phylogenetic relationships and classification of didelphid marsupials ...

2009 VOSS AND JANSA: DIDELPHID MARSUPIALS 69
ly of Marmosops (only moderately supported
by parsimony). However, Bayesian support is
weak for several nodes with moderate parsimony
bootstrap support, including the genus
Thylamys, the genus Caluromys, and the
genus Philander.
Most of the obvious differences between
these results and our previously published
analyses of didelphid morphological character
data are attributable to rooting. Whereas
we previously (Voss and Jansa, 2003; Voss et
al., 2004a; Jansa and Voss, 2005) rooted our
estimates of didelphine relationships using
Caluromys, Caluromysiops, and Glironia as
outgroups, these analyses are rooted using
nondidelphid marsupial outgroups. Considered
as an undirected network, the ingroup
topology of figure 27 is almost identical to
that obtained by Jansa and Voss (2005: fig.
1C) for the same set of didelphid terminal
taxa.
Single-gene Analyses
Maximum-likelihood topologies with superimposed
summaries of nodal statistics
from three analyses (MP, ML, and Bayesian)
of each single-gene dataset (figs. 28–32)
illustrate similarities and differences in clade
support among the five loci we sequenced.
Because our analytic results for IRBP and
DMP1 have already been published (Jansa
and Voss, 2005), only summary comments
are warranted here. Briefly, the monophyly
of all genera represented by two or more
terminal taxa is strongly supported by both
of these genes (figs. 28, 29) with the exception
of Gracilinanus (weakly to moderately supported
by IRBP, not recovered as monophyletic
by DMP1), Thylamys (only weakly
supported by Bayesian analysis of DMP1),
and Didelphis (inconsistently recovered as
monophyletic by analyses of IRBP). On the
assumption that the DMP1 tree (lacking
outgroup terminals) is appropriately rooted
within a node or two of Glironia, several
patterns of intergeneric relationships are also
supported by both genes, including the nested
clades (Metachirus (Chironectes (Lutreolina
(Didelphis + Philander)))); a group that
includes Lestodelphys and Thylamys; a group
that includes Cryptonanus, Gracilinanus, and
Lestodelphys + Thylamys; a group that
includes the latter four genera plus Marmosops;
and a group that includes Marmosa,
Monodelphis, and Tlacuatzin. As reported
elsewhere (Jansa and Voss, 2005), there are
no examples of hard incongruence to be
found in comparing analytic results between
IRBP and DMP1 because all conflicting
nodes (e.g., those resolving the position of
Hyladelphys) have weak support from one or
both genes.
Analyses of first and second codon positions
of RAG1 (fig. 30) support the monophyly
of most polytypic didelphid genera
(except Caluromys, Didelphis, andPhilander),
but some genera recovered as monophyletic
groups (e.g., Thylamys, Marmosops, and
Monodelphis) do not receive consistently
strong support. Many of the same intergeneric
relationships supported by IRBP and
DMP1 were also recovered, notably including
the branching patterns among Metachirus,
Chironectes, Lutreolina, and Philander
+ Didelphis. Additionally, Marmosops was
recovered as the sister group to a clade that
includes Cryptonanus, Gracilinanus, and Thylamys.
Unfortunately, the uncertain position
of the root (probably an artifact of incomplete
outgroup sequences; see above) is
reflected in the lack of strong support for
any basal relationships in this topology.
Analyses of sequence data from BRCA1
produced the most compelling single-gene
estimate of didelphid relationships recovered
to date, with strikingly consistent high nodal
support values and an almost completely
resolved consensus topology (fig. 31).
Among other salient features, every polytypic
opossum genus with the exception of Didelphis
was recovered with strong support, as
were almost all of the higher-level clades
recovered with strong support by any analysis
of other single-gene datasets (the only
exceptions are groups that include Lestodelphys
and Caluromysiops, taxa from which
BRCA1 sequences are not available). Three
of these merit particular attention. One is
‘‘clade H’’ of Jansa and Voss (2000), which
unites the Thylamys cluster with Metachirus
and the large opossums with 22 chromosomes
(Chironectes, Lutreolina, Philander,
and Didelphis). Another is the subfamily
Didelphinae of traditional usage (excluding
Hyladelphys, Caluromys, andGlironia), and