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The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data with dense sampling of Recent taxa, but few studies have combined both data types. Another dichotomy in the marsupial phylogenetic literature is between studies focused on New World taxa and those focused on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna based on combined analyses of morphology and molecular sequences for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 terminals representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) terminals represented by well-preserved fossils, and 5 outgroups (nonmarsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology including features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters (e.g., from the postcranium), and improved methods of phylogenetic analysis.
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