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.

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)

The ‘hedgehog’ tenrecs: they nest with hedgehogs

This is a think piece.
You’re going to be faced with

  1. a geographically inspired return of the cloaca (proposed heresy) or
  2. MASSIVE convergence involving everything but the cloaca (current and traditional paradigm)

Arguments will be presented.
You decide which is more parsimonious. We may need to bring in the DNA guys here, and I would welcome them! I don’t think such a study involving a wide range of purported and actual tenrecs has been proposed or done yet. Let me know as I am unaware of published work on this subject.

The present problem had its genesis in whale phylogenetic studies.
Earlier, from skeletal data, the the large reptile tree (LRT) nested odontocete (toothed) whales with tenrecs and mysticete (baleen) whales with hippos and desmostylians.

However
current DNA studies do not support the tenrec – odontocete relationship — perhaps because workers used the lesser hedgehog tenrec (Echinops telfairi, Martin 1838, Figs. 2, 3) in their DNA studies. Echinops is traditionally considered a tenrec, but it may not be one based on bones (Fig. 3) and massive homology/convergence with the European hedgehog, Erinaceus (Figs. 1, 3).

Figure 4. European hedgehog, a member of Glires.

Figure 1. European hedgehog, Erinaceus, a member of Glires.

It’s the cloaca that seems to matter most
in tenrec studies. Plus the location: Madagascar.

Figur3 5. Madagascar hedgehog, is not a tenrec, but another member of Glires.

Figure 2. Madagascar hedgehog tenrec, Echinops, perhaps not a tenrec, but another member of hedgehog family within Glires.

There are two extant hedgehog tenrecs (HHTs):
the greater HHT (Setifer = Ericulus setosus) and the lesser HHT (Echinops telfari). Their skulls are not that different from each other, except in size. They have similar skeletons and spines coats. So we’ll focus on the lesser HHT as other workers have done before.

The problem is
the large reptile tree (LRT) nests Echinops rather convincingly with hedgehogs, like Erinaceus, within Glires, not with tenrecs like Tenrec (Fig. 1). Shifting Echinops to the tenrecs adds 30 steps to the LRT. Shifting the entire tenrec clade (ncluding the odontocetes) to the hedgehogs adds only 12 steps.

We’ve seen something like this before
when the purported tenrec, Potamogale (Du Chaillu 1860, Nicoll 1985; extant), the giant otter shrew that was supposed to be a tenrec, instead nested rather convincingly with shrews, far from tenrecs. It, too, has a cloaca.

Maybe it’s because they’re all from Madagascar.
Not sure what it is about that island that takes a perfectly good set of genital and anal openings and reverts them back into a single primitive cloaca. But that appears to be happening here among unrelated taxa, by convergence.

Among mammals
monotremes have a cloaca and that is most likely the primitive condition, as a cloaca is found in all other reptiles. Most marsupials separate the anus and genitals, so no cloaca is present — except in the very derived marsupial moles. Marsupials are basal to placentals according to the LRT, so any appearance of a cloaca in placentals is a reversal. Thus the Madagascar hedgehogs, the African golden moles and giant otter shrews (Potamogale) that redevelop a cloaca are examples of phylogenetic reversals.

So you  have a choice in nesting these purported tenrecs:

  1. Do you follow the bones and other soft (and prickly, Fig. 2) tissue with the exception of the cloaca?
  2. Or do you follow the cloaca alone? Current taxonomy and experts for over a century favor this choice.

To my knowledge,
mtDNA studies have not been conducted yet to resolve interrelationships among tenrecs and other mammals. If Echinops is indeed a hedgehog, then tenrecs have not been genetically tested against odontocetes. In fact, tell me if I’m wrong, but this may be the first time such a study has been conducted on morphology alone. Asher and Hofreiter 2006 stated at the time: “Due in part to scarcity of material, no published study has yet cladistically addressed the systematics of living and fossil Tenrecidae (Mammalia, Afrotheria).”

Echinops was employed by Mouchaty et al. 2000. Echinops might have been used by Meredith 2011 and Song 2012 to nest tenrecs with golden moles (Chrysocloris) as Afrotheres, related to elephants (Elephas) and hyraxes (Procavia). I don’t see any other tenrecs being used in molecular studies.

Echinops was recently employed by
Suarez 2009 in a study of the vomernasal system (VNS). The distribution of both vomernasal pathways in Eutheria was found to be present in rodents and Echinops, but not in other tested eutherians, none of which included other tenrecs. Of course, hedgehogs nest with rodents in the LRT.

Figure 1. The skulls of Erinaceus (above), Echinops (middle) and Tenrec (below), compared. Note the large premaxillary teeth common to all members of the Glires to the exclusion of other clades, including Tenrecidae.

Figure 3. The skulls of Erinaceus (above), Echinops (middle) and Tenrec (below), compared. Note the large premaxillary teeth common to all members of the Glires to the exclusion of other clades, including Tenrecidae. The anterior maxillary tooth of Erinaceus might be a canine, but it is not at the anterior rim of the maxilla, where one expects a canine.

Let’s compare
a hedgehog, a tenrec and the lesser hedgehog tenrec and perhaps you’ll see that a mistake was made over 100 years ago that continues to adversely affect phylogenetic analyses today. Perhaps a member of Glires has been long considered a member of Tenrecidae by virtue of its location, Madagascar, and its cloaca.

The European hedgehog
Erinaceus europaeus (Linneaus 1758; 20-30cm; extant) this omnivore can roll itself into a ball, erecting its spines for defence. Unlike most Glires, the hedgehog does not have a diastema. The jugal is very tiny in this clade.

The lesser hedgehog tenrec
Echinops telfairi (Martin 1838; extant, 13-17 cm) the lesser or pygmy hedgehog tenrec is widely considered a tenrec, but here it nests with hedgehogs and other Glires including rodents. This omnivore is restricted to Madagascar, home of severalt tenrecs. Note the large canines, like tenrecs and unlike hedgehogs. Note the large premaxillary teeth, like hedgehogs and unlike tenrecs. Unlike tenrecs, the ears are prominent. Like tenrecs, the jugal is absent.

Given that the Madagascar mammals with a cloaca
all do some burrowing, I wonder if the genitals and anus retreated beneath the cover of a single opening in order to keep dirt out? If that’s not the answer, I wonder what the common thread is that these unrelated taxa have that caused that primitive trait to reappear? And I wonder if there are any analyses based on morphology that include several tenrecs and other eutherians for comparison? So far I have found none, so the LRT is shedding light where it may be needed.

If Echinops is indeed a hedgehog with a cloaca
then we have to go get some mtDNA from Tenrec to see if it is a good match for odontocete mtDNA. At present, Tenrec has not been tested for its mtDNA, that I know of, so the whale connection question remains open.

While we’re at it it
count the stomachs in Tenrec. Even odontocetes have subdivided stomachs. Let’s find out when that trait appeared.

References
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
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
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
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

Stem taxa: wider vs. narrower definitions

The following is as much a learning experience for me
as it may be for you, as I come to an understanding of a definition with which I was previously unfamiliar — Stem Taxa in the ‘wider sense’. There is also a ‘narrower sense’, with which I was more familiar (see below).

Stem taxa in the wider sense
are extinct taxa closer to one clade of living taxa than to any other living taxa. In more precise terms, according to Wikipedia: “A stem group is a paraphyletic group composed of a pan-group or total-group, above, minus the crown group itself (and therefore minus all living members of the pan-group).”

Figure 1. CLICK TO ENLARGE. Stem taxa are closest ancestors to living taxa. Here basal diapsids and marine enaliosaurs are stem archosaurs. Triceratops is a stem bird. Captorhinids are stem turtles. Pterosaurs are stem squamates.

Figure 1. CLICK TO ENLARGE and retrieve a PDF file. Stem taxa are the closest ancestors to living taxa, but not the living taxa. Here in the wider sense marine enaliosaurs, including ichthyosaurs, are stem archosaurs. Triceratops is a stem bird. Diadectids are stem turtles. Pterosaurs are stem squamates.

The stem reptiles
in the LRT (Fig. 1, click here for PDF enlargement) are not the same stem taxa found in traditional studies, like Benton 1999, who includes pterosaurs among the stem birds. In the LRT (Fig. 1) pterosaurs are stem squamates, not squamates, but closer to squamates than to Sphenodon, the extant tuatara. Stem amphibians are not listed here, because the only listed extant taxon in that clade is Rana, the bull frog. Here plesiosaurs, ichthyosaurs and mesosaurs are all stem archosaurs. All dinosaurs are stem birds. Diadectids are stem turtles.

Paleontological significance
According to Wikipedia, “Placing fossils in their right order in a stem group allows the order of these acquisitions to be established, and thus the ecological and functional setting of the evolution of the major features of the group in question. Stem groups thus offer a route to integrate unique palaeontological data into questions of the evolution of living organisms. Furthermore, they show that fossils that were considered to lie in their own separate group because they did not show all the diagnostic features of a living clade, can nevertheless be related to it by lying in its stem group.” Unfortunately, these benefits get fuzzier as the phylogenetic distance increases.

Stem group: the narrower sense
According to Wikipedia (referencing Czaplewski, Vaughan and Ryan 2000), “Alternatively, the term “stem group” is sometimes used in a narrower sense to cover just the members of the traditional taxon falling outside the crown group. Permian synapsids like Dimetrodon and Anteosaurus are stem mammals in the wider sense but not in the narrower one. From a cynodont ancestry, the stem mammals arose in the late Triassic, slightly after the first appearance of dinosaurs.”

That narrower definition
is the one I was following and is certainly more useful, more targeted, etc. Since both definitions are in play in the wider world, be sure you specify which one you are discussing. Dr. Naish embraced the wider one while ignoring the narrower one.

And that’s okay.

References
Benton MJ 1999. Scleromochlus taylori and the origin of the pterosaurs. Philosophical Transactions of the Royal Society London, Series B 354 1423-1446.
Czaplewski TA, Vaughan JM and Ryan NJ 2000. Mammalogy (4th ed.). Fort Worth: Brooks/Cole Thomson Learning. p. 61.

wiki/Crown_group#Stem_groups

 

Just ran the numbers: Eocasea is not a sister to Casea

Reisz and Fröbisch 2014
considered Eocasea martini (Late Pennsylvanian, Fig. 1) the basalmost caseid, despite its long slender appearance and small size.

Figure 1. Eocasea in situ with anterior skull imagined.

Figure 1. Eocasea in situ with anterior skull imagined based on phylogenetic bracketing. This long, low taxa does not nest with large, big-bellied caseasaurs but with more similar sister, including Delorhynchus. These are not wide dorsal ribs, but belong to a specimen with a standard, narrow torso.

And at the time (2 years ago), I wrote in ReptileEvolution.com,
“[Eocasea] had a long narrow torso and short legs. Note the resemblance to millerettids like Australothyris and Oedaleops.” 

Reisz and Fröbisch did not include those two
in their phylogenetic analysis because they were so sure they had a caseasaur. They also did not include Eunotosaurus, Acleistorhinus, Microleter, Delorhynchus, or Feeserpeton for the same reason.

But they should have done so, because
that’s where Eocasea nests in the large reptile tree (Fig. 2) close to, but not with caseasaurs.

Figure 2. Eocasea nests between Feeserpeton + Australothyris and Delorhynchus in this subset of the large reptile tree, not close to Casea.

Figure 2. Eocasea nests between Feeserpeton + Australothyris and Delorhynchus in this subset of the large reptile tree, not close to Casea.

The problems with the Reisz and Fröbish data set
is that it was too small. The authors presumed Eocasea would be a caseasaur and so included only the following taxa: Reptilia, Diadectes, Limnoscelis, Mycterosaurus, Varanops, Oromycter, Casea, Cotylorhynchus, Angelosaurus, Ennatosaurus and Eocasea. As you can imagine, providing scores to a clade named, “Reptilia” is inappropriate and, frankly, dangerous, whether cherry-picking traits or scoring all zeroes. Diadectes, Limnoscelis, Mycterosaurus, Varanops are not related to each other or to caseasaurs. Reisz and Fröbisch were making guesses without having a large gamut study from which to draw subsets.

Reisz and Fröbisch report,
“Eocasea changes significantly our understanding of the evolutionary history of both caseids and caseasaurs.” Not with the current nesting. The discovery of Eocasea extends the fossil record of Caseasauria and Caseidae significantly, well into the Pennsylvanian, in line with the fossil record of other early synapsid clades, indicating that the initial stages of synapsid diversification were well under way by this time.” Eocasea is not a caseid and caseids are not synapsids, so it doesn’t extend anything related to Caseidae.

“More significantly, Eocasea also allows us to re-evaluate the origin and evolution of herbivory within this clade, and terrestrial vertebrates in general.” It’s not an herby and it’s not a clade member. “Thus, we can identify Paleozoic herbivores because their rib cages are typically significantly wider and more capacious than those of their closest insectivorous or carnivorous relatives. Not in Eocasea. “Nevertheless, it is likely that the ability to process this kind of plant matter precedes the skeletal correlates that can be found in the fossil record.” This is an unsupported supposition in light of the new nesting. “It is therefore possible that we are underestimating the extent of herbivory that existed in the Paleozoic, but this does not invalidate our results because the clades of herbivores that we examine here are widely separated by successive clades of non herbivorous vertebrates.” There is no ‘therefore’ when the setup if invalid. 

To their credit, 
Reisz and Fröbisch did not nest Edaphosaurus or Protorothyris as outgroup taxa to the Caseasauria (Eothyris at its base). Perhaps that is so because they did not include these taxa! And I wonder why? But they did nest the unrelated Varanops and Mycterosaurus as caseasaur outgroups. Both nest about twenty nodes away on the other major branch of the Reptilia, the new Archosauromorpha.The Reisz and Fröbisch tree is bogus because their outgroup taxon list was based not on testing, but on tradition.

If you’re looking for
osteological evidence for herbivory in the ancestry of the Caseasauria, you won’t find big bellies and flat teeth, but you will find several herbivores arising from Milleretta (late Permian late survivor of a Carboniferous radiation) in the clade Lepidosauromorpha. These include diadectids and their allies bolosaurids (post-crania unknown) and procolophonids, pareiasaurs and their allies turtles, along with caseasaurs.

Working on their ‘wish list’
Reisz and Fröbisch continue with their hypothesis: “Whereas other caseids also show dental specializations, with leaf-like large serrations being present in the marginal dentition, Eocasea, Oromycter, and the undescribed Bromacker Quarry caseid lack these serrations. Interestingly, both Oromycter, and the Bromacker caseid show skeletal evidence for herbivory, raising the possibility that oral processing in the form of puncturing vegetation may have evolved within Caseidae after the acquisition of herbivory.”  Only the latter two are indeed caseasaurids. Eocasea definitely is not one. You can’t derive homolog conclusions from unrelated taxa.

Reisz and Fröbisch continue
“Late Pennsylvanian and Early Permian diadectids also show convincing evidence of dental and skeletal adaptations for herbivory. These enigmatic
[not any more] Paleozoic forms are part of Diadectomorpha, a sister group to crown Amniota  [not any more]. A preliminary phylogeny of diadectids indicates that Ambedus, a small diadectid from the Early Permian, tentatively identified as omnivorous because of its labiolingually expanded cheek teeth (but no evidence of dental wear) is the sister taxon to all other diadectids. Ambedus may not be a diadectid as noted here. However, the oldest known diadectid from the late Pennsylvanian of Oklahoma is already clearly an herbivore and older than the edaphosaur Edaphosaurus novomexicanus. As is the case with the caseid and edaphosaur synapsids, the sister taxon of Diadectidae, the Early Permian Tseajaia from New Mexico, was faunivorous.” That oldest known diadectid is not identified.

Reisz and Fröbisch add to their unsupported hypothesis with,
“Although the holotype of Eocasea certainly represents a juvenile individual [actually, and you can check this, it is the same size as sister taxa, but smaller than basal and other caseasaurs], it is diminutive, with an estimated snout-vent length of 125 mm. In contrast, the smallest known herbivorous caseid with a comparable ontogenetic age, based on level of ossification of the vertebrae and pedal elements, is a basal, undescribed form from Germany and has an estimated snout-vent length of 400 mm.” Not sure which specimen this is…

If Reisz and Fröbisch had just
increased the size of their taxon list, they would/could have correctly nested Eocasea, and avoided making the many subsequent mistakes based on that bad nesting, including the unfortunate and inappropriate naming of the taxon and the bogus headline that got tacked to the article and all the PR that attended it.

We don’t have a name yet
for the enanticaseasaurs or paracaseasaurs (Fig. 2), but we need one!

References
Reisz R and Fröbisch J 2014. The oldest caseid synapsid from the Late Pennsylvanian of Kansas, and the evolution of herbivory in terrestrial vertebrates. PLoS ONE 9(4): e94518. doi:10.1371/journal.pone.0094518

 

Basal Archosauromorpha paper – Ezcurra 2016

Another paper repeating the ‘sins’ of the past,
based on an incomplete taxon inclusion list (that also includes taxa that should not be included). And a huge amount of otherwise excellent work! It proves once again that first hand access to specimens and an overly large character list will not bring full resolution to a small taxon list cobbled together by tradition, rather than testing.

I envy, am proud of and have to feel sorry for 
Martin Ezcurra (2016). He went around the world gathering data, obviously took a huge amount of time studying the specimens and writing this paper, but he’s stuck with that less than adequate traditional taxon list rather than the testing offered by the wide gamut taxon list (large reptile tree) in ReptileEvolution.com. He’s using 96 taxa (vs. 674 at ReptileEvolution.com). He’s using 600 characters. That should be more than enough, and it is more than enough (less than half that number will do), but more taxa is really what Ezcurra needs.

Just a few notes
Ezcurra wrote: “Jesairosaurus lehmani was described in detail by Jalil (1997). Despite its short neck, this species has been considered since its original description as a member of “Prolacertiformes.” Nevertheless, the phylogenetic position of this species has not been further tested in more recent quantitative analyses.” Yes it has, Here Jesairosaurus nests with drepanosaurs at the base of the Lepidosauriformes, not with Macrocnemus, as shown by Ezcurra (Fig. 1). Drepanosaurs were excluded by Ezcurra.

Figure 1. Ezcurra 2016 tree of basal archosauromorphs. He has basically repeated the mistakes of Nesbitt 2011 here.

Figure 1. Ezcurra 2016 tree of basal archosauromorphs. He has basically repeated the mistakes of Nesbitt 2011 here. Colors denote taxa that lie outside the gamut of the Archosauriformes + Protorosauria under study here.

Ezcurra is still including the thalattosaur, Vancleavea which nests with Doswellia in the Ezcurra tree. It just doesn’t belong in a study on archosauriforms.

He still holds to the tradition of a monophyletic Diapsida proven invalid here.

Ezcurra is still including pterosaurs in an archosauriform study
Proterochampsia (now including Vancleavea) is still recovered by Ezcurra as the proximal outgroup. Phytosauria and Lagerpeton are sister taxa. How is this possible? What characters do they share? They certainly don’t look alike. He notes Peters (2000) then writes, “The phylogenetic analysis conducted here [Ezcurra 2016] constitutes the best data matrix compiled so far to test the position of pterosaurs within Archosauromorpha because of the broad sample of Permo-Triassic species, including the undoubted pterosaur Dimorphodon macronyx.”  Martin, but you’re not looking, really looking at your results. Your proximal outgroup should look kind of like a pterosaur. Right?

Ezcurra notes that 33 extra steps
are needed to place Dimorphodon with Tanystropheidae and 19 synapomorphies support the Ornithodira. That might be true in his study. Hard to imagine how that is possible though. I will try to plow through his 600 characters to figure it out.  Convergence is rampant in the Reptilia. More synapomorphies support pterosaurs outside the Ornithodira when pertinent taxa are not excluded (see below).

Ezcurra writes, “Future analyses focused on testing the higher-level phylogenetic relationships of pterosaurs should also incorporate a broader sample of early pterosaurs and some enigmatic diapsids that were found as more closely related to pterosaurs than to other archosauromorphs by Peters (2000) and are not included in the current taxonomic sample (i.e., Langobardisaurus pandolfi, Cosesaurus aviceps, Sharovipteryx mirabilis and Longisquama insignis). However, it seems extremely unlikely that the addition of these enigmatic diapsids, which are unambiguously considered to not be members of Archosauriformes (e.g., Peters, 2000Senter, 2004), will affect the higher-level phylogenetic position of pterosaurs.”

In Science, the word ‘seems” and “extremely unlikely” need to be tested, especially when Langobardisaurus, for instance, shares so many traits with Tanystropheus and Macrocnemus. And especially when they have been tested sixteen years ago (Peters 2000). The word “enigmatic” is inappropriate here, unless Ezcurra just preferred to avoid them and stay with the traditional nod and move on.

Many good color photos of specimens here.
Precise descriptions. Like Nesbitt (2011) he’s just not playing with a full deck — of taxa.

Ezcurra’s tree
had 1.8 million+ possible MPTs. The large reptile tree was fully resolved with a single tree and high Bootstrap values. His analysis 3 recovered 40 MPTs by dropping largely incomplete taxa. That’s often a good idea. No reconstructions were offered, except for some skulls. No gradual accumulations of derived traits for odd partners like pterosaurs, Vancleavea, Doswellia, etc. Many purported sisters do not look alike.

Still not sure how
these trees don’t nest Tropidosuchus and Lagerpeton together. They are virtually identical.

Figure 2. Ezcurra tree with Bremer supports AFTER pruning incomplete taxa.

Figure 2. Ezcurra tree with Bremer supports AFTER pruning incomplete taxa. Many oddly paired sisters still show up here.

Ezcurra comments on Choristodera
“The problematic phylogenetic position of choristoderans may be a result of an unsampled early evolutionary history. The phylogenetic position of choristoderans is also ambiguously resolved in this analysis, but is constrained to the base of either Lepidosauromorpha or Archosauromorpha.” Actually the early history is sampled (here), just not included in this analysis.

Ezcurra has to be feeling pretty confident.
He writes, “Much of the general topology of the phylogenetic trees recovered in this analysis agrees with that found by several previous workers (e.g., Sereno, 1991Dilkes, 1998Gottmann-Quesada & Sander, 2009Ezcurra, Lecuona & Martinelli, 2010Nesbitt, 2011Ezcurra, Scheyer & Butler, 2014).”

I’d feel more confident
if all sister taxa looked alike and a gradual accumulation of traits could be traced for every taxon. Ezcurra needs more taxa to weed out the problems here. This study carries with it the sins of past studies.

PS
I was unable to open the Ezcurra data files on either Mesquite or MacClade.

References
Ezcurra MD 016.The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriformsPeerJ 4:e1778https://doi.org/10.7717/peerj.1778
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352:1–292 DOI 10.1206/352.1.
Peters D 2000. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106:293-336

Excuses for not posting last week…

  1. I finally wrote another paper and submitted it. That took all week.
  2. There wasn’t much other paleo news to get excited about (unless I missed something?).

Now that I’m back to looking at other things,
all I see is a pachypleurosaur with small hands and feet of uncertain affinities, Dawazisaurus (Cheng, Wu, Sato and Shan 2016). I note the authors did not test it against Hanosaurus and Dianmeisaurus, where it nested in the large reptile tree.

I’m pleased and surprised to see that readership does not flag
on quiet weeks. And for some reason Sunday was a big day. Thank you all for your continued interest.

References
Cheng Y-N, Wu X-C, Sato T, Shan H-Y 2016. Dawazisaurus brevis, a new eosauropterygian from the Middle Triassic of Yunnan, China. Acta Geologica Sinica (English) 90:401-424.