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*Kharmerungulatum*, placental phylogeny, and stuff



*Kharmerungulatum* is an isolated tooth crown from an omnivorous or herbivorous tribosphenic mammal. I don't think much more can be said. I'm not an expert on that, but I wouldn't bet money on its being a eutherian, let alone a placental. (Although I do suspect that the *Protungulatum*-*Oxyprimus*-*Purgatorius* clade found by Wible et al. is an artifact of their failure to order any characters. Someone should test that...)

Where do the notoungulates and litopterns and pyrotheres and astrapotheres and xenungulates and whatnots come out these days? They don't. There is AFAIK no phylogenetic analysis that includes them. That's probably because any such analysis would have to be a complete morphological placental analysis, and such an analysis doesn't exist yet. It would have to be built from scratch, the way Livezey & Zusi did it for Neornithes, but with lots more fossils -- wait, not from scratch anymore, now that we have the *Maelestes* paper (and an SVP meeting abstract that alludes to also having done part of the work), but still we are talking about a Ph.D. thesis or two.

In the meantime, we will have to rely on the molecular analyses. Since 2001 they are no longer plagued by rampaging long-branch attraction, and even though they have been growing all the time, their results have been remarkably consistent.

One of the last points of contention was the trichotomy consisting of (Cet)artiodactyla, Perissodactyla, and Ferae ( = Carnivora + Pholidota). Some analyses found the first two as sister-groups (Euungulata -- what remains of the extant Ungulata after the removal of those that are afrotheres), others the last two (Zooamata; the molecular mammalologists don't name clades, they name hypotheses).

Then came this paper http://www.pnas.org/cgi/content/full/103/26/9929 (free online access). It uses a quasi-morphological character that is almost completely immune to convergence: retroposon insertion. The probability that the same retroposon inserts twice independently into the same random place in a genome sequence, and does so at the same random truncated length (replication of the very long retroposons of the family used here often stops prematurely), is negligible; reversals are just about impossible.

And here is the result (fig. 2; rest of Placentalia and the marsupial outgroups omitted; Pholidota was not included in the analysis):

Laurasiatheria
 |--Eulipotyphla
 `--Scrotifera
      |--Cetartiodactyla
      `--Pegasoferae
           |--Chiroptera
           `--Zooamata
                |--Perissodactyla
                `--Carnivora

Funnily, four retrotransposon insertions support Pegasoferae, but one supports

|--Chiroptera
`--+--Cetartiodactyla
  `--(Perissodactyla + Carnivora)

instead! The only reasonable explanation, which is adopted by the authors, is incomplete lineage sorting: "Namely, the L1 insertion at locus INT283 occurred in the genome of a common ancestor of Scrotifera, and the ancestral dimorphism of alleles containing or lacking L1 had been retained in the population during the divergence of at least three lineages such as Cetartiodactyla, Chiroptera, and a group of Carnivora + Perissodactyla, followed by random fixation of the alleles. Accordingly, the time period in which the divergences occurred is relatively shorter than the coalescence time of the ancestral population".

Euungulata is not an option.

(And within Afrotheria, the aardvark is the sister-group of Afrosoricida/Tenrecomorpha, and this clade is the sister-group to Macroscelidea, and all together form the sister-group of Paenungulata, which consists of the elephants on one side and Sirenia + Hyracoidea on the other. Even Pseudungulata is thus not an option.)

As the authors mention, Pegasoferae has occasionally also been found by conventional molecular analyses, though never with high support -- which is no surprise.

While I am at it, Xenarthra and Afrotheria are sister-groups (forming Atlantogenata) according to this paper http://mbe.oxfordjournals.org/cgi/content/abstract/24/9/2059 (only the abstract is free) which uses almost 2.17 million nucleotide positions, far more than any molecular phylogenetic analysis before.