On becoming a reptile: a new list of traits

With the nesting
of Gephyrostegus bohemicus as the last common ancestor to all other reptiles in the large reptile tree, it is worthwhile to list the traits that developed at this node versus the outgroup taxon, Silvanerpeton (Fig. 1). This new list becomes important because Gephyrostegus has no traditional amniote traits.

Traditional amniote traits include:

  1. loss/fusion of the intertemporal
  2. absence of the otic notch
  3. loss/reduction of palatal fangs
  4. appearance/expansion of the transverse flange of the pterygoid
  5. loss of labyrinthine infolding of the marginal teeth
  6. reduction of the intercentra
  7. addition of a second sacral vertebra
  8. narrowing and elongation of the humeral shaft
  9. appearance of the astragalus from fused tarsal elements.

many of the above traits are also found in microsaurs and seymouriamorphs, but not in basalmost amniotes. So there is an odd sort of homoplasy at play here.

Of course,
the chief and key trait of amniotes (= reptiles) is the development of the amniotic membrane,surrounding the embryo. The amnion is only the first of several membranes (later including the egg shell) that reduce egg fluid desiccation. This fragile layer of protection permits eggs to be laid on land, but at first only in moist environments.   Klembara et al. (2014) did not recognize Gephyrostegus as a basal amniote because they employed too few amniotes in their matrix. This was probably due to a mindset biased toward thinking about Gephyrostegus as a pre-amniote, in line with all other traditional paleontologists.

A new list of amniote/reptile traits
(Fig. 1) sets Gephyrostegus apart from its more primitive sister, Silvanerpeton. Yes, this is heretical thinking, but results from letting the matrix scores determine all taxon nestings.

Figure 1. Silvanerpeton and Gephyrostegus to the same scale. Each of the two frames takes five seconds. Novel traits are listed. This transition occurred in the early Viséan, over 340 mya. Gephyrostgeus is more robust and athletic with a larger capacity to carry and lay eggs.

Figure 1. Silvanerpeton and Gephyrostegus to the same scale. Each of the two frames takes five seconds. Novel traits are listed. This transition occurred in the early Viséan, over 340 mya. Gephyrostgeus is more robust and athletic with a larger capacity to carry and lay eggs.

Gephyrostegus bohemicus was more robust and athletic when compared to its phylogenetic predecessor, Silvanerpetion miripedes (Fig. 1). In G. bohemicus the skull, girdles and limbs were all larger relative to the torso. The carpus and tarsus were ossified. The ribs were longer, but fewer in number with a larger lumbar area. Thus the torso was capable of carrying more eggs more rapidly over terrestrial obstacles. The deeper pelvis could expel larger eggs. In summary, the evidence shows that basal reptiles were more fecund and agile than pre-reptiles and those traits were the keys to our success at that node. You can see a video highlighting the origin of humans, including the amniote transition, here.

Large reptile tree traits that appear in the basal amniote, G. bohemicus, 
not present in Silvanerpeton: 

  1. prefrontal (barely) separate from postfrontal
  2. premaxilla not transverse
  3. major axis of naris less than 30º above jawline
  4. naris lateral
  5. nasals and frontals subequal
  6. maxilla ventrally straight
  7. longest metatarsal is number four

Phylogenetic miniaturization
often occurs at the base of novel tetrapod clades. As a pattern, size reduction continued with the advent of amniotic eggs in reptiles, as we learned earlier here, despite the slightly larger size of Gephyrostegus, which may have been substantially larger than its thirty million years older Viséan sister. Certainly tiny reptiles were present in the Viséan in the form of Westlothiana and Casineri on the archosauromorph branch and later with Thuringothryis and Cephalerpeton on the lepidosauromorph branch. Phylogenetic miniaturization has also been overlooked by the latest studies, which generally disregard ‘size’ as a character trait.

Those who had access to the fossils themselves
(Klembara et al. 2014) were not able to make these conclusions because they did not have, nor did they choose to access online, a large gamut cladogram of amniotes. In this case, and many others, the large reptile tree proves again to solve problems despite lacking firsthand access to pertinent fossils. This is heresy, contra to traditional thinking.

On a side note, 
PterosaurHeresies wishes all those vertebrate paleontologists attending in Dallas, Texas, a grand convention filled with good cheer and camaraderie. Wish I could be there with y’all. We’ll review about two dozen published abstracts following the closing ceremonies.

Clack JA 1994. Silvanerpeton miripedes, a new anthracosauroid from the Visean of East Kirkton, West Lothian, Scotland. Transactions of the Royal Society of Edinburgh: Earth Sciences 84 (for 1993), 369–76.
Jaeckel O 1902. Über Gephyrostegus bohemicus n.g. n.sp. Zeitschrift der Deutschen Geologischen Gesellschaft 54:127–132.
Klembara J, Clack J, Milner AR and Ruta M 2014. Cranial anatomy, ontogeny, and relationships of the Late Carboniferous tetrapod Gephyrostegus bohemicus Jaekel, 1902. Journal of Vertebrate Paleontology 34:774–792.
Ruta M and Clack, JA 2006 A review of Silvanerpeton miripedes, a stem amniote from the Lower Carboniferous of East Kirkton, West Lothian, Scotland. Transactions of the Royal Society of Edinburgh: Earth Sciences, 97, 31-63.

When cladograms go bad…

Figure 2. Diandongosaurus exposed in ventral view, skull in dorsal view. Note the small size. At 72 dpi this image is 6/10 the original size.The last common ancestor of Diandongosaurus and Pachypleurosaurus was a sister to Anarosaurus at the base of the Sauropterygia.

Figure 1. Diandongosaurus exposed in ventral view, skull in dorsal view. Note the small size. At 72 dpi this image is 6/10 the original size.The last common ancestor of Diandongosaurus and Pachypleurosaurus was a sister to Anarosaurus at the base of the Sauropterygia.

A recent paper (Liu et al. 2015) on a new specimen (BGPDB-R0001) of the basalmost placodont, Diandongosaurus, (IVPP V 17761)brings up the twin problems of taxon inclusion/exclusion without the benefit of a large gamut cladogram, like the large reptile tree (580 taxa) to more confidently determine inclusion sets in smaller more focused studies (anything under 100 taxa).

Let’s start by making the large reptile tree go bad.  
Liu et al. used a traditional inclusion set (Fig. 1 on left) that included suprageneric taxa and taxa that were unrelated to one another in the large reptile tree (Fig. 1 on right). To illustrate inherent problems, I reduced the taxon list of the large reptile tree to closely match that of Liu et al. See them both here (Fig.1).

Figure 1. Click to enlarge. Left: Liu et al. cladogram. Diandongosaurus is in dark purple. Right: matching taxa from the large reptile tree. Note, this taxon mix is not a valid subset of the large reptile tree.

Figure 1. Click to enlarge. Left: Liu et al. cladogram. Diandongosaurus is in dark purple. Right: matching taxa from the large reptile tree. Note, this taxon mix is not a valid subset of the large reptile tree. “?” indicates probable transposition of taxa in the Liu et al tree as Rhynchosaurs typically nest with Trilophosaurus and Rhynchodephali typically nest with Squamates in traditional trees. They nest together in the large reptile tree. note the nesting of turtles (at last : ) with archosauriformes! This shows graphically how twisted cladograms can get with taxon exclusion issues.

Although many taxa on the left and right of figure one are similar, many nest differently.

Let’s start with the problems
in the cladogram on the right, in the reptileevolution.com incomplete cladogram

  1. Prolacerta nests basal to squamates (Iguana) and Triassic gliders (Kuehneosaurus).
  2. Trilophosaurus nests between squamates and rhynchocephalians.
  3. Turtles nest with archosauriforms and both close to rhynchosaurs, none of which are related to each other in the large reptile tree. This is the wet dream of many turtle workers intent on matching DNA studies that place turtles with archosaurs, a clear case of DNA not matching morphology.

Everything else
is basically in the correct topology, remarkable given that 540 or so taxa are missing.

The problems in the cladogram on the left,
from Liu et al include:

  • Turtles nest between Triassic gliders and placodonts (and not the shelled ones proximally). This is Rieppel’s insistence on a force fit. Is the insertion of turtles the reason for other tree topology disturbances here and on the right? Not sure…
  • Hanosaurus, a derived pachypleurosaur close to nothosaurs nests with Wumengosaurus, a pachypleurosaur/stem ichthyosaur.
  • Liu et al. nested Diandongosaurus with headless Majiashanosaurus (which is correct) but then nests both at the base of the nothosaurs (which is not validated by the large reptile tree). The large reptile tree nested Diandongosaurus at the base of the placodonts, between Anarorosaurus and Palatodonta + Majiashanosaurus. Shifting Diandongosaurus to the base of the nothosaurs adds 32 steps to the large reptile tree.

Perhaps what the Liu et al team need is a subset of the large reptile tree. That would help them drop those turtles from placodont studies. They don’t belong. When cladograms go bad, sometimes there are included taxa that should not be there. Colleagues, make sure to check your recovered sister taxa to make sure they look like they could be sister taxa. After all, evolution is about slow changes over time.

Liu X-Q, Lin W-B, Rieppel O, Sun Z-Y, Li Z-G, Lu H and Jiang D-Y 2015. A new specimen of Diandongosaurus acutidentatus (Sauropterygia) from the Middle Triassic of Yunnan, China. Vertebrata PalAsiatica. Online Publication.


News on the giant tube-snout sea turtle – Ocepechelon

The weird ones really are more interesting, aren’t they?
For awhile I’ve wanted to study this weird putative chelonid turtle to see where it nests in the large reptile tree (now at 580 taxa). It’s not a chelonid, as originally interpreted by Bardet et al. (2013). Ocepechelon bouyai OCP DEK/GE 516 (Fig. 1), the famous suction-feeding giant sea turtle, nests with the soft-shell turtles, Odontochelys (Late Triassic) and Trionyx (post-Cretaceous). They share a longer rostrum, and several other traits, that short-beaked chelonids just don’t have.

Figure 1. Ocepechelon bouyai OCP DEK/GE 516, the famous suction-feeding giant sea turtle.

Figure 1. Ocepechelon bouyai OCP DEK/GE 516, the famous suction-feeding giant sea turtle.Note the large orange bones are supratemporals, not squamosals. The skull roof retains post parietals, The occiput includes tabulars, as seen in Trionyx. Click to enlarge.

Trionyx and Odontochelys were not tested in the original phylogenetic analysis of Bardet et al. 2013, which only used sea turtles in the inclusion set. That taxon exclusion has become a problem with a solution (Fig. 2).

Figure 2. The family tee of turtles with Ocepechelon nesting with soft-shell turtles.

Figure 2. The family tee of turtles with Ocepechelon nesting with soft-shell turtles. High bootstrap support figures here.Taxon exclusion prevented this nesting in Bardet et al. 2013. 

The supplemental data
indicates Bardet et al. used an all-zero hypothetical outgroup and did not include Odontochelys or Trionyx. The supplemental data also includes a short movie of the turtle feeding on a fish, of which here is one frame (Fig. 3). Click here to view the very short movie on YouTube.

Ocepechelon feeding, one frame from the Bardet et al 2013 movie.

Ocepechelon feeding, one frame from the Bardet et al 2013 movie. Click to view on YouTube

A living turtle,
the long-necked mata-mata can be seen here suctioning it prey by expansion of the neck, with a wide open mouth. This is different, of course, from the pipette method used by Ocepechelon.

Postcrania support
the supplemental material of Bardet et al. 2013 reports: “The Maastrichtian Phosphates of the Oulad Abdoun Basin have yielded several very large Chelonioid elements (OCP collection): dorsal shells with large pleural disc fontanelles, widely U-notched and and and indented nuchal, various star-shaped plastral elements with deeply indented edges, shoulder and pelvis (neither protostegid nor dermochelyid) elements, as well as humeri and femurs. All these postcranial elements from Morocco may correspond to Ocepechelon, the only skull morphotype known in the Oulad Abdoun with a corresponding large size. As the skull, none of these postcranial elements can be surely referred to Protostegidae or Dermochelyidae and they could partly belong to Ocepechelon.”

So, the skull of Ocepechelon is not chelonioid, according to the large reptile tree and the disassociated post-crania is not chelonioid, according to the authors. Does anyone else want to look into the possibility that we have a giant soft-shell turtle here? Just add Ocepechelon to a large gamut turtle matrix. Publish the post-cranial bits and pieces. And fix those squamosal/supratemporal issues while you’re at it.

Bardet N, Jalil N-E, de Lapparent de Broin F, Germain D, Lambert O, et al. 2013. A Giant Chelonioid Turtle from the Late Cretaceous of Morocco with a Suction Feeding Apparatus Unique among Tetrapods. PLoS ONE 8(7): e63586. doi:10.1371/journal.pone.0063586
Li C, Wu X-C, Rieppel O, Wang L-T and Zhao L-J 2008.
An ancestral turtle from the Late Triassic of southwestern China. Nature 456: 497-501.
Gaffney ES 1975. A phylogeny and classification of higher categories of turtles. Bulletin of the American Museum of Natural History 155:387-436.
Meylan PA 1987. The phylogenetic relationships of the soft-shelled turtles (family Trionychidae). Bulletin of the American Museum of Natural History 186:1-101.


BPI 2871 has a new sister: Elachistosuchus huenei

Earlier we looked at a tiny basal choristodere, BPI 2871, which was derived from a line of much larger proterosuchids, according to the large reptile tree.

Recently a new PlosOne online paper (Sobral et al. 2015) reintroduces Elachistosuchus huenei (Janensch 1949, Late Triassicm, Norian, Germany; MB.R. 4520 (Museum für Naturkunde Berlin, Berlin, Germany)) with CT scans.

Figure 1. Elachistosuchus (Janensch 1949, Sobral et al. 2015) is a sister to BPI 2871, a basal choristodere.

Figure 1. Elachistosuchus (Janensch 1949, Sobral et al. 2015) is a sister to BPI 2871, a basal choristodere, has been misidentified for over fifty years.The left upper temporal fenestra has been largely closed by crushing here. Like BPI 2871, the nares were located on top of the skull, close to the snout tip. Note the vestige of the antorbital fenestra.

And they don’t know what it is. 
According to Sobral et al, Elachistosuchus could be “an archosauromorph, a lepidosauromorph or a more basal, non-saurian diapsid.” That confusion arises from using outdated matrices with too few generic taxa and too many suprageneric taxa.

Sobral et al. used the matrix from Chen et al. 2014, which nested Elachistosuchus in a polygamy with Choristodera, Prolacerta + Tanystropheus + Macrocnemus, and Trilophosaurus + Rhynchosauria + Archosauriformes. As readers know the large reptile tree found many of these taxa on opposite sides of the reptile cladogram.

Sobral et al. also used the matrix from Ezcurra et al. 2014, which nested Elachistosuchus with the gliding Permian lepidosauriform, Coelurosauravus.


Sobral et al. report: 
“These different placements highlight the need of a thorough revision of critical taxa and new character sets used for inferring neodiapsid relationships.” 

That’s why large reptile tree and reptileevolution.com are here. It’s good to have hundreds of specimen-based taxa for new taxa to nest with. More choice. More accuracy. Complete resolution.

To their credit,
a Sobral et al. analysis nested Elachistosuchus with choristoderes.

Figure 2. Dorsal, lateral and palatal views of BPI 2871 with bones colorized above. Below, reconstructed images of BPI 2871 tracings. It is more complete than illustrated by Gow 1975. Click to enlarge. Note the tiny remnant of the antorbital fenestra. The squamosal has been broken into several parts.

Figure 2. Dorsal, lateral and palatal views of BPI 2871 with bones colorized above. Below, reconstructed images of BPI 2871 tracings. It is more complete than illustrated by Gow 1975. Click to enlarge. Note the tiny remnant of the antorbital fenestra. The squamosal has been broken into several parts. This is a sister to Elachistosuchus.

Among earlier workers
Janensch (1949) considered Elachistosuchus a pseudosuchian archosaur with an antorbital fenestra. Walker (1966 ) considered  Elachistosuchus a rhynchocephalian lepidosaur.

The large reptile tree (now 575 taxa)
finds Elachistosuchus nests firmly as a sister to the BPI 2871 specimen (Fig. 3) that Gow mistakenly attributed to Youngina, but it nests far from Youngina at the base of the large and small choristoderes. And these two taxa are both derived from much larger proterosuchids in yet another case of phylogenetic miniaturization at the genesis of a new clade, in this case the Choristodera.

Elachistosuchus has a larger orbit and a maxilla with a straight, not convex, ventral margin of the maxilla than the BPI 2871 specimen. The former extends the geographic range of the latter, from southern Africa to Germany.

Both probably look like juvenile proterosuchids (whenever they are discovered, we can compare them). Phylogenetic miniaturization often takes juvenile traits and sizes and makes them adult traits and sizes to start new clades.

Janensch thought Elachistosuchus had an antorbital fenestra. As in BPI 2871, that is the vestige of the antorbital fenestra found in ancestors and lost in descendants.

Contra the title of the Sobral et al. paper
Elachistosuchus huenei has nothing to do with the origin of ‘Sauria.’

Sauria definition: “.Any of various vertebrates of the group Sauria, which includes most of the diapsids, such as the dinosaurs, lizards, snakes, crocodilians, and birds. Sauria was formerly a suborder consisting ofthe lizards” Rather, Elachistosuchus is a basal choristodere and a derived proterosuchid according to the large reptile tree. Based on the current definition of ‘Sauria’ ‘Sauria’ is synonymous with ‘Amniota’ which is a junior synonym for ‘Reptilia’ because the last common ancestor of lizards and dinosaurs is the basalmost reptile/amniote, Gephyrostegus bohemicus.

The reason why Sobral et al. were confused
with regard to their blurred nesting of Elachistosuchus is due to taxon exclusion. BPI 2871 is a rarely studied taxon and was not included in their analyses. Moreover, traditional paleontologists are not sure what choristoderes are. They don’t recognize them as being derived proterosuchids. And to make matters worse, traditional paleontologists prefer to think of Proterosuchus specimens as members of an ontogenetic series, when they should consider them as a phylogenetic series.

Figure 4. This is where Elachistosuchus nests, next to BPI 2871, at the base of the Choristodera.

Figure 3. This is where Elachistosuchus nests, next to BPI 2871, at the base of the Choristodera. Click to see the complete reptile cladogram.

The large reptile tree (Fig. 3) has proven itself time and again to solve paleontological problems in the reptile family tree. It is unfortunate that it has been rejected for publication so many times. If published, it can be use.

A MacClade file is available on request.

Chen X, Motani R, Cheng L, Jiang D, Rieppel O. 2014. The enigmatic marine reptile Nanchangosaurus from the Lower Triassic of Hubei, China and the phylogenetic affinities of Hupehsuchia. PLoS ONE. 2014; 9: e102361. doi: 10.1371/journal.pone.0102361 PMID: 25014493
Ezcurra MD, Scheyer TM, Butler RJ 2014. The origin and early evolution of Sauria: reassessing the Permian saurian fossil record and the timing of the crocodile-lizard divergence. PLoS ONE. 2014; 9: e89165. doi: 10.1371/journal.pone.0089165 PMID: 24586565
Gow CE 1975. The morphology and relationships of Youngina capensis Broom and Prolacerta broomi Parrington. Palaeontologia Africana, 18:89-131.
Janensch W 1949. Ein neues Reptil aus dem Keuper von Halberstadt. N Jb Mineral Geol Palaeont B. 1949:225–242.
Sobral G, Sues H-D & Müller J 2015. Anatomy of the Enigmatic Reptile Elachistosuchus huenei Janensch, 1949 (Reptilia: Diapsida) from the Upper Triassic of Germany and Its Relevance for the Origin of Sauria. PLoS ONE 10(9): e0135114. doi:10.1371/journal.pone.0135114
Walker AD 1966. Elachistosuchus, a Triassic rhynchocephalian from Germany. Nature. 1966; 211: 583–585.


History of reptile Interrelationship hypotheses: Meckert’s PhD thesis

There is a long history
of workers creating hypotheses of reptile interrelationships going back to the mid 18th century (Carl von Linneaus 1758). That history, up until 1995 (Laurin and Resiz 1995 and Meckert 1995), was summarized by Dirk Meckert in his PhD thesis, which otherwise  concentrated on all available specimens of Barasaurus. You can download that thesis here online and read that short but fascinating history for yourself.

Some interesting notes arise from Meckert’s short history:

  1. Some studies united pareiasaurs and turtles. Others did not.
  2. Other studies united pareiasaurs, diadectids and procolophonids (which happened here just yesterday). Meckert wrote: “The Procolophoniformes contain Procolophonia and Testudinomorpha as sister-groups. Testudines are the sister-group of Pareiasauria within the Testudinomorpha.”
  3. Mesosaurs are commonly considered of uncertain affinities. But not here.
  4. Many prior studies had the synapsids branch off first. That is incorrect as shown here.
  5. No prior studies recognized the original dichotomy of lepidosauromorphs and archosauromorphs.
  6. No prior studies recognized Gephyrostegus bohemicus as a sister to the basalmost amniote.
  7. Diadectomorpha have been nested in and out of the Amniota. They’re in here.

No studies prior to reptileevolution.com
have included as many as 571 individual species as taxa, not counting the therapsid tree (with 52 additional taxa) and pterosaur tree (with 228 additional taxa) for a total of 851 taxa.

Other studies more recent than 1995
(not included in Meckert’s history) include

  1. http://www.palaeos.org/Reptilia and http://palaeos.com/vertebrates/amniota/reptiles.html
  2. http://whozoo.org/herps/herpphylogeny.html
  3. https://en.wikipedia.org/wiki/Amniote as determined by Benton, M.J. (2004). Vertebrate Paleontology. Blackwell Publishers. xii–452.
  4. University of Maryland (John Merck)
  5. online pdf, Amniote Origins and Nonavian Reptiles
  6. YouTube video by Walter Jahn
  7. Tree of Life
  8. Hedges 2012
  9. Gauthier, Kluge and Rowe 1988 online
  10. Hill 2005
  11. Mikko’s phylogeny archive
  12. ReptileEvolution.com
  13. Let me know if I missed any. I’ll add them here.

A while back
we looked at the differences between astronomy and paleontology. As noted earlier, time is never of the essence in paleontology — and that extends to idea acceptance. So many hypotheses of reptile interrelationships are still floating around out there. A definitive and all encompassing demonstration, like the large reptile tree, will probably just float forever with the other several dozen hypotheses out there, hashed, rehashed and rehashed again without end.

This is one of the frustrations of paleontology. And many think it is largely ego driven.

On that note
In astronomy the data, be it observation or spectral analysis, is immediate and widespread. You just have to look up with the right tool in the right direction. Or study the shared data (photos, etc.) Everyone can confirm the observation.

In paleontology the data comes out piecemeal, in low resolution, or imprecise tracings, not from every angle of view. Some key parts are lost and others are hidden beneath other bones or matrix. Sometimes you have to assemble dozens or hundreds of specimens for a proper study. No one is interested in confirming observations or analyses perhaps for years if ever. They’re all too busy with their own projects. Checking the characters and scores of an analysis can take weeks, months or years (as long as it took to build originally), and to do so requires the same amount of globe-hopping to see all the specimens in all the museums. No one is going to do that. They’d rather be making their own discoveries… and adding their taxa to established trees created by hungry PhD candidates, like Dirk Meckert in 1995, done at the nadir or advent of their experience.

The paleo-mantra remains: you must see the specimen!
And even that is no guarantee.

And if you want to break a paradigm or two,
like Ostrom did in the 1960s, you might have to wait for widespread (but never universal) acceptance. Paleontologists like their paradigms. They don’t like to give them up.

Benton MJ 2004. Vertebrate Paleontology. Blackwell Publishers. xii–452.
Carroll RL 1988. 
Vertebrate Paleontology and Evolution, WH Freeman & Co.
Laurin M and Reisz R 1995. 
A reevaluation of early amniote phylogeny. Zoological Journal of the Linnean Society, 113: 165–223.
Linnaeus C 1758. 
Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Meckert D 1995.
 The procolophonid Barasaurus and the phylogeny of early amniotes. PhD thesis McGill University. Online Barasaurus dissertation




Loss of resolution in cladograms

A cladogram
is a graphic image (a diagram) typically generated from software, and typically based on a list of taxa and a list of characters, each one scored for each taxon. The cladogram is supposed to model actual evolutionary relationships among organisms. Ideally every cladogram will be fully resolved with every taxon sufficiently different from its sisters to merit its own node or branch. This is the basis for lumping and splitting. In practice loss of resolution occurs when sisters are not sufficiently different from one another. This can happen due to one or more of several problems:

  1. Three taxa are in reality too closely related. As an example, you may have input several specimens of the same genus and species, like “Tyrannosaurus rex,” without having characters in your characters list that could taxonomically separate them. Two identical taxa nest together, no problem. Three identical taxa produce loss of resolution. We saw something like this earlier in pterosaurs were two Rhamphorhynchus specimens had the same score and were deemed to be an adult and juvenile of the same species – but the third sister taxon (of the same putative species!) did not have the same score.
  2. Two sister taxa share no characters in common despite being closely related. This occurs most often when a skull-only taxon nests as a sister to a skull-less taxon, but it could also occur with other combinations of missing parts.
  3. One taxon is in a ‘by default’ nesting. It should not be in your taxon list because in reality it is not closely related to any other taxon in your taxon list. For instance, when one attempts to nest the pterosaurs “Pteranodon” or “Dimorphodon” with generic and specific members of the Archosauria or Archosauriformes, or when one attempts to nest “Homo sapiens” with generic and specific members of the Ichthyosauria. No telling what can happen in those instances, but anyone is able to try.
  4. Too few characters #1. If you have only 5 or 50 characters, there may not be a large enough list of traits to split your taxa apart. Statistically the list becomes large enough for 98% certainty at around 150 characters and becomes incrementally better with every character added thereafter. The large reptile tree uses 228 characters, many with more than two options, and has complete resolution (except for skull-less and skull-only taxa nesting as sisters (#2 above) with 546 taxa. Thus in practice there is no 3:1 character:taxon ratio as you may have learned about in theory.
  5. Too few characters #2. If your sister specimens are only represented by a few bones or parts of bones then two sister taxa may not resolve.
  6. Too few characters #3. Legless burrowing tetrapods appear to converge in their remaining traits so you better have a sufficient number of traits to lump and split the various clades. Otherwise the legless clades tend to be attracted to one another.
  7. Too few taxa. This goes back to #3 above because by throwing in one ‘by default’ taxon, like “Vancleavea” into an unrelated clade, like “Archosauriformes,” without also including the verified sisters of “Vancleavea,” like “Helveticosaurus” and “Askeptosaurus,” might produce loss of resolution because “Vancleavea” shares so few traits with any archosauriforms and the addition of the other thalattosaurs will clarify relationships. You may not have loss of resolution, but by adding taxa you’ll eliminate these ‘by default’ taxa.
  8. Using suprageneric taxa. If you can pick traits from one partial specimen AND another partial specimen to get enough traits to fill a suprageneric character list for a single taxon, then you’ve created a chimaera that can only lead to trouble. Even if your two taxa are incomplete, that’s better than creating a single cherry-picked chimaera taxon.
  9. Mistakes in scoring. Since humans are scoring all characters, mistakes can happen and they can affect nestings. Mistakes are often due to: 1) trying to maintain a paradigm or tradition; 2) too much leeway or opinion possible in a choice of possible scoring options; 3) inadvertent transpositions of data; 4) typos; 5) relying on the veracity of prior scorings, etc. Double and triple check your work and the work of others when you find loss of resolution. Errors are easy to make.
  10. Loss of resolution can occur at several levels: 1) in a simple heuristic search you need only one character score to lump and split sister taxa from your list of several dozen to several hundred traits; 2) in a bootstrap/jacknife search you need at least three character scores to lump and split taxa to raise your bootstrap score over 50%.

In my manuscripts,
when I report that my trees are fully resolved, that never seems to impress the referees (or they don’t believe it). Perhaps that is so because so many accepted manuscripts have loss of resolution at several nodes for many of the above reasons. That is not acceptable in most cases (exception: skull-only taxa will continue to occasionally nest with skull-less taxa).

We know better now.
We now have a large gamut “umbrella” study that continues to recover relationships within the Reptilia as it continues to increase in size. This large study provides a basis for smaller, more focused studies. When the old unverified traditions and paradigms have been replaced with verified models and relationships, then we’ll all have more confidence in recovered trees.

Nesting turtles with pterosaurs redux 2011-2015

For those who don’t read the ‘Letters to the Editor’,
a recent comment on sister taxa inspired me to revisit the old experiment that nested pterosaurs and turtles together as a result of taxon exclusion, which you can review here.

By default nestings
can be interesting and silly. The point behind nesting pterosaurs with turtles back then was to examine the folly behind nesting pterosaurs with archosaurs — only possible due to a similar taxon exclusion that’s been going on for at least fifteen years now, following the publication of a phylogenetic analysis that nested pterosaurs with fenestrasaurs (Peters 2000) and has been ignored ever since.

Back in the day (July 2011) with 360 taxa,
when all other taxa were removed from the lepidosauromorph side of the large reptile treeProganochelys, the turtle, nested with MPUM6009, the pterosaur at the base of the Sauropterygia. That’s bizarre, but interesting and hopefully enlightening by analogy to the achosaur-link question.

Today,with 508 taxa,
and deleting all other lepidosauromorphs, the pterosaur now nests between Cathayornis and Struthio, the ostrich, + Gallus, the chicken. The turtle now nests with the frogs, between Doleserpeton and Gerobatrachus + Rana.

Hmm. Let’s fix that.
Let’s delete the amphibians and add the basal lizard Huehuecuetzpalli and guess what happens?

The three lepidosauromorphs:
the turtle, the lizard and the pterosaur, all nest together again in their own clade at the base of the Sauropterygia… in other words, nowhere near dinos, pre-dinos, parasuchians, Lagerpeton or Marasuchus. Delete Huehuecuetzpalli and Proganochelys nests with the turtle-like placodont, Henodus, as you might imagine, while the basal pterosaur bounces back to the birds. So one taxon in-between the turtle and pterosaur were needed this time to glue them together in a single clade and to trump the attraction of other candidate sisters.

Bottom line:
by including more and more taxa the large reptile tree provides more and more nesting sites, and thus the large reptile tree minimizes unwanted ‘by default’ nestings. Up to now other workers have been relying an tradition and paradigm for their taxon lists, and many of those traditions have been tested (and falsified) at reptileevolution.com. When workers base their smaller, more focused studies on a larger umbrella study, they will have greater success and greater confidence that their cladogram is a good one = with no ‘by default’ nestings.