens lacking resolution are known from damaged skulls and a few post-cranial bones, so they can be scored for a relatively few character traits.

Curious readers
seeking more information for any genera listed above need only use it for a keyword in the search feature of this blog post (above).

Even though
the present tree has been improved, there is still room for improvement, probably around the weaker Bootstrap scores.

 

Heuristic testing
of just the basal tetrapods and lepidosauromprhs (370 taxa, 1 tree) took less than 51 seconds for a completely resolved subset of the LRT. Testing of just the archosauromorphs (781 taxa, 2 trees) took 8:45 minutes of computing time. So, 410 more taxa and one more tree take more time.

Taking it to the final step: Testing of the entire LRT (1151 taxa, 14 trees) took 1 hour 50 minutes. You can see computing time rises exponentially with increasing taxa, even with the next best thing to complete resolution.

So where did those 12 extra trees come from?
Should be from no more than 3 unresolved nodes. Here’s where PAUP fails (or becomes exhausted) with high taxon numbers:

Basalmost Synapsida  (Ellioitsmithia, Apsissaurus, Aerosaurus, etc.), Lepidosauria/Sphenodotia/Marine Younginiformes/Diadectomorpha + Pareiasauria/ Caseasauria/Basal Lepidosauromorpha/ Basal Archosauromorpha/ Basal Diapsida/ 13 more little clades/15 single taxa and…Hypuronector/Vallesaurus/Megalancosaurus

So with all those problems
(way more than expected) I ran PAUP again, sans mammals and terrestrial younginiforms (including protorosaurs and archosauriforms): so…. basically all the primitive taxa were included. Result: 565 taxa, 2 trees) took 5:54 minutes with loss of resolution between (Megazostrodon + Hadrocodium) and (Brasilitherium + Kuehneotherium), three of which are skull-only taxa just outside of the deleted mammals. No other tree topology changes are recovered.

Just so you know…
it seems that PAUP does exhaust itself in large cladograms, even in a simple Heuristic search.