Ozimek volans: long and skinny, but not a glider

Updated a few hours later
with a phylogenetic analysis nesting Ozimek with Prolacerta.

A new and very slender
Late Triassic (230 mya) reptile from lake sediment, Ozimek volans (Dzik and Sulej 2016; ZPAL AbIII / 2512; Figs. 1-3) appears to look like a variety of taxa on both sides of the great divide within the Reptilia: macrocnemids and protorosaurs. Based on the long, thin-walled neck bones, Ozimek was originally considered a possible pterosaur or tanystropheid, but Dzik and Sulej nested it with Sharovipteryx (Fig. 1), the Middle Triassic gliding fenestrasaur, and considered it a big glider (Fig. 3).

Figure 1. Three in situ specimens attributed to Ozimek. The largest humerus (purple) is scaled up from the smaller specimen. These are 80% of full scale when viewed at  72 dpi. To me, that 2012 ulna looks like a tibia + fibula and the 2012 humerus looks like a femur, distinct from the 2512 humerus.

The large reptile tree
(LRT) does not nest the much larger Ozimek with tiny Sharovipteryx, but with Prolacerta (Fig. 2). While lacking an antorbital fenestra, Dzik and Sulej consider Ozimek an archosauromorph. They also consider Sharovipteryx an archosauromorph.  Like all fenestrasaurs, Sharovipteryx has an antorbital fenestra by convergence with archosauromorpha.

Figure 2. Reconstruction of Ozimek with hands and feet flipped to a standard medial digit 1 configuration and compared to Sharovipteryx and Prolacerta to scale. Note the short robust forelimbs and elongate pectoral elements of Sharovipteryx, in contrast to those in Ozimek. Compared to Prolacerta the girdles are much smaller, indicating a much smaller muscle mass on the limbs, probably making it a poor walker. Perhaps it floated to support its weight.

Sediment
The authors report on the limestone concretion, “the fossils under study occur in the one-meter thick lacustrine horizon in the upper part where the dominant species are aquatic or semi-aquatic animals. These also include the armored aetosaur Stagonolepis, possible dinosauriform Silesaurus, crocodile-like labyrinthodont Cyclotosaurus, and the predatory rauisuchian Polonosuchus.”

Figure 3. 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 due to its weak musculature. The model was built based on crappy reconstructions of Sharovipteryx.

Forelimbs
Dzik and Sulej take the word of Unwin 2000, who did not see forelimbs in Sharovipteryx (and illustrated it with Sharov’s drawing), rather than the reports of Sharov 1971, Gans et al. 1987 and Peters 2000 who did see forelimbs. The latter three authors found the  forelimbs were short with long fingers, distinct from the gracile forelimbs and short fingers found in Ozimek. So, that’s one way to twist the data to fit a preconception. New specimens often get a free pass when it comes to odd interpretations, as we’ve seen before in Yi qi and others.

Manus and pes
In the reconstruction it appears that the medial and lateral digits are flipped from standards. This is both shown and repaired in figure 2.

According to the scale bars
the ZPAL AbIII/2511 specimen is exactly half the size of the ZPAL AbIII/2012 specimen. That issue was not resolved by the SuppData  The humerus shown in the 2012 specimen is not listed in the SuppData. Even so, the authors also ally another large humerus (2028) to Ozimek, and this provides the large scale seen in the fleshed-out model built for the museum and the camera (Fig. 3).

Built on several disassociated specimens
the reconstruction of Ozimek (Fig. 2) is a chimaera, something to watch out for.

Initial attempts at a phylogenetic analysis
based on the reconstruction pointed in three different directions, including one as a sauropterygian based on the illustrated dorsal configuration of the clavicles relative to the coronoids. If the clavicles are rotated so the vernal rim is aligned with the anterior coracoids the dorsal processes line up correctly with the indentations on the scapula (Fig. 2), alleviating the phylogenetic problem.

Lifestyle and niche
Sharovipteryx has an elongate scapula and coracoid, traits lacking in Ozimek. Sharovipteryx also has an elongate ilium and deep ventral pelvis, traits lacking in Ozimek. The limbs are so slender in Ozimek, much more so than in the much smaller Sharovipteryx, that it does not seem possible that they could support the large skull, long neck and long torso in the air – or on the ground. This is a weak reptile, likely incapable of rapid or robust locomotion. So instead of gliding, or even walking, perhaps Ozimek was buoyed by still water. Perhaps it moved its spidery limbs very little based on the small size of the available pectoral and pelvic anchors for muscles, despite those long anterior caudal transverse processes. Those might have been more useful at snaking a long thin tail for propulsion.

If we use our imagination,
perhaps with a large oval membrane that extended from the base of the neck to fore imbs to hind limbs Ozimek might have been like a Triassic water lily pad, able to dip its skull beneath the surface seeking prey, propelled by a flagellum-like tail. Not sure how else to interpret this set of specimens.

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.

wiki/Ozimek (in Polish)

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

It’s the single genital slit (similar to a monotreme cloaca) that seems to matter most
in tenrec studies. Plus the location: Madagascar.

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 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

Dr. David Unwin on pterosaur reproduction – YouTube

Dr. David Unwin’ talk on pterosaur reproduction 

was recorded at the XIV Annual Meeting of the European Association of Vertebrate Palaeontologists, Teylers Museum, Haarlem, Netherlands and are online as a YouTube video.

Dr. Unwin is an excellent and engaging speaker.
However, some of the issues Dr. Unwin raises have been solved at www.ReptileEvolution.com

The virtual lack of calcite in pterosaur eggs were compared to lepidosaurs by Dr. Unwin, because pterosaurs ARE lepidosaurs.  See: www.ReptileEvolution.com/reptile-tree.htm

Lepidosaurs carry their eggs internally much longer than archosaurs, some to the point of live birth or hatching within hours of egg laying. Given this, pterosaurs did not have to bury their eggs where hatchlings would risk damaging their fragile membranes while digging out. Rather mothers carried them until hatching. The Mrs. T external egg was prematurely expelled at death, thus the embryo was poorly ossified and small.

Dr. Unwin ignores the fact that hatchlings and juveniles had adult proportions as demonstrated by growth series in Zhejiangopterus, Pterodaustro and all others, like the JZMP embryo (with adult ornithocheirid proportions) and the IVPP embryo (with adult anurognathid proportions).

Dr. Unwin also holds to the disproved assumption that all Solnhofen sparrow- to hummingbird-sized pterosaurs were juveniles or hatchlings distinct from any adult in the strata. So they can’t be juveniles (see above). Rather these have been demonstrated to be phylogenetically miniaturized adults and transitional taxa linking larger long-tailed dorygnathid and scaphognathid ancestors to larger short-tailed pterodactyloid-grade descendants, as shown at: www.ReptileEvolution.com/MPUM6009-3.htm

Thus the BMNH 42736 specimen and Ningchengopterus are adults, not hatchlings. And the small Rhamphorhynchus specimens are also small adults.

More turtles with temporal fenestrae

Everyone knows that turtles are supposed to be ‘anapsids’.
In other words, they aren’t supposed to have temporal fenestrae. However, many extant taxa, like the box turtle, Terrapene, have such extensive posttemporal fenestrae that the entire posterior half of the skull can be greatly eroded as it is refilled with large jaw muscles.

Figure 1. Meiolania has a lateral temporal fenestra created by more bone encircling the tympanum (ear drum) at the quadrate. It could be that the top of the qj is actually the fused sq.

Sometimes more bone makes a fenestra
Earlier we looked at Meiolania a basal turtle with an unusual lateral temporal fenestra created by MORE BONE that encircled the eardrum and quadrate.

The extant leatherback,
Dermochelys (Fig. 2) also has a lateral temporal fenestra, but it lacks a lateral temporal bar. Dermochelys nests with Santanachelys, rather than Chelonia. Neither share this trait, nor do any other tested turtles.

Figure 1. Dermochelys, the leatherback turtle, has a lateral temporal fenestra, a product of bone reduction between the jugal and squamosal + quadrate. Adult at left, juvenile at right, not to scale. The elongate premaxilla is convergent with soft-shell turtles. Note the ontogenetic changes here. Pretty remarkable.

It’s interesting
to see the ontogenetic changes that take place in the skull bones of the juvenile Dermochelys as it matures. The lateral temporal fenestra appears to enlarge with age. Other bones change their shape as the turtle matures.

Figure 2. Chelus frmbiata, the mata-mata has a temporal fenestra. Not sure if it’s a lateral or upper type and I”m not looking, this time, at the hole leading into the quadrate. Just in front of those projections in dorsal view you’ll see the temporal fenestra of Chelus. Note the mistake made by Dr. Gaffney in overlooking the squamosal and quadratojugal (light green and yellow) while mislabeling the supratemporal (orange). The blue bones in ventral view are all hyoids used to anchor muscles that greatly expand the throat during prey capture.  Left image from Digimorph.org and used with permission. Right image from Gaffney 1979.

Another turtle with a lateral temporal fenestra
is Chelus frimbriata, otherwise known as the Mata-mata (Fig. 2), a side-neck turtle (pleurodire) with huge hyoids that help its neck expand quickly to suck in swimming prey items. This skull also qualifies for a top-ten position among the weirdest of all reptile skulls.

Dr. Eugene Gaffney, AMNH,
the dean of all turtle studies, unfortunately overlooked the squamosal and quadratojugal in Chelus (Fig. 2) while mislabeling the supratemporal in this and all other turtles he worked on (Fig. 3). That bone is typically very large in pareiasaurs and that mislabeling is likely one reason why some turtle workers are not recognizing the one and only valid pareiasaur – turtle relationship.

Here’s another example of the same mistake. 

Figure 3. This GIF movie of two frames changes every 5 seconds. Note the caption Dr. Gaffney provides as he misidentifies the supratemporal as the squamosal. The right side of the specimen, not illustrated, could represent a loss or, more likely fusion of the squomosal and quadratojugal cheekbones. Image from Gaffney 1979.

Pelomedusa
(Fig. 3) is a more plesiomorphic (basal) side-neck turtle without a lateral temporal fenestra and a very deep post-temporal fenestra. But note the ventral emargination in the cheek region. Gaffney noted the extra bone, but because he had already mislabeled the squamosal, he didn’t recognize the combination of the squamosal and quadratojugal in the cheek.

And speaking of pleurodires
(side-neck turtles), most traditional studies find a basal split between pleurodires and cryptodires (vertical neck flexure). By contrast, the LRT splits hard, dome-shelled turtles from flatter, soft-shelled turtles by the Triassic. Proganochelys represents the former while Odontochelys represents the latter. And each has their own small pareiasaur ancestor. So turtles are diphyletic, but the two clades are closely related.

References
Gaffney ES 1979. Comparative cranial morphology of recent and fossil turtles. Bulletin of the American Museum of Natural History 164(2):65-376.

wiki/Dermochelys
wiki/Chelus
wiki/Pelomedusa

The laughing hyena (Crocuta crocuta) is a ‘CatDog’

Traditionally
hyenas, like Crocuta crocuta (spotted or laughing hyaena, Kaup 1828, Erxleben 1777; up to 160 cm in length, Pliocene, 10 mya to present; Figs. 1,2), have been nested with palm civets, like Nandinia, and mongooses, like Herpestes. I hate to keep doing this, but adding Crocuta to the large reptile tree (LRT) nests this hyena rather strongly between dogs, like Canis (Fig. 3) and cats, like the African lion, Panthera leo (African lion, Linneaus 1758; up to 250 cm in length (sans tail), Pliocene, 10 mya to present; Fig. 4). So the hyena is something of a CatDog (see way below, Fig. 5). It is not a basal member of the Carnivora.

Figure 1. Crocuta skull is quite similar to that of Canis, its sister in the LRT. But also similar to Panthera, its other sister in the LRT.

And it’s easy to see why hyenas nest with dogs.
There is even a clade of widely recognized dog-like hyenas among fossil taxa. Wikipedia reports, “Although phylogenetically they are closer to felines and viverrids, hyenas are behaviourally and morphologically similar to canines in several aspects” So most workers consider this convergent evolution. Having examined the characters in detail, I call this nothing but rather typical evolution and sisterhood. There are only a few traits that separate the three sisters.

Figure 2. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2). Note the shorter torso and more robust limbs, perhaps the most obvious differences between hyenas and their sisters, cats and dogs.

From the  website of the
IUCN Hyaena Specialist Group “Although extant hyenas are rather dog-like in many aspects of their appearance, the family Hyaenidae actually belongs to the Carnivore suborder Feliformia, which also contains cats, mongooses, civets, and allies.”

Figure 3. Canis lupus, the wolf, nests as a sister to Crocuta in the LRT.

Contra that hypothesis of relationships,
the LRT nests civets, mongooses, moles, raccoons, seals and allies as basal carnivores. Cats, dogs and  hyenas nest as derived carnivores and sisters to the extinct taxa, Miacis and Hyopsodus.

Figure 4. Panthera leo skull and skeleton. This taxon nests basal to hyenas + wolves. Note the relatively large scapula and slender limbs with retractable claws.

Perhaps more reasons to distrust DNA studies
The IUCN website notes: “Fossil data suggest that members of the family Hyaenidae last shared a common ancestor with their Feliform sister taxon in the Oligocene, around 25 million years ago (MYA) (Werdelin & Solounias 1991), and recent molecular data suggest this divergence occurred even earlier, approximately 29 MYA (Koepfli et al. 2006). The molecular data further suggest that the sister group to the Hyaenidae is a Feliform clade containing the mongooses (family Herpestidae) and the fossa (genus Cryptoprocta), a small, civet-like Malagasy carnivore that was assigned to the family Viverridae until quite recently (Yoder et al. 2003).”

Sisters to the dog-cat split, Miacis and Hyopsodus, 
were found in Late Paleocene to Late Eocene strata. So phylogenetic bracketing pushes the cat-dog + hyena split back to that era.

Figure 5. CatDog is a cartoon character that in no way resembles the extant hyena.

The cartoon
CatDog is a animated television character (Fig. 5) with two heads that in no way resembles the extant hyena. As you might imagine, they often want to go their separate ways and this leads to frustration and fun.

While we’re on the subject of hyenas…
Proteles crostata (aardwolf; Fig. 6; Sparrman 1783; extant), is in the same family as hyenas, according to Wikipedia. And it is, in a way… except the LRT nests this long-legged termite-eater closer to Canis than Crocuta.

Figure 6. The extant aardwolf, Proteles, nests as a sister to Canis in the LRT and this clade is a sister to Crocuta, the hyena. Note the tiny teeth, except for the large canines, of this long-legged termite eater.

And this footnote:
The weasel or stoat (Mustela erminea; Linneaus 1758) nests basal to all six above named taxa in the LRT, derived from a sister to the raccoon (Procyon).

References
Erxleben J 1777. Systema regni animalis.
Kaup JJ 1828. Über Hyaena, Uromastix, Basiliscus, Corthaeolus, Acontias. Isis 21, columns 1144–1150.
Linnaeus C von 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Sparman A 1783. 

wiki/Canis
wiki/Carnivora
wiki/Crocuta
wiki/Hyena
wiki/Panthera
wiki/Aardwolf

Phylogeny of the Carnivora – its topsy-turvy!

The large reptile tree
(LRT) presents a novel topology for many clades within the Reptilia. Among them is the Carnivora (Fig.1). The LRT uses fossil taxa and, you’ll note by comparison, is virtually upside-down (topsy-turvy, backwards) when it comes to trees recovered in molecular studies. That major difference MIGHT be traced to the choice of outgroup, as you will see…

Figure 2. Subset of the LRT focusing on the Carnivora.

Using molecular phylogenetics
(no fossils) Eizirik et al 2010 recovered a cladogram of the Carnivora that used Manis, the pangolin (Fig. 2), as the outgroup. Does this surprise you? …especially considering the fact that Manis has bounced around various nodes on the mammal family tree for decades. …and since it is toothless! And since it has scales instead of hair! etc. etc.

Figure 2. Manis, the Chinese Tree Pangolin along with other views of other pangolins

That, in itself, is very strange
to have a highly derived taxon used as a plesiomorphic outgroup. By contrast, in the LRT the outgroup is Monodelphis (Fig. 3), a tiny very plesiomorphic, opossum-like basal placental with origins in the Jurassic. And it has teeth!  And hair!

Figure 3. Entire skeleton of Monodelphis from Digimorph.org and used with permission. This little taxon makes a great outgroup for the Carnivora that will flip topologies on their head when employed.

Using a pangolin as the outgroup
the Eizirik team recovered a basal split between feliforms and caniforms.

Feiliforms include Nandinia, then a split between cats and civets + hyenas + mongooses + fossas.

Caniforms include a basal split between wolves and bears + seals + raccoons + minks. Essentially these topologies are quite similar to the LRT, only in the opposite order with cats and dogs nesting in basal nodes, while minks and mongooses nest in derived nodes.

Notice the relatively flipped topologies
Can we blame this on the choice of an outgroup? On the lack of fossil taxa? On the inadequacies of DNA analyses across large clades? Or a little of all three?

Note that
Talpa, the extant Eastern mole, and Mondelphis, the extant gray short-tailed opossum were excluded a priori from the Eizirik study, but revealed by the large gamut analysis of the LRT, which minimizes a priori assumptions such as these.

Also using molecules
Wesley-Hunt and Flynn 2005 found a similar topology to the Eizirik study, turning the order recovered by the LRT on its head, with opossum-like carnivores (civets, minks) in derived nodes. This study used a variety of outgroups (Manis, Elephas, Loxodonta, Equus, Bos, Sus, Homo) rather than Monodelphis. Results did not change the topology within the Carnivora.

Now is a good time to ask yourself,
Why did they use such silly, useless and obviously wrong outgroups rather than seek the one true plesiomorphic outgroup?

This is exactly why
this blog and ReptileEvolution.com were created — to throw back the curtain on such odd practices, methods and choices — AND produce viable alternative answers. These are experiments you can repeat yourself, BTW.

Let’s not forget
moles (Fig. 3) are carnivores, too!

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

References
Eizirik E, Murphy WJ, Koepfli KP, Johnson WE, Dragoo JW and O’Brien SJ 2010. Pattern and timing of the diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Molecular Phylogenetics and Evolution 56:49–63.
Wesley-Hunt GD and Flynn JJ 2005. Phylogeny of the Carnivores. Journal of Systematic Palaeontology. 3:1–28.

Zygorhiza mandible issues

Zygorhiza kochiii (Late Eocene, 36mya; 5.2m; Kellogg 1936) is a dorundontine odontocete, smaller than Zeuglodon (Basiliosaurus), but larger than Maiacetus. Like its tenrec ancestors, Zygorhiza had long, slender toothy jaws.

Figure 1. (above) Zygorhiza kochi from George Mason University website, likely captured from Kellogg 1936. To make the jaws fit and teeth occlude the mandible had to be reduced and the cranium had to tilted down posteriorly.

Today’s problem involves the jaws
which were presented, apparently, in a scale that did not permit the teeth to occlude properly when reattached to the skull. By reducing the mandible and lowering the rear of the skull all the parts mesh and match. Not sure what the fossil looks like, but this is what happens when you test the restoration and create a reconstruction.

Perhaps
the mandible and skull come from two different specimens. It’s also worth noting how this odontocete whale’s teeth appear to be evolving back to primitive shapes, that is, cusps aligned all in a row, rather than W -shaped in occlusal view. And, of course, extant odontocete teeth have no distinct cusps, but have all reverted to a complete arcade of canine-like pegs largely made up of former premolars.

References
Kellogg R 1936. A review of the Archaeoceti. Washington: Carnegie Institution of Washington. pp. 100–177.

wiki/Zygorhiza

Weirdest skull of all: Eubalaena australis (Southern right whale)

There are few mammal skulls
that depart from the basic placental pattern (bauplan) like that of Eubalaena australis (Desmoulins 1822; 15-18 m in length; extant), the Southern right whale (Fig. 1). All the parts are there. They just have weird shapes and are shifted around a bit.

The giant mouth
is much deeper than in Caperea (Bisconti 2012, Fordyce and Marx 2013 ) or Balaenoptera (Fig. 2; Linneaus 1758), with much longer baleen. The skull is relatively larger and the postcrania shorter and deeper with relatively larger forelimbs than Balaeonoptera. The mandible moves relatively little. The coronoid process is absent. The lower lip rises to meet the upper jaw, as in Caperea (Fig. 2), but much more so due to the great height of the giant skull.

Note the hammerhead cranium in dorsal view
creating a T-shape with the addition of that long triangular rostrum (Fig. 1). The mandible is much wider than the rostrum. That resulting space between them is where the water exits after entering from the front and after being filtered by the tall baleen strips.

Surprisingly,
five digits are present on the manus following a long lineage of thumb-less ancestors. So the reappearance of the thumb here is a minor atavism.

Figure 1. Eubalaena australis skeleton with several bones colorized and eyeball added. Note the reappearance of an atavistic thumb after a long run of four-fingered ancestors.

The cervical series
is tightly interwoven, like a stack of bent playing cards. The caudal transverse processes have broad tips. The chevrons are longer than deep.

Figure 2. Caperea, the pygmy right whale, is a much smaller sister to Eubalaena. Only the skeleton with the ribs angled back fits the stranded in vivo specimen and the skull is a better fit when it is slightly larger.

The pygmy right whale (Caperea marginata)
(Fig. 2; Gray 1846; 6m; extant) looks like a small, slender right whale with tiny flippers. While it nests with Eubalaena in the LRT (Fig. 9), it retains something of a gray whale (Eschrichtius, Fig. 4) appearance. Caperea is the smallest of all baleen whales, by far.

The cervicals are all fused to one another. The dorsals have paddle-shaped ribs, but don’t be fooled by the museum mounts (Fig. 2, above). Such ribs cannot fit into a living Caperea without rotating posteriorly about 45º (Fig. 2, below). The lumbars are reduced to one. The chevrons are shorter than long, as in right whales and cetotheres.

The dorsal fin is above the sacral vertebrae, distinct from odontocetes, in which the dorsal fin is above the dorsal ribs.

By comparison
Balaenoptera (Fig. 2) the blue whale, is longer, with a relatively smaller, shallower skull. It feeds by expanding a giant throat sack with water inflow then expelling it with the tongue and by throat constrictions.

Figure 3. Blue whale (Balaenoptera musculus) skull and skeleton. Note the lack of a thumb goes back to Mesonyx.

The California Gray Whale
(Eschrichtius robustus; 15m; extant; Gray 1864; Fig. 7) nests at the base of all tested mysticetes (Fig. 9) and provides the best clues to envision the post-crania of Behemotops, and other derived desmostylians.

Figure 6. Eschrichtius-robustus, the gray whale is the most basal mysticete tested in the LRT with a skull similar to Desmotylus and Beheomotops.

The maxilla of the gray whale retains a tooth alveolus
for the canine which is aligned along the jawline in Desmostylus (Fig. 8), a trait not found elsewhere among mammals. The dentary tip also retains a tooth alveolus, similar to that found in Desmostylus.

Figure 7. Gray whale (Eschirctius) anterior rostrum. Green arrow points to the canine alveolus lacking a tooth. Missing mandible teeth would have appeared along anterior rims of the mandibles (blue arrow), as in desmostylians. See figure 8. I wonder if we’ll someday find teeth in a dissection of the Gray Whale. Someone should look for them.

Note the maxilla of this Desmostylus
(Fig. 8) shares many traits with basal mysticetes, including a general toothlessness (molars still are present below the orbit), a concave maxilla ventral margin, and a dorsal naris. The dentary has anteriorly oriented, tusk-like incisors, growing from alveoli similar to those in the gray whale (Fig. 7).  I wonder if we’ll someday find teeth in a dissection of the Gray Whale. Someone should look for them. I wonder if someday someone will find teeth in a dissection of the Gray Whale. Someone should look for them.

Figure 8. Desmostylus jaws with green and blue arrows pointing to buried canine and anterior dentary tusks. Compare to gray whale rostrum in figure 6.

The evidence keeps mounting
that mysticetes and odontocetes had separate origins among desmostylians and tenrecs, respectively.

Figure 9. Subset of the LRT showing mesonychids including hippos, anthracobunids, desmostylians and mysticete ‘whale.’

References
Desmoulins C 1822. Baleine. Dictionnaire Classique d’Histoire Naturelle 155-165
Gray JE 1864. “Eschrichtius“. Annals of the Magaztine Natural History. 3 (14): 350.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Balaenoptera
wiki/Eubalaena
wiki/Caperea
wiki/Eschrichtius

 

 

Mammal evolution analyses using molecules

Now that
the large reptile tree (LRT) has grown to encompass a large gamut of mammals based on shared morphological traits, it’s time to compare it with prior studies based on molecules. Some scientists say that molecular studies that do not include fossil taxa should take precedence over morphological studies that do include fossils. Some studies combine extant DNA and extinct morphological data. In any case, it is important that all pertinent taxa are included and that unrelated taxa are excluded — and that suprageneric taxa are avoided. And finally, stand back and check your work to make sure it makes sense (more on that below).

The base of the Placentalia in the LRT
begins with small, omnivorous. plesiomorphic Monodelphis. This taxon gives rise to a number of small fur balls, all similar in size and shape, but differing subtly and nesting at the bases of more diverse and derived clades. In succession the following clades split off: Carnivora (includes moles), Glires, arboreal mammals, tenrecs/odontocetes, edentates and finally the large herbivores splitting mesonychids, desmostylians and mysticetes from elephants, sirenians and ungulates. This study provides a gradual accumulation of traits from small plesiomorphic generalists to large derived specialists and includes extinct taxa. Importantly, the basalmost taxon is very much like a basal marsupial — as it should be!

By comparison
Meredith 2011 – begins with Afrotheria (elephants/ sirenians/ elephant shrews/ tenrecs/ golden moles) + edentates, arboreals (sans bats)/ Glires, and finally moles/shrews/hedgehogs + pangolins/carnivores + bats + artiodactyls (including hippos + whales).  This study does not provide a gradual accumulation of traits from small plesiomorphic generalists to large highly derived specialists and does not include extinct taxa. The basalmost taxa are not close to any marsupials in appearance.

Margulies et al. 2007 – essentially repeat this topology. This study has the same problem.

Tree of Life project 1995 – begins with edentates + pangolins, then Glires + arboreals + insectivores + (carnivores + creodonts) + artiodactyls and whales +  aardvarks, + perissodactyls + hyracoids + tethytheres (elephants, embrithopods, desmostylians and sirenians).. This study has the same problem.

Song et al. 2015 – begins with edentates + elephants/ tenrecs, insectivores + bats + ungulates + carnivores + other ungulates + whales, Glires, tree shrews, primates. This study has the same problem.

In a condescending tone
Asher, Bennett and Lehmann 2009 added their research to the topic of mammal phylogeny. Note how often these authors use the word ‘believe’ with regard to the best efforts of prior scientists, none of whom put faith ahead of evidence.

“In the not so distant past, there was a lot of uncertainty regarding how clades of living mammals were interrelated. Many mammalian systematists believed that sengis (Macroscelididae or ‘elephant shrews’) were closely related to rabbits and rodents, that pangolins (Pholidota) were ‘edentates’ along with anteaters, or that tenrecs (Tenrecidae) and golden moles (Chrysochloridae) were ‘insectivorans’ along with shrews and hedgehogs. Some believed that hyraxes (Procaviidae) were part of the Perissodactyla, and others thought that bats were so close to primates that the non-echolocating ones actually were primates, or at least close enough to make Chiroptera paraphyletic. In contrast, the consensus today on each of these issues is not only quite different, but also resolved with a substantial level of confidence. Questions regarding character evolution among living mammals now have the decisive advantage of a relatively well-resolved tree.”

Asher, Bennett and Lehmann 2009 – begin with a basal split between Atlantogenata (edentates + elephants + elephant shrews) and Boreoeutheria (primates/ rodents + insectivores + carnivores + bats + ungulates (including whales). This study has the same problem(s). And I, for one, have no ‘substantial level of confidence’ in its results. A ‘relatively well-resolved tree’ that does not provide a series of taxa with gradually accumulating derived traits is no match for a completely resolved tree topology that does provide that gradual accumulation. Let’s keep our thinking caps on. 

Does anyone else see
that in each of these studies, bats and ungulates nest as closely related? That the highly specialized edentates and elephants nest basal to the little furry opossum-like omnivores? The LRT does not have these problems. And yes, I’m picking the low-hanging fruit, but those kinds of problems are your clue that it is best to ditch DNA for major clade interrelationships (but keep DNA for congeneric and criminal studies) and stick to morphology when you create your own tree topology). That way you can visually check your results! Stand back from your cladogram before you publish it and see if all nodes and branches form a continuous and logical sequence with only gradual changes apparent between sister taxa. And that basal taxa look like outgroup taxa. That’s why I show my work.

When it comes to whales
Geisler et al. 2011 – nested fossil and extant odontocetes and mysticetes arising from Zygorhiza. and Georgiacetus, two archaeocetes. The toothed taxa, Janjucetus, Mammalodon and Aetiocetus were nested as basal mysticetes. Sus (pig), Bos (cattle) and hippopotamidae (hippos) were outgroup taxa. This study appears to be accurate when it comes to extant whales. But this team assumed whales were monophyletic and thus haven them a common ancestor with fins and flukes. By contrast the LRT found toothed whales arising from toothed tenrecs and baleen whales arising from desmostylians, all of which have a long diastema (toothless region of the jawline) and dorsal nares.

References
Asher RJ, Bennett N and Lehmann T 2009. The new framework for understanding placental mammal evolution. BioEssays 31:853–864.
Geisler JH, McGowen MR, Yang G and Gatesy J 2011. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evolutionary Biology 11:112.
Margulies EH et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Meredith RW et al. 2011. Impacts of the Cretaceous terrestrial revolution and KPg Extinction on Mammal Diversification. Scence  334(6055):521-524.
Song S, Liu L, Edwards SV and Wu S 2015. Resolving conflict in eutherian mammal phylogeny using phylogenomics and multi species coalescent model. PNAS 109(37)14942-14947.

The first Jurassic feather – SVP abstract 2016

Pittman et al. 2016
describe a new way of looking at fossils, with laser stimulated fluorescence. I can’t show you what attendees saw at SVP as it is awaiting publication, but other examples can be seen here online. This image from Tom Kaye (Fig. 1) was bumped by me with Photoshop to increase contrast and perhaps reveal a wee bit more detail.

Figure 1. Archaeopteryx feather from T. Kaye. Second image is Photoshop contrast bump created here. Pittman et al. laser stimulated fluorescence imagery was shown at SVP and is awaiting publication. 

From the Pittman et al. 2016 abstract
“The single feather initial holotype of Archaeopteryx lithographica is one of the world’s most iconic fossils, but contains a 150 year old mystery. The specimen’s 1862 description by Hermann von Meyer shows that the calamus is 15 mm long and 1 mm wide. However, the calamus is no longer visible on the fossil, and there is no record of when or how it disappeared. The specimen is a rare example of a lone Archaeopteryx feather, giving access to its entire morphology, as opposed to only parts of it in the overlapping feathers of articulated specimens. This makes it an important addition to the anatomical record of Archaeopteryx and basal birds more generally. After 150 years, laser stimulated fluorescence has recovered the calamus as a chemical signature in the matrix and reveals preparation marks where the original surface details have been obliterated. The feather has recently been imaged by others under UV light as well as with X-rays at the Stanford Linear Accelerator Center, with no reports of the existence of the calamus. This demonstrates the capability of laser stimulated fluorescence to visualize important data outside the range of current methodologies. The feather has at different times, been cited as a primary, secondary and covert, and has even been suggested to belong to another taxon. With the new calamus data in hand, the morphology of the feather was examined within the framework of modern feather anatomy. The percentage of calamus length to overall feather length, when plotted against a histogram of 30 phylogenetically and ecologically diverse modern birds, comes out in the middle of the range, placing it in the flight feather regime. The most recent identification of the feather as a primary dorsal covert can be discounted because the rachis is in line with the calamus rather than curving upwind of the calamus centre line. The curvature of the rachis is also too pronounced to function as a primary or tail feather. If the feather is scaled as a secondary in the wing of Archaeopteryx, only five feathers fit the reconstruction along the ulna, rather than the 9-13 that have been estimated for this taxon and the 7-14 that are found in modern birds. These inferences suggest that the isolated feather is fundamentally inconsistent with those of Archaeopteryx and is instead a secondary of another early bird taxon or potentially even a feather of a non-avialan pennaraptoran theropod.”

Kaye’s work with fossil imaging
has revealed many interesting and otherwise invisible traits. Let’s call this one more ‘feather in his cap.’

References
Pittman M, Kaye TG, Schwarz D, Pei R and Xu X 2016. 150 year old Archaeopteryx mystery solved. Abstract from the 2016 meeting of the Society of Vertebrate Paleontology.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125923