Craniodental morphology and phylogeny of marsupials

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.