Morphological, mtCOI DNA, and luciferase DNA data are analyzed individually and simultaneously for phylogenetic signal. Analysis of 16 characters traditionally used in species identification for 317 individual Microphotus specimens yields 5000 trees with poor resolution. Although mtCOI and luciferase data conflict in basal clades, both contribute to the phylogeny of Microphotus. Based on lack of morphological variation and geographic and temporal proximity of collection localities, M. decarthrus Fall 1912 and M. fragilis Oliver 1912 are synonomized. Microphotus octarthrus Fall occurs throughout the southwestern United States in discontinuous pinyon-juniper and juniper-oak habitats. Wide geographic distribution, discontinuous habitat and limited dispersal capabilities of females makes this species ideal for the study of genetic variation. Mantel’s approximate t test indicates that populations are both geographically and genetically isolated. Twenty-six haplotypes are found among 28 individuals; haplotypes are unique for the populations studied. When subjected to a 2.3% sequence divergence rate, mean branch lengths suggest segregation of populations began in the Holocene, before Pleistocene glaciation. Although these data suggest greater species diversity, more data, including mating behavior and more genes are required to further elucidate species limits.

Extant monotremes have a combination of plesiomorphic and apomorphic characters that causes ambiguity about their basic anatomy and evolutionary history. The problem is compounded by the lack of extinct and extant specimens of monotremes available for study. Only five species of monotremes are currently recognized, and all are endangered. The most speciose subclade, the long-beaked echidna, Zaglossus, has few specimens archived in mammalogy collections relative to the platypus, Ornithorhynchus anatinus, and the short-beaked echidna, Tachyglossus aculeatus. As a result, researchers sample from Ornithorhynchus and Tachyglossus, excluding species of Zaglossus from analysis. An equally depauperate fossil record consisting primarily of fragmentary jaws and isolated molars over a broad temporal range (~125 Ma) has led to controversies surrounding the origin and evolution of Monotremata and its major subclades. As new fossils attributable to Monotremata have been discovered, they are placed in conflicting positions on either the crown or the stem. I used CT scans of skeletally immature and mature specimens of Zaglossus bruijni and Zaglossus bartoni, respectively, to describe the cranial osteology of Zaglossus in detail. New insights about the anatomy of Zaglossus were then utilized in a phylogenetic analysis. Zaglossus and the extinct echidna, Megalibgwilia were added to a previously published morphological character matrix, along with 42 new skeletal characters. For the first time, I illustrated the cranial anatomy of Zaglossus bruijnii and Zaglossus bartoni, and described the endocranial morphology and individual variation among the two species. I described patterns of ossification throughout ontogeny that may explain a preservation bias against echidnas. My phylogenetic analysis placed the Early Cretaceous monotremes either on the stem of Ornithorhynchidae or in the monotreme crown, supporting an Early Cretaceous divergence estimate between platypuses and echidnas. I provide the first phylogenetic definition and diagnosis of Monotremata, Ornithorhynchidae, and Tachyglossidae. Based on the distribution of characters of extant monotremes, the ancestral monotreme was likely a terrestrial, scratch-digger capable of electroreception. The ancestral population gave rise to the semi-aquatic platypuses and the large, terrestrial echidnas. Tachyglossus is the most derived of the extant echidnas; it is more appropriate to include Ornithorhynchus and Zaglossus in future phylogenetic analyses. / text