Vintana and the vain search for the clades Allotheria and Gondwanatheria

Figure 1. Vintana as originally illustrated. I added colors to certain bones. Note the high angle of the ventral maxilla and the deep premaxilla. Lateral view reduced to scale with other views.

Figure 1. Vintana as originally illustrated. I added colors to certain bones. Note the high angle of the ventral maxilla and the deep premaxilla. Lateral view reduced to scale with other views.

Earlier we looked at Vintana (Fig. 1, Krause et al. 2014a, b). To Krause et al. Vintana represented the first specimen in the clades Allotheria and Gondwanatheria to be known from more than teeth and minimal skull material.

To Krause et al. 
Allotheria included Multituberculata and nested between the clade Eutriconodonta (including Repenomamus and Jeholodens) and the clade Trechnotheria (including the spalacotheres Maotherium and Akidolestes) and Cronopio, Henkelotherium, Juramaia, Eomaia, Eutheria and Metatheria.

Taxon exclusion issues
The large reptile tree (LRT, 1005 taxa) did not recover the above clades or relationships. Alotheria does not appear in the LRT.

  1. Multituberculata, Henkelotherium and Maotherium nest within Glires (rats and rabbits and kin) in the LRT.
  2. Repenomamus and Jeholodens nest within the pre-mammalian trityllodontid cynodonts in the LRT.
  3. Akidolestes nests within basal Mammalia, close to Ornithorhynchus in the LRT.
  4. Cronopio and Juramaia nest within basal Mammalia between Megazostrodon and Didelphis in the LRT.
  5. Eomaia nests at the base of the Metatheria in the LRT.
  6. Vintana nests with Interatherium among the derived Metatheria (marsupials), with wombats, like Vombatus and Toxodon in the LRT.

Despite a paper in Nature
and a memoir of 222 pages in the Journal of Vertebrate Paleontology; despite CT scans and firsthand examination with electron microscopes; despite being examined and described by many of the biggest name and heavy hitters in paleontology… Krause et al. never understood that Vintana was just a derived wombat, evidently due to taxon exclusion problems.

Figure 3. Interatherium does not nest with notoungulates or other purported interotheres. Rather cat-sized Interatherium nests with wombats, between Vombatus and the giant Toxodon.

Figure 2. Interatherium does not nest with notoungulates or other purported interotheres. Rather cat-sized Interatherium nests with wombats,with Vintana,  between Vombatus and the giant Toxodon

The large reptile tree now includes
1005 taxa, all candidates for sisterhood with every added taxon. Despite the large gamut of 74 taxa employed by Krause et al. they did not include the best candidates for Vintana sisterhood. Perhaps the fault lies in the reliance of prior studies and paradigms. Perhaps the fault lies in the over reliance by Krause et al. and other mammal workers, on dental traits. Perhaps the fault lies in the absence of pertinent sisters to the above-named taxa, including Interatheriium for Vintana.

In any case
Vintana does not stand alone as the only taxon in its clade represented by skull material. Based on its sisterhood with Interatherium, we have  pretty good idea what its mandibles and post-crania looked like. Yes, Vintana is weird. But Interatherium is also weird in the same way, just not as weird.

The LRT has dismantled and invalidated
several other clades, too, Ornithodira and Parareptilia among them.

References
Krause DW, Hoffmann S, Wible JR, Kirk EC, and several other authors 2014a. First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism. Nature. online. doi:10.1038/nature13922. ISSN 1476-4687.
Krause DW et al. 2014b. Vintana sertichi (Mammalia, Gondwanatheria) from the Late Cretaceous of Madagascar. Journal of Vertebrate Paleontology Memoir 14. 222pp.

wiki/Vintana
pterosaur heresies – Vintana

Yanoconodon: Proximal sister to the Mammalia

This post was composed several weeks ago.
After all the intervening excitement I’m glad to bring Yanoconodon to your attention.

Yanoconodon alllini (Luo, Chen, Li and Chen 2007; Early Cretaceous, 122 mya; 13 cm in length; Figs. 1, 2) is known from a nearly complete and articulated crushed fossil. It is traditionally considered a eutriconodont, a clade that traditionally includes Spinoletes, Repenomamus, GobiconodonLiaoconodonJeholodens and Volaticotherium. Unfortunately that clade is paraphyletic in the large reptile tree (LRT). Here Yanoconodon was derived from a sister to Pachygenelus and nested between that clade and the Mammalia (Fig. 3).

Yanoconodon had a semi-sprawling posture
and a a long, robust torso with an unusually thick lumbar vertebrae provided with very short ribs. The limbs were short. The canines were quite narrow. The posterior jaw bones were still attached to the jaw. They had not yet become completely reduced to middle ear bones and completely separated from the jaw bones. So, by definition and cladogram (Fig. 3), Yanoconodon was not a true mammal. Wikipedia disagrees as that author reports, “Despite this feature Yanoconodon is a true mammal.”

See below for some thoughts on that.

FIgure 1. Yanaconodon nests as the proximal outgroup to the Mammalia in the LRT.

FIgure 1. Yanoconodon nests as the proximal outgroup to the Mammalia in the LRT. Even so it has several autapomorphies (differences from the actual  hypothetical ancestor.)

from the Luo, Chen and Chen abstract
“Detachment of the three tiny middle ear bones from the reptilian mandible is an important innovation of modern mammals. Here we describe a Mesozoic eutriconodont nested within crown mammals (1) that clearly illustrates this transition: the middle ear bones are connected to the mandible via an ossified Meckel’s cartilage. The connected ear and jaw structure is similar to the embryonic pattern in modern monotremes (egg-laying mammals) and placental mammals, but is a paedomorphic feature retained in the adult, unlike in monotreme and placental adults. This suggests that reversal to (or retention of) this premammalian ancestral condition is correlated with different developmental timing (heterochrony) in eutriconodonts. (2) This new eutriconodont adds to the evidence of homoplasy of vertebral characters in the thoraco-lumbar transition and unfused lumbar ribs among early mammals. (3) This is similar to the effect of homeobox gene patterning of vertebrae in modern mammals, making it plausible to extrapolate the effects of Hox gene patterning to account for homoplastic evolution of vertebral characters in early mammals.” (4)

Notes

  1. The LRT nests Yanoconodon just outside the crown mammals. Not sure why the authors say this, given what they report about the posterior jaw bones as posterior jaw bones.
  2. Curious that the retention of “this pre-mammalian ancestral condition” does not indicate to the authors that Yanoconodon is indeed a pre-mammal.
  3. Yanoconodon does not nest as an early mammal in the LRT.
  4. …or…not, if Yanoconodon is indeed a non-mammalian trithelodont. Other non-mammalian cynodonts lived alongside Jurassic mammals. Only one purported eutriconodont listed above is a mammal, Volaticotherium. It nests as a basal placental. Triconodon is a mammal, too, a monotreme known from just a dentary and teeth.
Figure 2. From Luo et al. the posterior jaw bones of Yanoconodon. These are not middle ear bones, so Yanoconodon is not a mammal.

Figure 2. From Luo et al. the posterior jaw bones of Yanoconodon. These are not middle ear bones, so Yanoconodon is not a mammal. The malleus is the articular. The incus is quadrate.

Yanoconodon is a great transitional fossil.
You can call it a mammal, if you want to slightly stretch the current definition. You can call it a mammal if you want to describe it as the last common ancestor of all living mammals.  But as soon as a better transitional candidate comes along, it will be demoted.

Figure 3. Basal mammals begin with Ornithorynchus, the most primitive living mammal. Yanoconodon nests just outside this clade.

Figure 3. Basal mammals begin with Ornithorynchus, the most primitive living mammal. Yanoconodon nests just outside this clade.

References
Luo Z, Chen P, Li G, and Chen M 2007. A new eutriconodont mammal and evolutionary development in early mammals. Nature 446:15. online Nature

wiki/Yanoconodon

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 1. Carnivora subset of the LRT with Monodelphis, a basal placental, as the outgroup, not Manis the pangolin.

Figure 1. Carnivora subset of the LRT with Monodelphis, a basal placental, as the outgroup, not Manis the pangolin.

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

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 4. Entire skeleton of Monodelphis from Digimorph.org and used with permission.

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, ElephasLoxodonta, 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.

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.

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.

Docodon and molar count

The genus Docodon (Marsh 1881; Late Jurassic, 170 mya; Fig. 1) is represented by a jaw with several more molars than typical (Fig. 1). Hard to tell the premolars from the molars in lateral view. See the dorsal view for the distinct difference. Even so, the count may be off, because molars are not molars based on shape, but on the fact that they appear once and are not replaced during growth. I cannot tell, note have I found references that say where the division is in Docodon.

Figure 1. The holotype of Docodon has 4 incisors, 4 premolars and a whopping 7 molars.

Figure 1. The holotype of Docodon has 4 incisors, 4 premolars and a whopping 7 molars. diplocynodon has 8 according to Osborn, who confirms the 7 in Docodon.

More than four molars in a mammal jaw is relatively rare.
But not rare in ancestral monotremes. Among tested taxa  Amphitherium, Kuehneotherium and Akidolestes have 6.

Figure 1. The addition of teeth in Kuehneosaurus and Akidolestes led to the loss of teeth in Ornithorhynchus.

Figure 1. The addition of teeth in Kuehneosaurus and Akidolestes led to the loss of teeth in Ornithorhynchus.

There is also “a rule” that says
only one canine appears, but the other teeth can vary greatly in number. I’m wondering if that is true. Sometimes there will be a small, simple tooth arising between the canine and the double-rooted premolars. Is that a tiny canine? or a tiny premolar? Maybe someone out there has not only the answer, but the reason why.

And yes,
I’m aware of the convention that numbers premolars 1-4. But the anterior one, is almost always the smallest, as if it just arrived.

References
Marsh OC 1881. Notice of new Jurassic mammals. American Journal of Science. (3) xxi: 511-513.

wiki/Docodon

 

The Eutriconodonta is also paraphyletic in the LRT

Triconodon, Docodon, and Kuehneotherium are known form dentary bones with most of their teeth in place. Generally I avoid adding such partial specimens to the large reptile tree (LRT-updated at 848 taxa) because so few scores are generated for them with the current character list that they lead to loss of resolution at their nodes…

But curiosity won out
when wondering about members of the putative clade Eutriconodonta (Kermack et al. 1973), a clade that ostensibly replaces the paraphyletic Triconodonta. Some of these mandible-only taxa I added to the tree only to delete them later, just to see where they nested (often at the base of the Monotremata, as one would guess given their Mid-to Late Jurassic ages).

According to Wikipedia
“The Eutriconodonta  is a [presumeably monophyletic] order of mammals” broadly, though not exclusively characterized by molar teeth with three main cusps on a crown that were arranged in a row.  “Eutriconodonts retained classical mammalian synapomorphies like epipubic bonesvenomous spurs and sprawling limbs. Eutriconodonts had a modern ear anatomy, the main difference from therians being that the ear ossicles were still somewhat connected to the jaw via the Meckel’s cartilage.

“Phylogenetic studies conducted by Zheng et al. (2013), Zhou et al. (2013) and Yuan et al. (2013) recovered monophyletic Eutriconodonta containing triconodontids, gobiconodontids, Amphilestes, Jeholodens and Yanoconodon. The exact phylogenetic placement of eutriconodonts within Mammaliaformes is uncertain.”

“Traditionally seen as the classical Mesozoic small mammalian insectivores, discoveries over the years have ironically shown them to be among the best examples of the diversity of mammals in this time period, including a vast variety of bauplans, ecological niches and locomotion methods.”

Traditional Eutriconodont taxa (see Martin et al. 2015) presently included in the LRT nest in a variety of clades:

  1. Gobiconodon – pre-mammal tritylodontid
  2. Repenomamus – pre-mammal tritylodontid
  3. Spinolestespre-mammal tritylodontid
  4. Jeholodens – pre-mammal tritylodontid
  5. Volaticotherium basal placental 
  6. Triconodonbasal monotreme
  7. Trioracodon – basal monotreme
  8. Yanoconodonpre-mammal (Fig. 1).

We’ve seen this sort of splitting
of traditionally established clades based chiefly on tooth traits before with the Docodonta (Fig. 1). As in molecule trees, tooth trees are not replicated in the LRT, which recovers a distinctly new tree topology without the odd logic jumps that traditional clades, like Afrotheria, produce.

Figure1. Repeat of an early subset of the LRT, this time highlighting putative eutriconodonts and where they nest. No wonder they are described as a diverse clade!

Figure1. Repeat of an early subset of the LRT, this time highlighting putative eutriconodonts and where they nest. No wonder they are described as a diverse clade!

For the most part
eutriconodonts nest more or less together very close to the base of the Mammalia, whether in or out. Those slender posterior jaw bones are not typically preserved, but the long groove in which they are attached is typically preserved. Caution must be exercised, as fully mammalian taxa like Monodelphis, can also preserve a remnant of this groove despite the complete evolution of the post-dentary bones into tiny ear bones.

Figure 4. Mondelphis domestics with its posteromedial jaw groove highlighted in red. The ear bones are tiny and enclosed within the auditory bulla beneath the cranium.

Figure 2. Mondelphis domestics with its posteromedial jaw groove highlighted in red. The ear bones are tiny and enclosed within the auditory bulla beneath the cranium.

So.. about those venomous ankle spurs…
Ornithorhynchus, the platypus, has them and likely so do its sisters. The authors of the Volaticotherium paper make no mention of either venom nor spur and score it as a “?”. The Yanoconodon tarsi are a challenge to reconstruct based on their preservation. The authors and yours truly note no spur-like bones present.

A new evolution website has launched
Check out www.TimeTree.org for a tremendous amount of phylogenetic information. For instance, one can input two well-known taxa, like Gallus and Homo, and the tree will determine the estimated date of their last common ancestor, in this case Vaughnictis (which is a taxon not in their current database).

References
Editors: Carrano MT et al. 2006. Amniote Paleobiology: Perspectives on the Evolution of Mammals, Birds and Reptiles. University of Chicago Press.  online here.
Kermack KA, Mussett F, Rigney HW 1973. The lower jaw of Morganucodon. Zoological Journal of the Linnean Society.53 (2): 87–175.
Martin T et al. 2015. A Cretaceous eutriconodont and integument evolution of early mammals. Nature 526:380-384. online.

wiki/Eutriconodonta

Imagining the unknown: the skulls of Amphitherium and Docodon

Often enough
tiiny Jurassic synapsids, like Amphitherium prevosti  (von Meyer 1832; Middle Jurassic, 170 mya) and Docodon victor (Marsh 1881; Late Jurassic, 2 cm skull length), are known only from mandibles with teeth (Fig. 1).

We can guess what the skull looks like
because the molars occlude and the rest of the teeth interlock, slide past one another or meet at or near their tips. Plus we have clues from sister taxa that set parameters for possibilities in a method known as phylogenetic bracketing. In such cases some scores are less risky to guess, like the number of molars. Others are more risky, like the presence of caniniform canines.

Figure 1. Amphitherium and Docodon with skulls imagined.

Figure 1. Amphitherium and Docodon with skulls imagined. The large number of molars nests both these taxa with Monotremata.

References|
Marsh OC 1881. Notice of new Jurassic mammals: American Journal of Science, ser. 3, 21: p. 511-513.
Meyer H von 1832. Palaeologica, zur Geschichte der Erde und ihrer Geschöpfe. Schmerber, Frankfurt a/M, xi, 560 pp.