Compared to just a decade ago, there is now a broad level of agreement on the basic topology of the extant mammalian radiation [e.g., [8-14]]. Using a relatively large DNA-indel-morphology dataset based on [8,9,17], this study has made a number of changes to both molecular and morphological homology (see additional file 1), yet recovers the same basic pattern of living placental phylogeny (Figs. 1, 2, 3), dividing the unrooted tree into Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria.
The same level of agreement cannot yet be said to exist for all fossil clades. In this study, Ukhaatherium, Centetodon, Hyopsodus, Meniscotherium, Phenacodus, Arsinoitherium, Moeritherium, and Anagale are placed with some consistency across analyses. The remaining four fossils (Leptictis, Paleoparadoxia, Plesiorycteropus, and Zalambdalestes) vary in their position depending on the analysis, indicating that at present the morphological data sampled here are not sufficient to reconstruct the phylogeny of these taxa. I concur with [25] that the current morphological sample could be expanded significantly. Nevertheless, this study demonstrates that even a small morphological dataset can influence a much larger body of DNA sequences. Here, morphology not only improves resolution in some clades that remain poorly resolved based on DNA sequences alone (e.g., favouring sea cow-elephant), but can also shift the placental root from Muridae to Afrotheria (Fig. 4). The combined data favour a placental root at either Afrotheria or Xenarthra (Table 1; Figs. 1, 2, 3). Both Atlantogenata and Muridae receive suggestively low p-values with third coding positions excluded; Glires and Erinaceus are the least favoured root-taxa among the alternatives tested with the present dataset.
The morphological web-database presented here will make it easier for researchers to incorporate these data into larger phylogenetic matrices that sample additional fossils. In the long term, such representations will be essential to reconstruct the morphology of the placental common ancestor. Towards this end, morphological character matrices should be easily accessible and understandable across institutions and generations of scientists; and they should build upon previous work in order to offer an ever-expanding character database. Many kinds of molecular data have enjoyed such accessibility for well over a decade. The relatively infrequent presentation of graphic character databases limits the utility and appreciation of morphological character matrices, a condition that in recent years has, fortunately, begun to change.
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