Seriously trying to nest turtles with archosaurs

Recent molecule analysis of tetrapods
by Iwabe et al. 2005 report that turtles are closer to archosaurs than to any other tested extant taxa.

Okay, given that genomic goal…
let’s figure out which archosaurs are closer to turtles.

We can do this
in the taxon-rich LRT by deleting all other candidate taxa but turtles and archosaurs (crocs + dinos). We did something like this before when we successfully nested turtles with pterosaurs using taxon deletion. Hone and Benton (2007-2009) also did something similar when they deleted the closest sisters to pterosaurs, the fenestrasaurs of Peters (2000) to connive a way to nest pterosaurs uncertainly with basal archosauriformes, like Erythrosuchus. And they did not check their work for possible problems.

You just can’t learn as much from taxon exclusion
and you can be led down unproductive paths. So, it’s much better to expand your taxon list if there is any doubt as to where your taxon will nest… as you’ll soon see.

In experiment #1
only turtles and archosaurs (crocs + dinos) were included. Ichthyostega and Pederpes were chosen as outgroup taxa. Eight MPTs were recovered from the 192 non-deleted taxa. Unfortunately, turtles nested between the basal tetrapods and the archosaurs, in other words, outside the archosaurs.

So, now let’s expand the taxon list to include all archosauriformes.

In experiment #2
only turtles and archosauriformes (includes the basalmost archosauriform, Youngoides UC FMNH 1528 and all descendants. 2 MPTs were recovered (Niolamia + Meiolania currently unresolved) from the 266 non-deleted taxa. Unfortunately, turtles again nested between the basal tetrapods and the archosauriformes, outside the archosauriformes. Interestingly, the basalmost archosauriform clades were reversed, so they included the small choristoderes at the base, not the proterosuchids, which still nested with erythrosuchids, UC FMNH 1528 and Euparkeria.

So, let’s expand the taxon list to include the new archosauromorphs.

In experiment #3
only turtles and the new archosauromorphs (including enaliosaurs) were included. Turtle-like sauropterygians from within the Enaliosauria have been promoted as turtle sisters. I stopped the search after 220 million rearrangements were tried. 6 MPTs were recovered from 635 non-deleted taxa. Interestingly, turtles nested with the Anomodontia, the herbivorous basal therapsids, now shifting their nesting to between Titanophoneus and Procynosuchus — NOT with basal sauropterygians or shelled placodonts!

Now, after all that frustration,
let’s expand the taxon list to include all tested tetrapods. 

In experiment  #4
giving turtles every possible opportunity with the current list of 889 total taxa, turtles arise in two clades from two clades of small pareiasaurs, Sclerosaurus for flat-soft-shelled turtles and Elginia for  dome-hard-shelled turtles. Both of these hypotheses of relationships are heretical and unprecedented, but continue to be validated  in the LRT. And when you look at the pertinent transitional taxa (Fig. 1), the long overlooked transition from pareiasaurs to turtles is almost painfully obvious.

Figure 1. The palate and lateral skulls of Elginia, a small toothed pareiasaur, and Niolamia, a large, toothless turtle to scale. These taxa nest a the origin of turtles.

Figure 1. The palate and lateral skulls of Elginia, a small toothed pareiasaur, and Niolamia, a large, toothless turtle to scale. These taxa nest at the origin of hard-shelled turtles. No other taxa are closer. Soft-shelled turtles have their own origin. From this perspective, using these taxa, the origin of turtles is pretty clear. Here it is clear that the supratemporal horns and tabular plate/horns are large elements that become reduced shortly before turtles were able to pull the skull beneath the shell.

Meiolaniidae
is a clade of extinct turtles restricted to the Cenozoic of Patagonia and Australasia. Sterli and de la Fuente 2012 report, “Historically, meiolaniids have been described as being related to both living groups of turtles – Pleurodira and Cryptodira – or were even placed outside the crown (Joyce 2007; Sterli 2010; Sterli & de la Fuente 2011a), but only recently have other fossil turtles been allied with this group.”

Not Meiolaniidae
Peligrochelys, Chubutemys and Mongolochelys were considered Meiolaniidae by Sterli and de la Fuente 2012, but that is not a recovered topology in the LRT. All of these taxa lack horns, which disappear phylogenetically in this lineage with Proganochelys or an earlier, as yet unknown, Triassic taxon. These taxa nest between Proganochelys and sea turtles like Chelonia. Earlier authors assumed the skull horns were derived, largely because they did not include the taxon Elginia in their studies. So they got their phylogenetic order backwards. Yes, the hornless taxa currently precede Meiolaniidae in the fossil record. Elginia, which they ignore, precedes all known turtles chronologically.

Those giant horns
Here (Fig. 1) it is clear that the lateral supratemporal horns and posterodorsal tabular plate/horns are large elements that become reduced shortly before or as turtles learned to pull the skull beneath the shell. Niolamia nests closer to Elginia than smaller-horned Meiolania does in the LRT.

On another note… Guillon et al. used molecules
to lump and separate extant turtles. They found a basal dichotomy between cryptodires (vertical-neck turtles) and pleurodires (side-neck turtles), and within cryptodires a split between soft-shell turtles (Trionychia) and all remaining hard-shell cryptodires  Of course, they had no outgroup because they were testing extant taxa. Contra Guillion et al. the LRT indicates that Trionychia had a separate but parallel origin from pareiasaur ancestors without a shell and pleurodires are a clade within the cryptodires. Thus the first line of text in Guillon et al.Turtles (Testudines) form a monophyletic group with a highly distinctive body plan.” is not supported by the LRT.

References
Guillon J-M, Guéry L, Hulin V and Girondot M 2012. A large phylogeny of turtles (Testudines) using molecular data. Contributions to Zoology, 81 (3) 147-158 (2012)
Iwabe N, Hara Y, Kumazawa Y, Shibamoto K, Saito Y, Miyata T. and Katoh K 2005. Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins, Molecular Biology and Evolution 22(4):810–813.
Sterli J and de la Fuente MS 2012. New evidence from the Palaeocene of Patagonia (Argentina) on the evolution and palaeo-biogeography of Meiolaniformes (Testudinata, new taxon name) Journal of Systematic Palaeontology 11(7):835–852.

Do gliding lizards (genus: Draco) actually grab their extended ribs?

Figure 1. Extant Draco flying with hands either grabbing the leading edge of the membrane or streamlining their hands on top of it.

Figure 1. Extant Draco flying with hands either grabbing the leading edge of the membrane or streamlining their hands on top of it. Images from Dehling 2016.

Gliding lizards
of the genus Draco (Figs. 1, 2) come in a wide variety of species. Similar but extinct gliding basal lepidosauriformes, like Icarosaurus (Fig. 2), form a clade that arose in the Late Permian and continued to the Early Cretaceous.

Figure 2. Two Draco species fully extending their rib membranes without the use of the hands.

Figure 2. Two Draco species fully extending their rib membranes without the use of the hands.

A recent paper
(Dehling 2016) reported, “the patagium is deliberately grasped and controlled by the forelimbs while airborne.” Evidently this ‘membrane-grab’ behavior has not been noted before. I wondered if the rib skin is indeed grasped, or does the forelimb merely fold back against the leading edge of the patagium in a streamlined fashion? Photographs of climbing Draco specimens (Fig. 2) show that the patagium  can fully extend without the aid of the forelimbs to stretch them further forward.

Figure 3. Icarosaurus. Note the tiny ribs near the shoulders. The bases for the strut-like dermal bones are the ribs themselves flattened and transformed by fusion to act like transverse processes, which sister taxa do not have. Note the length of the hands corresponds to the base of the anterior wing strut.

Figure 3. Icarosaurus. Note the tiny ribs near the shoulders. The bases for the strut-like dermal bones are the ribs themselves flattened and transformed by fusion to act like transverse processes, which sister taxa do not have. Note the length of the hands corresponds to the base of the anterior wing strut, a great place to rest the manus or grab the membrane.

A quick review of prehistoric gliding keuhneosaurs
(Fig. 3) show that the manus unguals are not quite as large and sharp as those of the pes and that the manus in gliding mode extends just beyond the shorter two anterior dermal struts so that the glider -may- have grasped the anterior struts in flight. Or may have rested the manus there. Remember, these are taxa unrelated to the extant Draco, which uses actual ribs to stretch its gliding membrane. The same holds true for the more primitive Coelurosauravus and Mecistotrachelos, which have not been traditionally recognized as basal kuehneosaurs.

* As everyone should know by now…
the so-called transverse processes in kuehneosaurs are the true ribs, only fused to the vertebrae. The ribs remain unfused to the vertebrae in the older and more primitive coelurosauravids. No sister taxa have transverse processes elongate or not.

References
Dehling M 2016. How lizards fly: A novel type of wing in animals.

Paravian phylogeny revisited – SVP abstracts 2016

Pei et al. 2016
reveal the origin of birds in a new phylogenetic analysis. Some aspects confirm earlier recoveries in the large reptile tree (LRT) made about a year ago. Not sure about other aspects given the brevity of the abstract and lack of cladogram imagery.

From the Pei et al. 2016 abstract
“Paraves are theropod dinosaurs comprising of living and fossil birds and their closest fossil relatives, the dromaeosaurid and troodontid dinosaurs. Traditionally, birds have been recovered as the sister group to Deinonychosauria, the clade made up of the two
subclades Dromaeosauridae and Troodontidae. However, spectacular Late Jurassic paravian fossils discovered from northeastern China – including Anchiornis and Xiaotingiapreserve anatomy that seemingly challenges the status quo. (1) To resolve this debate we performed an up-to-date phylogenetic analysis for paravians using the latest Theropod Working Group (TWiG) coelurosaur data matrix which we supplemented with new data from recently described Mesozoic paravians from Asia and North America (e.g., Zhenyuanlong and Acheroraptor). This includes data from the unnamed dromaeosaurid IVPP V22530 and Luanchuanraptor, which are included in a phylogenetic analysis for the first time. We also incorporate new data from iconic paravians such as Archaeopteryx and Velociraptor based on firsthand study. (2) The analysis adopted the maximum parsimony criterion and was performed in the phylogenetic software TNT. Our preliminary results support the monophyly of each of the traditionally recognized paravian clades. (3) The Late Jurassic paravians from northeastern China (e.g., Anchiornis and Xiaotingia) are recovered as avialans rather than deinonychosaurians, at a position more basal than Archaeopteryx and other derived avialans (4). The traditional sister group status of Troodontidae and Dromaeosauridae is reaffirmed (5) and is supported by a laterally exposed splenial and a characteristic raptorial pedal digit II. Recently reported Early Cretaceous dromaeosaurids from northern and northeastern China, including Zhenyuanlong, Changyuraptor and IVPP V22530, are closely related to other microraptorines as expected. (6) Luanchuanraptor, a dromaeosaurid from the Late Cretaceous of central China is recovered as a more advanced eudromaeosaurian. By tracing character evolution on the current tree topology we report on the latest insights into the adaptive radiation amongst early paravians, including the origin of flight and changes in body size and diet. (7)

Notes

  1. In the LRT Xiaotinigia and Anchiornis have nested as derived troodontids, basal to birds since their insertion into the LRT more than 3 years ago. So that’s confirmation that troodontids are basal to Archaeopteryx and other birds with Xiaotinigia and Anchiornis as proximal outgroup taxa.
  2. But did they include five or more Archaeopteryx specimens, as in the LRT? They don’t say so…
  3. In the LRT there is a clade that includes Velociraptor, but the Troodontidae does not produce a clade that does not include birds. Rather birds are derived troodontids in a monophyletic clade.
  4. If avialans are usually defined as all theropod dinosaurs more closely related to modern birds (Aves) than to deinonychosaurs, all troodontids are avialans in the LRT. Since Troodontidae was named by Gilmore in 1924, the term Avialae (Gauthier 1986) is a junior synonym.
  5. Troodontidae and Dromaeosauridae are also sisters in the LRT.
  6. This confirms the topology recovered in the LRT from about a year ago. Microraptorines, like Microraptor and basal tyrannosauroids like Zhenyuanlong are not related to troodontids or birds, but to tyrannosaurs and compsognathids.
  7. I’d like to see their tree whenever it is published to compare the two.
Figure 7. Bird cladogram with the latest additions. Here the referred specimen of Yanornis nests with enantiornithes while Archaeovolans nests within the Scansoriopterygidae, not with Yanornis.

Figure 1. Bird cladogram from several months ago. Here Avialae is a junior synonym for Troodontidae.

References
Pei R, Pittman M, Norell M and Xu X 2016. A review of par avian phylogeny with new data. Abstract from the 2016 meeting of the Society of Vertebrate Paleontology.

Notoryctes the marsupial mole

Wikipedia reports, “Marsupial moles are a family (Notoryctidae) of cladotherian mammals of the order Notoryctemorphia. They are rare and poorly understood. Once classified as monotremes, they are now thought to be marsupials. Their precise classification was for long a matter for argument.”

Earlier we looked at other mammal moles.

  1. Eastern mole – Talpa  (Carnivora, Placentalia)
  2. Docofossor (basal Placentalia)
  3. Golden mole – Chrysochloris (Glires, Placentalia)

And some reptilian ‘moles’.

  1. Mexican mole lizard – Bipes (Scincomorpha, Squamata)
  2. Mermaid skink – Sirenoscincus mobydick (Scincomorpha, Squamata)
  3. Texas blind snake – Leptotyphlops dulcis (Serpentes, Squamata)

Today we’ll round out this topic
with the extant marsupial mole (Notoryctes; Stirling 1888, 1891;  Figs. 1-3; 12-16 cm long) which nests with Anebodon at the base of the Marsupialia in the large reptile tree. The two-teat pouch opens backwards to keep dirt out.

Figure 2. Notoryctes skeleton. The hind limbs were not included so the femur and tibia are added here.

Figure 1. Notoryctes skeleton. The hind limbs were not included so the femur and tibia are added here.

We see burrowing synapsids
all the way back to Thrinaxodon, but moles spend all their time underground.

FIgure 3. Notoryctes in vivo.

FIgure 2. Notoryctes in vivo.

Notoryctes typhlops (Stirling 1891; extant; up to 16 cm in length) is the marsupial mole.  This taxon is blind with eyes reduced to vestigial lenses and without external ears. Three molars are present. Several neck vertebrae are fused, as are the sacrals. The tail verts are quite robust, especially for a mole. Tiny epipubes are present. A cloaca is present, a trait otherwise seen in monotremes and tenrecs. The forelimb has transformed to support the two large digging claws.

Figure 1. Notoryctes skull from copyright Digimorph.org, used with permission.

Figure 3. Notoryctes skull from copyright Digimorph.org, used with permission. Colors added. Although the orbit portion of the confluent lateral temporal fenestra, the eyeball is small and blind.

The claws of the third and fourth digits
are enormous. The canine (orange, Fig. 1) is considered by some as a 4th upper and 3rd lower incisor.

Figure 2. Anebodon partial skull. This is the only known and tested sister to Notoryctes.

Figure 4. Anebodon partial skull. This is the only known and tested sister to Notoryctes.

 

 

References
Bi S-D, heng X-T, Meng J, Wang X-L, Robinson N and Davis B 2016. A new symmetrodont mammal (Trechnotheria: Zhangheotheriidae) from the Early Cretaceous of China and trechnotherian character evolution. Nature Scientific Reports 6:26668 DOI: 10.1038/srep26668
Gadow H 1892. On the systematic position of Notoryctes typhlops. Proc. Zool. Soc. London 1892, 361–370.
Stirling EC 1888. Transactions of the Royal Society, South Australia 1888:21
Stirling EC 1891. Transactions of the Royal Society, South Australia 1891:154

wiki/Notoryctes

Modifying characters in phylogenetic studies: Simoes et al. 2016

This blog post will hold a special interest
for those who do not like the character list of the large reptile tree. Simoes et al. 2016 attempt to show that large studies, even those created by universally respected and dedicated PhDs (Gauthier et al. 2012 and Conrad 2008), may not be “of the highest quality.” They report, “Our results urge caution against certain types of character choices and constructions.”

Nice to know someone else out there
is also testing cladograms with critical insights. But, as you’ll see, the Simoes corrections, no matter how praise-worthy, well-intentioned and insightful, do not solve several problems.

At least one of the two tested analyses HAS to be of poor quality,
because the prior two analyses (Gauthier et al. 2012 and Conrad 2008) do not agree with one another (see below) in major and minor ways. When the LRT is introduced as a third candidate, now at least two are of poor quality, because the LRT provides yet a third topology. Which one best reflects actual evolutionary events? Or are all three ‘poor’?

Simoes et al. 2016
modified two competing scleroglossan studies (Gauthier et al. 2012, Conrad 2008) by culling ‘poor’ characters while keeping the original ordering of remaining character states and then by making all character states unordered. They report, “the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures.” 

This has been a frequent criticism
of the large cladogram at ReptileEvolution.com, despite the fact that it continues to grow organically (with no cuts and grafts over the past several years) with additional taxa that all continue to resemble one another. And that it is developed by someone who is learning as he goes, with no a priori expertise or even knowledge of every new clade added to the LRT.

Simoes et al. 2016 found in the Gauthier et al. and the Conrad studies
“more than one-third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations.These characters were removed or recoded, and the data matrices re-analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies.”

Note the Simoes team did not,
apparently, attempt to reexamine problematic taxa and re-score any errors they might have found. While constructing the LRT, scoring errors are corrected constantly.

Simoes et al. 2016 conclude:
“The modified versions of Conrad’s (2008) and Gauthier et al.’s (2012) matrices do not provide revised phylogenetic hypotheses that we claim to be “fixed” or “superior” versions of the same—that would also require a re-analysis of the scorings performed for all terminal taxa that are well beyond the goals of this study. In addition, these results still reflect the original authors’ notions of primary homologies for many characters. Our main goal was to identify general problems with character conceptualizations and constructions for morphological characters for all morphological data sets, and then to identify these problematic characters within our area of expertise, specifically studies of squamate phylogeny. The results of this study provide a different perspective of squamate relationships and indicate how specific issues with character construction may deeply affect our current notion of the squamate tree of life.”

No word yet on what Gauthier et al. and Conrad have to say
about the criticism and changes to their matrices and tree topologies.

Four basic rules from Simoes et al. 
“We have identified four basic operational rules for the construction of characters, and accurate coding and scoring, but note there may well be more:

  1. utilization of as many similarity sub-criteria as possible in order to create characters that are more likely to reflect similarity due to recency of common ancestry;
  2. avoidance of logically inconsistent character construction, such as logically dependent characters, exemplified by our character type series I A;
  3. take into consideration previous studies suggesting possible biological dependency/independency among distinct morphological attributes used as characters; 
  4. acknowledge that continuous variation is widespread in nature and that such data must be treated as such. In the case of phylogenetic analyses, measurement characters must not be treated as discrete when there is a continuous range of variation.

When there is evidence for a disjoint distribution of data, and authors wish to treat them as discrete, a clear statement must be made supporting the disjoint nature of that data.”

These are good ideals to strive for.
The problem with related traits such as, longer vertebral column and short underdeveloped limbs, will always be with us. On the other hand, continuous variation sometimes leads to personal choice when judging those that are on the margins of one and another. Character construction is not perfect and never will be. Neither will scoring. But we can still strive for those — to a point. At some stage, all thinking has to stop and the SEND button must be pressed to upload the data and results to an editor or to the public.

Thankfully
the tree figures provided by Simoes et al 2016 were color coded for simplicity.  Unfortunately neither study includes taxa published after 2012. For their time, both the 2008 and 2012 studies were laudable efforts, but with the LRT, things have changed. Neither study recognized the Tritosauria and Protosquamata, although both correctly nest tritosaurs outside the crown group Squamates. Some protosquamates, like Dalinghosaurus, nested within derived clades by default.

Result: Gauthier et al. 2012
Both revisions retain snakes and amphisbaenids as sister taxa and highly derived burrowing snakes that open the jaws laterally as basal taxa. The modified and unordered tree correctly nest pro-snakes closer to snakes, but both fail to separate them from mosasaurs, which should arise from varanids. The unordered tree correctly moves geckos closer to snakes, but not close enough. Eicthstaettisaurus incorrectly moves further from geckos. Legless pygopodid geckos move to the base of legless amphibaenids + snakes and legged pro snakes + mosasaurs. This is where reconstructions would help workers see the red flags.

Results: Conrad 2008
Gekkos did not shift when this dataset was modified and unordered. All versions of the Conrad study retain the amphisbaenid – snake relationship, which was not repeated in the LRT. The clades Scincomorpha and Anguimorpha disappeared. The clade Diploglossa appeared in the modified version. Anguimorpha reappeared in the unordered version.

Conrad 2008 vs. Gauthier et al. 2012
These two studies did not agree with one another, despite having first hand access to most of the taxa, having extensive character and taxon lists and both had PhDs as authors.

  1. Conrad nested Eicstattisaurus at the base of the Squamata. Gauthier did not.
  2. Conrad nested gekkos as basal squamates. Gauthier did not.
  3. Conrad nested skinks and snakes next. Gauthier did not. 
  4. Conrad nested mosasaurs as highly derived. Gauthier did not.
  5. And there are a dozen+ other differences.

So, which one of these is valid?
That means the other is not valid (does not echo evolutionary events). The LRT indicates that both have problems because it presents a third topology based on traits that apply not only to lizards, but to all reptiles in general. Similarities appear within all major clades. Differences appear between all major clades. Since all three studies are based on genera, one wonders how such differences arise.

And what happens when ALL the changes are made by Simoes et al. 2016?

  1. The Conrad and Gauthier studies do not look more like each other after the changes
  2. Gauthier nests geckos as more derived, with Sineoamphisbaena, apart from other amphisbaenids but closer to the pro-snakes (still not allied with Eichstaettisaurus or snakes) and mosasaurs (still not allied with varanids).
  3. Conrad major squamate clades don’t change much, but genera change sisters quite a bit. At all stages Conrad allies varanids with mosasaurs, but it is not clear if that includes Aigialosaurus, Pontosaurus and Adriosaurus, which all nest with mosasaurs in the Gauthier studies, but the last two nest apart and with snakes in the LRT.

Concluding remarks

Even with the best minds, the best characters and firsthand access to data, Conrad 2008 and Gauthier 2012 could not come to one accord, even with the help of Simoes et al. 2016. And the LRT provides yet a third tree topology for squamates that takes into account the nesting of prosquamates and tritosaurs, something prior workers were unaware of based on their limited gamuts and paradigms. Simoes et al. were correct in unordering character traits, but that did not improve their trees. The LRT is unordered because ordering makes a priori assumptions that may not be valid

It is apparent that Conrad, the Gauthier team and the Simoes team trusted their numbers because they followed a ‘plug and go’ philosophy, lacking the critical reinspection of every relationship to make sure all sister taxa looked alike, did not quickly redevelop lost bones, or reverse the order of evolution (going from exotic and highly derived to simple and plesiomorphic). All taxa were reconstructed in the LRT and that makes for great ease in re-inspecting scores and traits. In the last four years several squamates unavailable to prior workers, like Tetrapodophis, have clarified relationships in the LRT.

Large studies that load lots of taxa and characters together and then push the start button don’t have the benefit of making sure every additional taxon fits and continues to make sense. Neither the Conrad nor the Gauthier originals nor their Simoes modifications were able to become fully resolved like the LRT is. In large studies, such as these, partial taxa should be included only if parsimony informative traits are preserved. Otherwise you blur the big picture.

One of the strengths of the LRT is that it grew slowly from a few taxa to many. Just like an imperfect child, it had and continues to have imperfections, yet it also continues to deliver new insights into reptile interrelationships that can be read, appreciated, confirmed and/or refuted by others. At present it is the only voice raised in heresy to all the traditional paradigms that cannot be validated, are poorly resolved and can be readily modified by others.

I don’t expect ANYONE to use my character list. No PhD in his/her right mind will ever use it. And we all know that. It would be like adopting an older child. It’s not yours, you didn’t raise it and you have to adapt your thinking to understand it. Better to grow your own analysis, like I did.

On the other hand, I DO hope and encourage others to use various subsets of the taxon list that the LRT recovers. It’s just a list of genera and specimens. No controversy there. Add my sisters to your trees and see where they take you. So far, several PhDs have done so with success and that’s great. Hopefully others will follow.

The taxa are flawless. The characters and scoring will always be flawed to some degree. That’s the world we all live in and paleontology will always have to deal with sometimes crumby (literally crumby) data.

References
Conrad JL 2008. Phylogeny and systematics of Squamata (Reptilia) based on morphology. Bulletin of the American Museum of Natural History 310: 1–182.
Gauthier JA, Kearney M, Maisano JA., Rieppel O and  Behlke ADB 2012. Assembling the squamate tree of life: Perspectives from the phenotype and the fossil record. Bull. Peabody Mus. Nat. Hist. 53, 3–308.
Simoes TR , Caldwell MW, Palci A and Nydam RL 2016. Giant taxon-character matrices: quality of character constructions remains critical regardless of size. Cladistics (2016) 1–22. doi: 10.1111/cla.12163. Online here.

Thanks to Dr. Neil Brocklehurst
for bringing this paper to my attention. I’m sure his intention in doing so was not satisfied.

Ozimek volans: homology and analogy

Earlier we looked at the new protorosaur
Ozimek volans (Fig. 1) here and determined by phylogenetic analysis that it was a sister to Prolacerta, not Sharovipteryx.

Today, just a short note
about its homology with Prolacerta and its purported and invalid analogy with the unrelated membrane gliders Sharovipteryx and Cynocephalus.

Figure 1. Ozimek volans compared to its homolog sister, Prolacerta, and to two putative analogs, Sharovipteryx and Cynocephalus, all to scale. Note the lack of climbing claws and the weakness of the limbs and girdles in Ozimek.

Figure 1. Ozimek volans compared to its homolog sister, Prolacerta, and to two putative analogs, Sharovipteryx and Cynocephalus, all to scale. Note the lack of climbing claws and the weakness of the limbs and girdles in Ozimek, adorned here with hypothetical membranes.

Floating is just one niche possibility
based on the weakness of the muscle anchors in Ozimek. I have never seen such skinny arms and legs, so I am at a loss for a suitable niche for it.
I don’t see large climbing claws,
long manual digits, large muscles and their anchors on Ozimek that one finds on Cynocephalus. If it were it otherwise, I might support the gliding hypothesis.
Gliding animals need strong limbs
and muscle anchors not only for supporting their total weight in the air, but also for climbing trees and the momentum shock of both take-off and landing. In this regard, Ozimek appears to be quite a bit weaker than either Cynocephalus or Sharovipteryx. If it was like Sharovipteryx the diameter of the limb bones should have been scaled up to deal with the magnitude greater mass.
Sharovipteryx has elongate ilia and pectoral elements with short arms, plus seven sacrals, all lacking in Ozimek, its putative sister.
Sharovipteryx does not have a lateral membrane
Old and bad reconstructions of Sharovipteryx used to add a membrane between imagined long forelimbs with short fingers and the longer hind limbs. No one has ever seen such a membrane in the fossil. No sisters have such a membrane. Rather a uropatagium trails each hind limb, as in pterosaurs and Cosesaurus. Phylogenetic bracketing adds a pterosaur-like brachiopatagium behind each tiny Sharovipteryx forelimb, but it is likewise not visible in the fossil. The Dzik and Sulej team counts on the validity of the fantasy lateral membrane between the limbs to make their Ozimek a glider. But it was never there in any case.
Figure 1. Dzik and Sulej are so sure that their Ozimek was a spectacular big sister to Sharovipteryx that they gave a model gliding membranes and used the largest disassociated humerus for scale. More likely it was an aquatic animal that did not move around much underwater.

Figure 2. Dzik and Sulej are so sure that their Ozimek was a spectacular big sister to Sharovipteryx that they gave a model gliding membranes and used the largest disassociated humerus for scale. No membranes are present lateral to the pancaked ribs in Sharovipteryx and so this patagium on Ozimek, lacking such ribs, is also based on fantasy.

Prolacerta is also hollow-boned,
and is the sister of Ozimek in the LRT. No tested taxon, including Sharovipteryx, is phylogenetically closer.
Langobardisaurus analogy
Overall, Ozimek looks like a big, skinny Langobardisaurus (Fig. 3).
Figure 2. Langobardisaurus compared to Ozimek and its sister, Prolacerta.

Figure 3. Langobardisaurus compared to Ozimek and its sister, Prolacerta to scale. Structurally, Ozimek was similar to Langobardisaurus, but had much longer, weaker limbs and girdles and despite a long list of similarities, still nested with Prolacerta.

Langobardisaurus had the same long neck
and big skull as seen in Ozimek, but is not related, The girdles are larger and the limbs are more robust in the smaller Langobardisaurus than in the larger Ozimek. So, whatever Langobardisaurus was doing, Ozimek might have been doing, but more slowly, cautiously and secretly, perhaps like a spider.

Protorosaurs and Tritosaurs
appear on opposite sides of the LRT, but closely resemble one another such that macrocnemids and langobardisaurs were both considered protorosaurs (even by me) before the LRT showed macorcnemids and langobardisaurs actually nested with tritosaur lepidosaurs. The convergence is amazing and potentially confusing unless a rigorous analysis is performed. The LRT has been successful in separating such convergent taxa and continues to do so.

References
Dzik J and Sulej T 2016. An early Late Triassic long-necked reptile with a bony pectoral shield and gracile appendages. Acta Palaeontologica Polonica 61 (4): 805–823.

Splitting up the Tenrecidae

Everyone agrees
that the current list of genera within the clade Tenrecidae are a diverse lot. Asher and Hofreiter 2006 report, With the exception of a single genus of shrew (Suncus), insectivoran-grade mammals from Madagascar are members of the family TenrecidaeThis group of placental mammals consists of eight genera endemic to Madagascar and two from equatorial Africa and is remarkably diverse, occupying terrestrial, semi-arboreal, fossorial, and semiaquatic niches.” Finlay and Cooper 2015 sought to quantify that diversity. They report, “There are tenrecs which resemble shrews (Microgale tenrecs), moles (Oryzorictes tenrecs) and hedgehogs (Echinops and Setifer tenrecs). The small mammal species they resemble are absent from the island.”

Olson and Goodman 2003 report,
“Morphological studies have not support [genomic studies], however and the higher-level origins of both tenrecs and golden moles remain in dispute.” However, they limited their report to tenrecs, assuming a single origin.

According to Poux et al. 2008
Tenrecidae includes the following clades:

  1. Potamogalinae includes the genera Potamogale and Micropotamogale
  2. Tenrecinae includes the genera Tenrec, Echinops, Setifer and Hemicentetes;
  3. Oryzorictinae includes the genera Oryzorictes, Limnogale and Microgale;
  4. Geogalinae: includes Geogale. 

What makes a tenrec a tenrec?
Wikipedia provides no clue. And the academic literature has been similarly bereft. Instead all authors emphasize the diversity in this clade. The traditional and recent hypotheses of common ancestry are based on genomic studies that provide no clues to skeletal similarities and differences. As mentioned earlier, the anus and genitals revert to a single cloaca, as in golden moles and the scrotum reverts to an internal arrangement, distinct from many other mammals, but similar to odontocetes and hippos + mysticetes. The permanent dentition in tenrecs tends not to completely erupt until well after adult body size has been reached. Some tenrecids [which ones?] erupt their molars before shedding any deciduous teeth other than the third milk incisors.

Helping to define tenrecs, MacPhee 1987 reported,
“Shrew tenrecs are sometimes considered to be the most primitive members of Tenrecoidea. They outwardly resemble other unspecialized soricomorph insectivores (e.g., Crocidura) in possessing dense, rather velvety fur, abundant vibrissae, tiny eyes, short pentadactyl limbs slung under a long, fusiform body, and an elongated skull tapering into a narrow rostrum. Notably, like other tenrecs they retain ancient plesiomorphies that have been lost in virtually all other eutherian lineages (including true shrews), such as variable and rather low body temperature and cloacae in both sexes.”

Genomic analysis
by Asher and Hofreiter 2006 found Tenrecidae to be monophyletic. The proximal outgroup taxon was  Chrysospalax, a highly derived genus within the Chrysochloridae, or golden moles. In like fashion, Elephantulus, an elephant shrew, and Procavia, the hyrax, were successive outgroups as members of the Afrotheria, a diverse clade that only arises in genomic analyses and seems to provide a long list of oddly matched sister taxa.

Figure 1. Subset of the LRT highlighting tenrecs and former tenrecs

Figure 1. Subset of the LRT highlighting tenrecs and former tenrecs

By contrast
The large reptile tree (LRT, Fiig. 1) found the members of the former Tenrecidae so diverse that they nested in three different clades, apart from one another.

  1. Potamogale and Micropotamogale (both from Africa) nested with the shrew, Scutisorex within Glires.
  2. Echinops, Limnogale and Microgale (all from Madagascar) nested with the hedgehog, Erinaceus, despite lacking spines and also within Glires,
  3. Hemicentetes and Tenrec (both from Madagascar) nested with several fossil leptictids basal to odontocetes (toothed whales)  among extant taxa.

Those taxa nesting in Glires
have enlarged central incisors lacking in Hemicentetes and Tenrec, which have a longer, more pointed rostrum with relatively tiny incisors. Shifting aquatic Limnogale to nest with aquatic Potamogale adds 13 steps, so water habits are convergent.

Genomic sequencing lumps

  1. Limnogale and Microgale, as in the LRT.
  2. Micropotamogale and Potamogale, as in the LRT.
  3. Hemicentetes and Tenrec, as in the LRT.

Dissimilarities in DNA and trait-based tree topologies arise
with greater phylogenetic distance. The LRT permits one to include fossil taxa and to observe changes in traits that genomic codes can not do.

In the LRT
Hemicentetes and Tenrec are surrounded by fossil lepitictids. Asher and Hofreiter do not list odontocetes in their analysis, but these nest with Hemicentetes and Tenrec among living taxa in the LRT. Rose 1999 ran an analysis of postcranial traits that included Leptictidae and Tenrecidae. It nested Tenrecidae between Solenodon and shrews and Leptictidae between Tupaia and Zalambdalestes, distinct from the LRT which includes more characters, more body parts and more taxa. In the LRT Lepticitis and Lepticitidium nest with Andrewsarchus and Tenrec between them.

See what happens when you include more taxa? Topologies change.

Body masses of tenrecs
Finlay and Cooper 2015 report, “Body masses of tenrecs span three orders of magnitude (2.5 to >2,000 g): a greater range than all other families, and most orders, of living mammals.” The new phylogenetic set will not include the tiniest shrew tenrecs, but it will include the sperm whale weighing in at 57,000 kg.

If anyone has access to 
skeletal images of Geogale and/or Oryzorictes, please send them my way in order to add them to the LRT.

When you use molecules

  1. you don’t use traits. Therefore you lump and divide taxa based on combinations of DNA you can’t see or argue about.
  2. you don’t use fossils. Therefore you can’t tell which fossil taxa gave rise to which other fossil and extant taxa.
  3. you often recover very odd sister taxa that anti-evolutionists love to use in their PowerPoint lectures. That gives them power over audiences who want to see the evidence of evolution, which the LRT provides.

We have to own up to the shortcomings of DNA
while we still can. Great for criminals and baby daddies, bad for turtles and archosaurs. I think we need to get back to morph studies in mammal phylogeny. Molecules have given us very weird and unwieldy answers that don’t start small, extinct and simple and end large, extant and exotic, like the LRT does.

 

Authority
Granted if have not seen any specimens first hand, nor am I anywhere near a tenrec expert. Like Galileo, I am metaphorically tossing balls off the Tower of Pisa, coming to my own conclusions following repeatable observations. Because you can do that in Science. Others may argue methods and observations, but they will have to duplicate the list of taxa before they can do so with their own authority. This post provides an expanded taxon list and tentative insights for future studies.

References
Asher RJ and Hofreiter M 2006. Tenrec phylogeny and the noninvasive extraction of nuclear DNA. Systematic Biology 55(2):181-194. 
Asher RJ 2007. 
A web-database of mammalian morphology and a reanalysis of placental phylogeny. BMC Evol Biol. 7: 108-10 online
Asher  RJ and Helgen KM 2010. Nomenclature and placental mammal phylogeny. BMC Evolutionary Biology 10:102 online
Du Chaillu P 1860. Descriptions of mammals from equatorial Africa. Proceedings of the Boston Society of Natural History, 7, 358–369.
Eisenberg JF and Gould E 1970. The tenrecs: a study in mammalian behavior and evolution. Smithsonian Institution Press, Washington, DC. 138 pp. PDF online
Finlay S and Cooper N 2015. Morphological diversity in tenrecs (Afrosoricida, Tenrecidae): comparing tenrec skull diversity to their closest relatives. PeerJ 3:e927; DOI 10.7717/peerj.927
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
MacPhee RDE 1987. The shrew tenrecs of Madagascar: systematic revision and Holocene distribution of Microgale (Tenrecidae, Insectivora).
Martin WCL 1838. On a new genus of insectivorous mammalia. Proceedings of the Zoological Socieety, London, 6:17.
Mouchaty SK, Gullberg A, Janke A, Arnason U 2000. Phylogenetic position of the Tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi. Zoologica Scripta. 2000, 29 (4): 307-317. 10.1046/j.1463-6409.2000.00045.x.
Nicoll M 1985. The biology of the giant otter shrew *Potamogale velox*. National Geographic Society Research Reports, 21: 331-337.
O’Leary, MA et al. 2013. The placental mammal ancestor and the post-K-Pg radiation of  placentals. Science 339:662-667. abstract
Olson LR and Goodman SM 2003. Phylogeny and biogeography of tenrecs. Pp. 1235-1242 in Natural History of Madagascar, SM Goodman & JP Benstead (eds.), University of Chicago Press, Chicago.
Poux C, Madsen O, JGlos J, de Jong WW and Vences M 2008. Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses. BMC Evolutionary Biology 8:102. Open Access
Rose KD 1999. Postcranial skeleton of Eocene Leptictidae (Mammalia), and its implications for behavior and relationships. Journal of Vertebrate Paleontology 19(2):355-372.
Suárez R, Villalón A, Künzle H and Mpodozis J 2009. Transposition and Intermingling of Gαi2 and Gαo Afferences into Single Vomeronasal Glomeruli in the Madagascan Lesser Tenrec Echinops telfairi. PLoS ONE 4(11): e8005. doi:10.1371/journal.pone.0008005

 

Tenrec bones website here (Microgale and Tenrec skulls and jaws)