Reviewing old and new news from Brazil on the origin of mammals and ictidosaurs

Figure 1. Brasilodon nests with Sinoconodon as a stem mammal.

Figure 1. Here Brasilodon nests with Sinoconodon as a stem mammal (mammaliaformes).

Bonaparte et al. 2003
discovered two taxa close to the origin of mammals, Brasilodon  (Fig. 1) and Brasilitherium (Fig. 2). Originally both were considered stem mammals. In the large reptile tree (LRT, 1025 taxa, subset figure 4) Brasilodon nests with the stem mammal, Sinoconodon. However, Brasilitherium, also from the Late Triassic, nests at the base of the monotremes a clade including Akidolestes, Ornithorhynchus and Kuehneotherium. So it’s not a stem mammal. It’s a mammal. Bonaparte et al. 2003 missed that nesting due to taxon exclusion and a very interesting jaw joint that did not fit a preconceived pattern (Fig. 2 and see below).

Figure 2. Brasilitherium compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus.

Figure 2. Brasilodon compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus.

Bonaparte et al. 2003
nested Brasilodon between Pachygenelus and Morganucodon + Brasilitherium, basically matching the LRT which did not exclude monotremes and Sinoconodon.

The key skeletal trait
defining Mammalia (unless it has changed without my knowledge) has been the disconnection of the post dentary bones from the dentary coincident with the dentary articulating with the squamosal producing a new mammalian jaw joint and the genesis of tiny ear bones.

Note: that’s not happening yet
in Brasilitherium despite its phylogenetic nesting as a basal monotreme. In Brasilitherium the articular, a post dentary bone, still articulates with the quadrate (Fig. 2). So, going by the jaw joint, Brasilitherium is not a mammal. However, going by its phylogenetic nesting in the LRT, it is a mammal.

Figure 4. Therioherpeton nests at the base of the Mammaliaformes with Brasilodon, between Yanaconodon and Sinoconodon, not far from Megazostrodon.

Figure 3. Therioherpeton nests at the base of the Mammaliaformes with Brasilodon, between Yanaconodon and Sinoconodon, not far from Megazostrodon.

We’ve seen something similar occurring
at the origin of mammals, where amphibian-like reptiles (without reptile traits) have not been recognized as amniotes, based on their phylogenetic nesting in the LRT.

And, of course,
traditional workers still consider pterosaurs to be archosaurs based on their antorbital fenestra (by convergence), not their phylogenetic nesting (first documents in Peters 2000) in the LRT which solves earlier taxon exclusion problems by introducing a wider gamut of candidate sister taxa.

Th late appearance of the now convergent mammalian jaw joints
after the phylogenetic origin of mammals helps explain the two sites for ear bones in monotremes (below and medial to the posterior dentary) versus in therians (posterior to the jaw joint).

Tooth count
Basal monotremes have more teeth than any other mammals. Derived monotremes, like the living platypus and echidna, have fewer teeth, with toothless anterior jaws. This is a pattern of tooth gain/tooth loss we’ve seen before in other toothless taxa like Struthiomimus.

Recently, Bonaparte and Crompton 2017
concluded that ictidosaurs (Pachygenelus and kin) originated from more primitive procynosuchids rather than probainognathids. Pachygenelus likewise has a squamosal dentary contact, but it also retains a quadrate/articular contact as a transitional trait. They write: “We suggest a revision to the overwhelmingly accepted view that morganucodontids arose from probainognathid non- mammalian cynodonts (sensu Hopson & Kitching 2001). We suggest two phylogenetic lines, one leading from procynosuchids to ictidosaurs and the other from procynosuchids to epicynodonts and eucynodonts. One line evolves towards the mammalian condition, with a loss of circumorbital bones prefrontal, postfrontal, and postorbital), retention of an interpterygoid vacuity, a slender zygomatic arch, dentary/squamosal contact, and a long snout. The second evolves towards advanced non-mammalian cynodonts and tritylodontids with loss of the interpterygoid vacuity (present in juveniles), formation of a strong ventral crest formed by the pterygoids and parasphenoid, a very deep zygomatic arch, a tall dentary, and a short and wide snout.”

Talk about heretical!
Unfortunately, with the present taxon list, the LRT does not concur with Bonaparte and Crompton 2017, but instead recovers a more conventional lineage (Fig. 4).

Ictidosauria according to Bonaparte and Crompton:
The diagnostic features of Ictidosauria are as follows:

  1. absent postorbital arch, postorbital, and prefrontal;
  2. a slender zygomatic arch with a long jugal and short squamosal;
  3. a dorsoventrally short parietal crest and transversally wide braincase;
  4. interpterygoid vacuity;
  5. ventral contact of the frontal with the orbital process of the palatine;
  6. an unfused lower jaw symphysis;
  7. a well-developed articular process of the dentary contacting the squamosal;
  8. and a petrosal promontorium.
Figure 5. Basal Cynodont/Mammal cladogram focusing on the nesting of Brasilodon and Brasilitherium in the LRT.

Figure 4. Basal Cynodont/Mammal cladogram focusing on the nesting of Brasilodon and Brasilitherium in the LRT.

Therioherpeton (Bonaparte and Barbierena 2001; Fig. 3) also enters the discussion as a stem mammal.

Therioherpetidae according to Bonaparte and Crompton:
share several features with mammaliaforms:

  1. a slender zygomatic arch
  2. squamosal dentary contact
  3. unfuseddental symphysis
  4. petrosal promontorium
  5. transversely narrow postcanines with axially aligned cusps and an incipient cingulum
  6. and a transversely expanded brain case
  7. Therioherpetidae lack procumbent first lower incisors occluding between the first upper incisors
  8. lack an edentulous tip of the premaxilla
  9. and lack transversely widened postcanines

According to the Bonaparte team
Three distinct groups have been included in Mammaliformes.

  1. Morganucodon, Megazostrodon and Sinoconodon;
  2. Docodonta
  3. Haramiyids such as Haramiyavia

They report,
“Brasilitherium is closer to the first group than the more derived second and third groups. Brasilitherium is almost identical to Morganucodon, except that the latter has a mammalian tooth replacement pattern (single replacement of the incisors, canines, and premolars, and no replacement of the molars), double rooted molars, and the orbital flange of the palatine forms a medial wall to the orbit (Crompton et al. 2017).”

“Several features present in Procynosuchus are absent in probainognathids (sensu Hopson & Kitching 2001), but present in Ictidosauria.

  1. Interpterygoid vacuities (present only in juvenile probainognathids);
  2. a slender zygomatic arch;
  3. incisiforms present at the junction of premaxilla and maxilla;
  4. a low and elongated dentary;
  5. and an unfused lower jaw symphysis.”

Hopefully it will be seen as a credit to the LRT 
that it nested each new taxon about where the three Bonaparte teams nested them (sans the unusual Procynosuchus hypothesis), only refined a bit with the addition of several overlooked monotreme taxa, several of which have similar (to Procynosuchus) low, long skulls and rather low-slung post-crania.

Bonaparte JF and Barbierena MC 2001. On two advanced carnivorous cynodonts from the Late Triassic of Southern Brazil. Bulletin of the Museum of Comparative Zoology 156(1):59–80.
Bonaparte JF, Martinelli AG, Schultz CL and Rubert R 2003. The sister group of mammals: small cynodonts from the Late Triassic of Southern Brazil. Revista Brasileira de Paleontologia 5:5-27.
Bonaparte JF and Crompton AW 2017. Origin and relationships of the Ictidosauria to non-mammalian cynodonts and mammals. Historical Biology. https://doi.


Is Phascolotherium a basal mammal? Perhaps not…

Yesterday we looked at the origin of mammals and noted the Rowe 1988 considered the fossil mandible Phascolotherium bucklandi (Middle Jurassic; Owen 1838; Fig. 1) one of the earliest known mammals. Unfortunately, the mandible specimen does not have enough traits to nest Phascolotherium in the large reptile tree (LRT, 1011 taxa) with complete resolution.

that doesn’t stop one from visually comparing Phascolotherium to more complete taxa.

Figure 1. Phacolotherium compared to the tritylodontid Jeholodens.

Figure 1. Phacolotherium compared to the tritylodontid Jeholodens. The smaller Jeholodens image is to scale with the much larger Phacolotherium specimen.

There’s a pretty good match for Phascolotherium
with Jeholodens  (Ji et al. 1999); non-mammalian cynodont/tritylodontid/mammaliaform known from the Middle Cretaceous. The Jeholodens mandible is smaller than Phascolotherium, It has an unerupted 4th molar, which would indicate immaturity if it was a mammal. Only mammals do not replace molars.

Of Jeholodens
Ji et al. 1999 reported, “The postcranial skeleton of this new triconodont shows a mosaic of characters, including a primitive pelvic girdle and hindlimb but a very derived pectoral girdle that is closely comparable to those of derived therians. Given the basal position of this taxon in mammalian phylogeny, its derived pectoral girdle indicates that homoplasies (similarities resulting from independent evolution among unrelated lineages) are as common in the postcranial skeleton as they are in the skull and dentition in the evolution of Mesozoic mammals.”

There’s a postscript
Take another look at the mandible of Jeholodens (Fig. 1). Note the giant incisor 1 and the robust jaw articulation. Where else do we see this combination in small mammals? In Multituberculata and Haramiyidae, but both nest with rodents, plesiadapids and carpolesteids in the LRT. Traditional cladograms nest Multituberculata and Haramiyidae either before Mammalia or between monotremes and therians as very basal mammals. I have long wondered, if this was so, which basal pre-mammals or mammals look most like multituberculates and might therefore be most closely related? Could it be Jeholodens? So it was time for a test. Shifting the multituberculates to Jeholodens currently adds 34 steps to the LRT. Let’s see what happens when multis are re-scored with prejudice toward Jeholodens

So what happened?
The multis and haramiyids did not shift. The tree topology did not change. Apparently any resemblance between Jeholodens and these two clades must have been by convergence. Or the amount of convergence is overtaking the true relationship. Since everything in science is provisional we’ll keep testing.

Ji Q, Luo Z and Ji S 1999. A Chinese triconodont mammal and mosaic evolution of the mammalian skeleton. Nature 398:326-330. online.
Owen R 1838
. On the jaws of the Thylacotherium prevostii (Valenciennes) from Stonesfield. Proceedings of the Geological Society of London 3, 5–9.

The Origin of Mammals: Rowe 1988

Rowe 1988
provided a list of skeletal traits found in mammals not found in their proximal outgroups. Here they are broken down into digestible categories. Noteworthy are the many traits associated with improvements and refinements to hearing and smelling. Noticeable by their absence are any dental traits.


  1. Premaxilla internasal process absent (external nares confluent
  2. Ethmoid and maxillary turbinals ossified
  3. Internasal septum ossified
  4. Ossified quadratojugal absent
  5. Sclerotic ossicle absent


  1. Ectotympanic horizontal (former reflected lamina rotates from vertical
  2. Squamosal suspensorial notches absent – sites of former connections to quadrate and quadratojugal
  3. Cribiform plate (ethmoid ossifies below olfactory bulbs)
  4. Pterygoid transverse process vestigial (muscles now fill the gap)
  5. Tegmen tympani (thin plate of bone spread over the cochlear capsule forming a new side wall for the cranium)
  6. Hyoid arch evolves to become petrosal bridge


  1. Occipital condyles expanded upwards and laterally, far apart from one another
  2. Hindbrain greatly expanded overlies fenestrae vestibuli
  3. Paroccipital process directed ventrally (no longer sloping ventrolaterally)
  4. Pneumatic mastoid process (no longer solid)
  5. Styloid process – no longer a separate bone, the stylohyal fuses the otic capsule, joining the paroccipital process
  6. Craniomandibular joint positioned anterior to fenestra vestibuli (hearing organ opening)


  1. Craniomandibular joint formed only by squamosal and dentary
  2. Meckelian sulcus (trough) enclosed – when open it held the post dentary elements
  3. Coronoid bone vestigial or absent – the dentary takes over
  4. Splenial vestigial or absent
  5. Articular, prearticular, surangular and angular suspended from the skull (as tiny ear bones and ectotympanic bulla respectively)


  1. Proatlas not ossified
  2. Atlas intercentrum and neural arches fused to form one ring-like bone, vertebra #1.
  3. Atlas rib absent (actually fused to the atlas)
  4. Axis prezygopophyses absent
  5. Postaxial cervical ribs fused to vertebrae


  1. Styloid processes on dstial ends of radius, tibia and fibula
  2. Patella present along with patellar facet on femur
  3. Entocuneiform–Hallucial (distal tarsal 1 and m1.1) articulation saddle-shaped permitting greater mobility
  4. Secondary ossifications on long bones and girdles – ossified joints
  5. Flexor sesamoids

Under this guidance
and prior to the use of software in cladisitic analysis Rowe 1988 indicated that
“Morganucodontidae, Kuehneotherium, Dinnetherium, Sinoconodon and Haramiyidae can no longer be considered mammals.” In Rowe’s tree Multituberculata nest between monotremes and metatherians. (Contra Novacek 1997, who nested that clade outside the Mammalia.)

The LRT does not agree with parts of this topology
In the LRT haramiyidans nest with multituberculates, both with rodents. There are no pre-rodent, pre-placental or pre-mammal taxa with such derived traits. Attempts to put a cynodont-like middle ear on the multituberculate Megaconus are largely the product of hope, bias and imagination, not data.

Living monotremes have tiny ear bones below and internal to the mandible, distinct from placentals and marsupials that have tiny ear bones just posterior the jaw joint. This indicates that monotremes had a separate, but convergent (parallel) evolutionary history with regard to the tiny ear bones. In the LRT. Kuehneotherium nests at the base of the monotremes and thus within Mammalia, at its base. Based on the very derived character of all monotremes, including Kuehneotherium, the very first mammals had a much earlier origin.

According to Rowe 1988
Phascolotheriium bucklandi
(Middle Jurassic, Owen 1838, Clemens et al. 1977) is the oldest known mammal.  Amphitherium (de Blainville 1838) is from the same strata. Both were discovered within the first few decades of modern British paleontology. Unfortunately there are not enough traits in Phascolotherium to nest it in the LRT without massive loss of resolution.

Butler P M Clemens, W. A. (2001). Dental Morphology of the Jurassic Holotherian Mammal Amphitherium, with a Discussion of the Evolution of Mammalian Post-Canine Dental Formulae. Palaeontology. 44 (1): 1–20.
Novacek MJ 1997. Mammalian evolution: An early record bristling with evidence. Current Biology 7(8):pR489–R491. DOI: 
Owen R 1838.
On the jaws of the Thylacotherium prevostii (Valenciennes) from Stonesfield. Proceedings of the Geological Society of London 3, 5–9.
Rowe T 1988.
Definition, diagnosis, and origin of Mammalia. Journal of Vertebrate Paleontology 8(3):241-264.

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.

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.

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)


  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.

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


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 and used with permission.

Figure 3. Entire skeleton of Monodelphis from 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 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.

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.

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.