Cladistic phylogeny reconstruction of mammals has its roots in publications by Malcolm McKenna [1] and was more explicitly algorithmic in the 1980s [2,3]. In the latter publications, discrete characters were analysed with an explicit optimality criterion, and were in principle observable by anyone with access to relevant material, in order to make specific, testable hypotheses regarding mammalian interrelationships. In retrospect, debate about mammalian interrelationships following these publications moved away from competing authoritarian statements on how mammalian groups are interrelated and towards a more focused discussion of the actual characters upon which such interrelationships are hypothesized [e.g., [4]].
Objections to algorithmic approaches to phylogeny reconstruction, particularly regarding its practice among morphologists [e.g., [5]], have occasionally noted the uninformative and/or low quality of character descriptions. Individual investigators are not necessarily to fault for the format in which their character lists are published, as editorial standards for such information vary widely, not to mention the capacity of different journals to publish graphic and/or textual appendices. Nevertheless, calls for the improvement of standards by which morphological character data are published, and by which they are selected for inclusion in a given study, have been made [e.g., [6]].
Web-based databanks offer an ideal means by which the information content of anatomical character sets can be maximized. Initiatives such as: digimorph [36], morphobank.org [37] and morphbank.net [38] have for several years taken advantage of this medium [7] , and have made it easier for investigators to evaluate morphological data with the ultimate goal of better understanding character evolution and phylogeny. However, as of this writing, a databank focusing on the skeletal anatomy of placental mammals is still lacking.
Hypotheses of placental mammal phylogeny
A widely cited dataset consisting primarily of nuclear DNA sequences [8,9] has been interpreted to contain an unambiguous signal dividing placental mammals into four main clades: Xenarthra (armadillos, sloths, and anteaters), Afrotheria (sea cows, elephants, hyraxes, elephant shrews, aardvarks, tenrecs, and golden moles), Euarchontoglires (primates, tree shrews, colugos, rodents, and lagomorphs), and Laurasiatheria (lipotyphlans, bats, carnivorans, pangolins, perissodactyls, whales, and artiodactyls), with a root separating Afrotheria from the remaining placental mammals. Studies of mtDNA that include both coding and non-coding sequences [10], as well as the longest concatenation of nuclear DNA to date [11], with ca. 200,000 aligned nucleotides for 18 terminal taxa, support this topology.
Other DNA datasets, including analyses of rare molecular features such as the presence/absence of retroposons [12] and sequence analysis of LINEs [13], provide independent support for the same unrooted topology, but disagree on the location of the root. This falls either at Atlantogenata (Afrotheria+Xenarthra) [13,14], Xenarthra [12], or Glires (Rodentia+Lagomorpha) [15]. Earlier analyses of mitochondrial protein-coding genes [16] and of a combined morphology+DNA dataset [17] have also supported a basal (and often paraphyletic) position of rodents, although in [16] erinaceids were located at the placental root, adjacent to murid rodents. The most recent molecular phylogenetic analyses of placental mammals support a relatively basal position of afrotherians and xenarthrans (except for [15]), and a monophyletic Rodentia and Glires [18], but the precise identity of the basal-most placental taxon remains elusive.
Palaeontological work continues to yield fossil mammals that are relevant to debates on mammalian phylogeny and the placental root [19-21]. Some have argued that certain Cretaceous eutherians comprise the sister taxon to Glires [22]. If Cretaceous eutherian lineages could be definitively linked with modern rodents and lagomorphs, this could be interpreted to support to the hypothesis of Glires basal within Placentalia [15]. However, the most taxon- and character-rich phylogenetic analyses including Cretaceous eutherians [20,21] do not support their placement within crown Placentalia, nor are they unanimous in identifying a basal-most crown placental clade.
In this paper, I present an image-rich, morphological character-database focusing on placental mammals, in tandem with a reanalysis of morphological and sequence data that bear on placental mammal phylogeny. The morphological character list is based on [17], which was in turn based on the work of many other publications, as cited therein. I combine these morphological data with the DNA sequence dataset (19 nuclear and 3 mitochondrial genes) of [9], and for the first time include information on 221 indels from their DNA sequence alignment. I apply a number of corrections to both the sequence- and morphological data sets; and using both maximum parsimony (MP) and a Bayesian algorithm, I investigate the support of these data for the aforementioned hypotheses on mammalian interrelationships and the placental root.
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