Nomenclature proposals for hypothetical relationships within the Mammalia

Updated August 17, 2016 with corrections to some of the nomenclature and graphics .Thanks to M. Mortimer for some valuable suggestions.

Now that several dozen mammal
and stem-mammal taxa have been added to the large reptile tree, and it recovered a distinct topology (Fig. 1), it is not only appropriate but a duty to propose new names for novel clades. Of course, we’ll retain all still-valid clade names.

Introducing new clade names also happened earlier
with the introduction of the clade name, Tritosauria, here online, and in a peer-reviewed academic publication (Peters 2000), when I introduced the Fenestrasauria for Cosesaurus through Pterosauria, long with other clade names for fenestrasaur outgroups, all recovered in phylogenetic analysis.

The new mammal tree topology
(Fig. 1) flips and mixes up the current paradigm (Kriegs et al. 2006) in which (untenably) carnivores are sisters to ungulates and ungulates are sisters to bats and elephants nest between marsupials and primates. None of that makes sense. Where are the gradual accumulations of derived traits? Evidently that was not important to Kriegs et al.  As a remedy we now have this cladogram:

Figure 1. New mammal family tree, a subset of the large reptile tree. Here one can trace a gradual accumulation of derived traits, something the traditional paradigm fails to do. Here the clade names in black refer to small discrete clades in the gray column at right. The red clade names refer to taxa identified by color bars

Figure 1. New mammal family tree, a subset of the large reptile tree. Here one can trace a gradual accumulation of derived traits, something the traditional paradigm fails to do. Here the clade names in black refer to small discrete clades in the gray column at right. The red clade names refer to taxa identified by color bars. Liaoconodon now nests with Maotherium, Repenomamus and Gobiconodon (see updated cladogram in figure 2)

Here a gradual accumulation of derived traits can be demonstrated.
All basal taxa are tiny furry arboreal forms that look like each other and later evolve in various ways. Both the major (red) and minor (black) clades are discussed below.

The Red List (Fig. 1)
Each of these major monophyletic clades extend to the ungulates.

A. Kynodontia – Therapsida sans Anomodontia; Hipposaurus, Hippopotamus, their last common ancestor and all  descendants; named for the large canine found in many and most basal clade members

B. Cynodontia – Owen 1861 named Cynodontia, which he assigned to Anomodontia as a family. That is not valid, but the name is retained and in common use. Here, confirming Ruta et al. 2013, the clade is defined as: Procynosuchus, Hippopotamus their last common ancestor and all escendants.

C. Probainognathia – confirming Ruta et al. 2013, the clade includes Probainognatbus and the chiniquodontids and is defined as Probainognathus, Hippopotamus their last common ancestor and all descendants.

D. Trithelodontia – Broom 1912 named this clade, but here it also includes mammals. The clade is defined as Pachygenelus, Hippopotamus their last common ancestor and all descendants.

E. Mammalia – this goes back to Linneaus 1758; provisionally this clade is defined as Sinoconodon, Hippopotamus their last common ancestor and all descendants.

F. Theria – named by Parker and Haswell 1897, include all live-bearing mammals (sans Prototheria); Juramaia has been reported (Luo et al. 2010) as the earliest known therian, but it is not possible to know if it laid eggs or not. Provisionally this clade is defined as Juramaia, Hippopotamus, their last common ancestor and all descendants.

G. Panmetatheria – includes Metatheria (Huxley 1880, taxa more closely related to marsupials than to placentals) + Eutheria. Among tested taxa, Didelphis and the marsupials are also basal therians, traditionally known as metatherians.

H. Eutheria – include all placental mammals (sans Metatheria). The putative marsupial, Monodelphis, lacks a pouch. Eomaia has been reported (Ji et al. 2002) as the earliest known eutherian. Provisionally this clade is redefined as Monodelphis, Hippopotamus, their last common ancestor and all descendants. Basal taxa appear to have been small and arboreal.

I. Pancarnivora – Here the basalmost placental split is between the clade Carnivora and Eomaia. Provisionally this clade is defined as Vincelestes, Hippopotamus, their last common ancestor and all descendants.

J. Panprimates – The next split produced Ptilocercus, Primates, Demoptera, Chiroptera and Pholiodota. Provisionally this clade is defined as Ptilocercus, Hippopotamus, their last common ancestor and all descendants.

K. Panglires – The next split produced rabbit and rodent-like taxa with reduced canines and often enlarged incisors. Provisonally this clade is defined as Asioryctes, Hippopotamus, their last common ancestor and all descendants.

L. Pantenreccetacea – The next split produced long-snouted tenrecs and their sisters the Cetacea (whales). Provisionally this clade is defined as Leptictis, Hippopotamustheir last common ancestor and all descendants.

M. Pancondylarthra – The next split produced the larger basal herbivores, all lacking claws. Provisionally this clade is defined as Onychodectes, Hippopotamustheir last common ancestor and all descendants.

N. Panxenarthra – The next split produced the odd xenarthrans. Provisionally this clade is defined as Orycteropus, Hippopotamustheir last common ancestor and all descendants.

O. Panungulata – (not Paenungulata) The next split produced elephants, sirenians and hyraxes. Provisionally this clade is defined as Elephas, Procaviatheir last common ancestor and all descendants.

P. Ungulata – This is a traditional clade (Linneaus 1766), but now includes only odd-toed and even-toed ungulates, not aardvarks, hyraxes, sirenians, elephants and/or whales. Provisionally this clade is defined as Tapir, Hippopotamustheir last common ancestor and all descendants.

Q. Phenacodonta – The final split produced Uintatherium and Arsinoitherium on one branch, Hippopotamus and Mesonyx on the other branch. Provisionally this clade is defined as Phenacodus, Hippopotamustheir last common ancestor and all descendants.

The Black List (Fig. 1)
These are the smaller monophyletic clades that branch off sequentially from the main line of descent that ultimately leads to ungulates. Single node taxa are not listed here.

  1. Chiniquodontidae – is represented here by Chiniquodon, Probainognathus and Castorocauda.
  2. Tritheledontidae– includes Pachygenelus, Repenomamus and the Tritylodontidae
  3. Monotremata – includes Sinoconodon and Ornithorhynchus.
  4. Morganucondonta – includes Megazostrodon and tiny Hadrocodium.
  5. Metatheria – includes the marsupials, of course, but not the traditional marsupials, Didelphis or Monodelphis.
  6. Carnivora – includes the larger meat-eating placentals with a carnassial tooth, like Canis and Phoca.
  7. Ptilocercia – includes the smaller omnivorous fanged placentals, like Pteropus and Proconsul, but also the termite-eater, Manis. This is a new clade composed of primates, bats, flying lemurs and pangolins.
  8. Asioryctitheria – named by Novacek et al. 1997, but here includes the smaller omnivorous fangless placentals, like Rattus and Plesiadapis.
  9. Tenreccetacea – includes the long-snouted omnivorous fangless placentals, like Leptictis and now whales, with stem-whale Maiacetus retaining limbs.
  10. Condylarthra – includes large herbivores, like
  11. Xenarthra – a traditional clade includes the anteaters, sloths (Bradypus), armadillos (Dasypus) and now aardvarks (Orycteropus), but not pangolins.
  12. Paenungulata – a traditional clade with Elephas, Dusisiren and Procavia, but no longer Paleoparadoxia and Arsinoitherium, which nest as basal ungulates.
  13. Perissodactylia – a tradional clade of odd-toed ungulates, including Tapirus and Chalicotherium.
  14. Artiodactylia – a traditional clade of even-toed ungulates, including Giraffa and Micromeryx.
  15. Phenacodontidae – Cope 1881 named this clade here expanded to include Uintatherium and Arsinoitherium.
  16. Mesonychidae – Cope 1880 named this clade, but here is redefined by Mesonyx, Hippopotamus, their last common ancestor and all descendants.
Figure 1. Subset of the LRT focusing on the Kynodontia and Mammalia. Non-eutherian taxa in red were tested in the LRT but not included because they reduce resolution. Eutherian taxa in red include a basal pangolin and derived xenarthran, clades that extend beyond the bottom of this graphic. The pink clade proximal to mammals was considered mammalian by Lautenschlager et al. due to a convergent mammalian-type jaw joint.

Figure 1. Subset of the LRT focusing on the Kynodontia and Mammalia. Non-eutherian taxa in red were tested in the LRT but not included because they reduce resolution. Eutherian taxa in red include a basal pangolin and derived xenarthran, clades that extend beyond the bottom of this graphic. The pink clade proximal to mammals was considered mammalian by Lautenschlager et al. due to a convergent mammalian-type jaw joint.

Of course this means
that the following traditional and molecule-based clades (Kriegs et al. 2006) have lost their utility due to paraphyly. See if these clades make sense to you. They were not recovered in the LRT.

  1. Atlantogenata – Afrotheria + Xenarthra
  2. Afrotheria – (from Africa): golden moles, elephant shrews, tenrecs, aardvarks, hyraxes, elephants, and extinct forms (not from Africa) sea cows (sirenians)
  3. Boreoeutheria – ungulates, carnivores, primates, rodents, rabbits, tree shrews, flying lemurs
  4. Euarchontoglires – primates, rodents, rabbits, tree shrews, flying lemurs
  5. Laurasiatheria – shrews, pangolins, bats, whales, carnivorans, odd- and even-toed ungulates.
  6. Scrotifera – same as Laurasiatheria sans shrews.
  7. Cetartiodactyla – whales and even-toed ungulates
  8. Ferae – carnivores and pangolins

Earlier studies by McKenna and Bell 1997
listed Xenarthra as the basalmost placental taxon, but they seem a little too derived to show up so early (but then, so are extant monotremes).

Recent restudy 
re-nested Haldanodon (Kühne and Krusat 1972) between Probainognathus and Liaoconodon (Fig. 1). These taxa are basal to Pachygenelus and the Tritylodontia and cannot be considered mammaliaforms, unless Pachygenelus and the Tritylodontia are also considered mammaliaforms. Read more about Haldanodon and the Docodonta here.

I realize that online publication without peer-review
is not going to be accepted, but this hypothesis of interrelationships has to start somewhere. Then again, even with peer-review, after 16 years, Peters 2000 is still not accepted, tested or debated, except for this one totally botched and biased attempt that landed its junior author a PhD.

References
Broom R 1912. On a new type of cynodont from the Stormberg. Annals of the South African Museum. 7: 334–336.
Cope ED 1880. On the genera of the Creodonta. Proceedings of the American Philosophical Society. 19: 76–82.
Ji et al 2002. The earliest known eutherian mammal, Nature 416:816-822.
Kriegs JO, Churakov G, Kiefmann m, Jordan U, Brosius J and Schmitz J 2006. Retroposed Elements as Archives for the Evolutionary History of Placental Mammals. PLoS Biology. 4 (4): e91. doi:10.1371/journal.pbio.0040091. PMC 1395351free to read. PMID 16515367.
Kühne and Krusat 1972. Legalisierung des taxon Haldonodon (Mammalia, Docodonta). Neues Jahrbuch für Geologie, Paläontologie and Mineralogie, Monatshefte 5: 300-302.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Linneaus C 1766. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio duodecima, reformata. Holmiae. (Laurentii Salvii).: 1-532.
Luo Z-X, Yuan C-X, Men Q-J and JiQ 2011.A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature 476: 442–445. doi:10.1038/nature10291.
McKenna MC, Bell SG 1997. Classification of Mammals above the Species Level. New York: Columbia University Press.
Novacek MJ, Rougier GW, Wible JR, McKenna MC, Dashzeveg D and Horovitz I 1997. Epipubic bones in eutherian mammals from the Late Cretaceous of Mongolia. Nature 389:483-486
Owen R 1861. Palaeontology, or a systematic summary of extinct animals and their geological relations. 2nd ed. Adam and Charles Black, Edinburgh, xvi + 463 p.
Peters D 2000. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.

wiki/Mammalia
wiki/Mammaliaformes

Several traits indicate pterosaurs were aerobic and endothermic (warm-blooded)

Pterosaurs, by all accounts, were not your ordinary saurians.
Pterosaurs arose from a previously unreported clade of extinct lepidosaurs, the Tritosauria, not from any living squamates. They could fly and some were fantastically adorned with crests and soft tissues that enabled flight. Moreover, many, if not all, had hair/fibers/fur. The origin of these fibers appears to be in non-volant Middle Triassic fenestrasaurs at the level of Sharovipteryx and Cosesaurus, long before dinosaurs and birds developed protofeathers.

Living lizards are ectothermic (cold-blooded). Pterosaurs are widely considered to be endothermic (warm-blooded) due to their fur-covering, but that’s not the complete story. There’s more:

Jeholopterus2013-588

Figure 1. Jeholopterus in lateral view. Note the extreme length of the dermal fibers, unmatched by other pterosaurs, likely to keep biting insects away from its sensitive skin as it exploited and made wounds on dinosaurs.

1. Ptero fur — aka: pycnofibers, covered pterosaur bodies according to several well-preserved fossils of small pterosaurs. Most of our evidence for a pelage comes from small German and Chinese pterosaurs, but at least some specimens of Zhejiangopterus, a large azhdarchid, had ptero-fur. Preservation of hair apparently depends on subtle differences in substrate geochemistry. Like feathers, ptero-fur could have had uses other than trapping body heat, like keeping flying insects (mosquitoes and flies) from biting sensitive skin, as in Jeholopterus (Fig. 1) and, or course, could be considered decoration or camouflage if striped, spotted or colored.

2. Tiny adult size and even tinier hatchlings — We’ve seen in phylogenetic analysis that tiny pterosaurs succeeded fading larger clades and preceded expanding larger clades. Thus reducing adult size was a survival mechanism for the gene pool. Since moisture loss and heat loss would have been more stressful for tiny pterosaurs and especially the hatchlings of tiny pterosaurs, a pelage might have been useful to keep the wee ones warm, but mostly moist. “Endothermy originated in smaller, active eurythermal ectotherms living in a cool but variable thermal environment,” according to Clarke and Pörtner 2010. Desiccation is the main problem facing today’s tiniest reptiles, all of whom are restricted to moist leaf litter environs (Hedges and Thomas 2001). Unfortunately, we have no examples of tiny pterosaurs with ptero-fur.

Pterodactylus with hair in life pose, preparing to take off.

Figure 1. Pterodactylus with hair in life pose, preparing to take off.

Conversely large pterosaurs with soft and hard crests and extremely long necks and wings increased their surface-to-volume ratios, expanding these natural passive heat radiators when deploying their wings, evidently reducing the need for insulation and fur. We don’t see the body diameter length ptero-hair on large pterosaurs, like we do on Jeholopterus. Rather large pterosaurs, like Zhejiangopterus, appear to have had a short pelage.

3. Flying — Active muscle rapidly gets warm and steady activity due to flying gets a boost from an endothermic aerobic metabolism. The most widely accepted explanation for the evolution of endothermy has been selection for enhanced aerobic capacity.

On the flip side, flying by its very nature, requires a constant airstream and with it, heat loss by convection — if the ambient air is cooler than the body. This is emphasized in pterosaurs with their long wings laced with blood vessels, perhaps acting like giant gills, if not in oxygenation, then in heat exchange.

4. Short, laterally stiff torso — Most lizards cannot breathe while running quadrupedally. Undulating lizards experience Carrier’s constraint because their lungs cannot fill with air while laterally undulating (one lung compresses as the other expands then vice versa beneath the expanding and contracting ribcage). Short torso pterosaurs (and Sharovipteryx) did not undulate. Like birds, they don’t use their tail muscles to retract their hind limbs. Femora retractors have shifted to the enlarged hips. Pterosaurs breathed like we do and like birds do, by expanding both sides of their ribcage at once. (Not but rotating their prepubes back and forth! Gaak!)

5. Hollow bones –- Like warm-blooded birds, many pterosaurs had hollow bones that probably contained air sacs that inflated and cooled the bones with air from their advanced lungs.

6. Erect hind limbs —  Like warm-blooded birds, pterosaurs walked with more or less erect hind limbs that elevated their bellies far above the substrate. Maintaining this configuration required more energy than belly-floppers typically muster.

Clarke and Pörtner (2010) declared the metabolic status of pterosaurs remains unresolved. They reported, “Endothermy has evolved at least twice, in the therapsid-mammal and theropod-bird lineages. The benefits of endothermy are clear: a high and relatively constant internal body temperature allows a fine tuning of metabolism, high muscular power output, fast growth, and a significant degree of independence from environmental temperature. The costs are also well understood: the high rate of metabolism needed to sustain endothermy requires a great deal of food. Undoubtedly the most successful hypothesis, however, has been the suggestion of Bennett & Ruben (1979) that the key factor in the evolution of endothermy was selection for an enhanced aerobic capacity to allow increasingly sustained locomotor activity. The evolution of a higher body temperature and endothermy followed as secondary events. This proposal, the aerobic scope hypothesis, has withstood two decades of further research, and it remains the most widely accepted theory for the evolution of endothermy.”

Benefits of a warmer body

  1. Processing of food proceeds more rapidly
  2. Speed of nervous conduction is temperature dependent
  3. Higher growth rates in the young
  4. Improved food-gathering capability by adults for provisioning developing young. [This is likely not important for pterosaurs, who were likely independent from the moment of hatching because they could fly.]

Embryo development
Like other lizards, pterosaur mothers held eggs within their bodies until just before hatching. This warmth likely decreased the in-utero period by accelerating the embryo’s development, enabling flying shortly after hatching. Since pterosaurs likely laid only one egg at a time, (none have been found in clutches), accelerating embryo development would have increased the reproductive rate, especially among tiny pterosaur adults, which reached adulthood more rapidly.

References
Clarke A and Pörtner H-O 2010. Temperature, metabolic power and the evolution of endothermy. Biological Reviews online.
Hedges SB and Thomas R 2001. At the Lower Size Limit in Amniote Vertebrates: A New Diminutive Lizard from the West Indies. Caribbean Journal of Science 37:168–173.