the base and stem of the mammal clade are showing some nomenclature problems relative to traditional results.
First, I added a few mammals
(Mus, Taeiniolabis, Paulchaffatia) just be sure I was comparing listed taxa (see below) with listed taxa. If you know of any pertinent taxa that will change the current tree topology back to traditional topologies, please let me know. So far, I’m coming up short. These are the changes recovered so far:
Carrano et al. (editors) 2006
reports the following pertinent definitions. Comments follow (not in boldface).
Mammalia Linneaus 1758
The least inclusive clade containing Ornithorhynchus and Mus. In the LRT, Sinoconodon is the last common ancestor and Pachygenelus nests at the base of the outgroup clade, the Trithelodontidae (including the Tritylodontidae). So, no problems with this definition.
Trithelodontidae Broom 1912
The most inclusive clade containing Pachygenelus, but not Tritylodon and Mus. In the LRT Pachygenelus is basal to both Tritylodon and Mus, so the most inclusive clade containing Pachygenelus includes Mammalia and Tritylodontidae, contra prior studies.
Tritylodontidae Kühne 1956|
The most inclusive clade containing Tritylodon, but not Pachygenelus or Mus. In the LRT, this clade is monophyletic, and now includes Repenomamus.
Mammaliamorpha Rowe 1988
The least inclusive clade containing Tritylodon, Pachygenelus and Mus. In the LRT this clade is a junior synonym of the Trithelodontidae (see above).
Mammaliformes Rowe 1988
The most inclusive clade containing Mus, but not Tritylodon or Pachygenelus. In the LRT, this clade is a junior synonym for the clade Mammalia because Pachygenelus is the proximal outgroup taxon to Mammalia.
Theria Parker and Howell 1897
The least inclusive clade containing Mus and Didelphis. In the LRT this clade is monophyletic and unchanged.
Theriimorpha Rowe 1988
The most inclusive clade containing Mus but not Ornithorhynchus. In the LRT this clade is a junior synonym for Theria.
Metatheria Huxley 1880
The most inclusive clade containing Didelphis, but not Mus. This definition was meant to include all marsupials, but in the LRT the clade that includes most marsupials does not include Didelphis, which nests basal to and outside both monophyletic Marsupialia and Placentalia. So, strictly speaking, Metatheria in the LRT currently includes only Didelphis and perhaps its sister, Ukhaatherium.
Allotheria Marsh 1880
The most inclusive clade containing Taeniolabis, but not Mus or Ornithorhynchus. This was meant to indicate that Taeniolabis nested outside the Mammalia, but in the LRT Taeniolabis nests with Plesiadapis and Carpolestes and this clade is a sister to the clade containing Mus and the Multituberculata — within the Glires and Placentalia.
Multituberculata Cope 1884
The least inclusive clade containing Taeniolabis and Paulchofattia. This was meant to include all the multituberculates and have them nest outside of the Mammalia, but in the LRT Taeniolabis nests with Plesiadapis and Paulchofattia nests with Carpolestes. So that is a clade of four taxa at present and it does not include Ptilodus and other multituberculates, the clade with a large and grooved lower last premolar. These traditional multis now need a new clade name. They are derived from a sister to the rodent clade in the LRT and they leave no descendants. Carpolestes is a sister to the ancestor of rodents and multis and Carpolestes (Fig. 1) has a large and barely-grooved lower last premolar, a precursor to that identifying trait in that second clade of multis.
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.