Phylogenetic relationships within marsupials were investigated based on a 20.1-kilobase molecular supermatrix comprising 7 nuclear and 15 mitochondrial genes analyzed using both maximum likelihood and Bayesian approaches and 3 different partitioning strategies. The study revealed that base composition bias in the 3rd codon positions of mitochondrial genes misled even the partitioned maximum-likelihood analyses, whereas Bayesian analyses were less affected. After correcting for base composition bias, monophyly of the currently recognized marsupial orders, of Australidelphia, and of a clade comprising Dasyuromorphia, Notoryctes, and Peramelemorphia, were supported strongly by both Bayesian posterior probabilities and maximum-likelihood bootstrap values. Monophyly of the Australasian marsupials, of Notoryctes Dasyuromorphia, and of Caenolestes Australidelphia were less well supported. Within Diprotodontia, Burramyidae Phalangeridae received relatively strong support. Divergence dates calculated using a Bayesian relaxed molecular clock and multiple age constraints suggested at least 3 independent dispersals of marsupials from North to South America during the Late Cretaceous or early Paleocene. Within the Australasian clade, the macropodine radiation, the divergence of phascogaline and dasyurine dasyurids, and the divergence of perameline and peroryctine peramelemorphians all coincided with periods of significant environmental change during the Miocene. An analysis of “unrepresented basal branch lengths” suggests that the fossil record is particularly poor for didelphids and most groups within the Australasian radiation.
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