phylogenetic relationships and classification of didelphid marsupials ...

2009 VOSS AND JANSA: DIDELPHID MARSUPIALS 67
TABLE 11
Results of Maximum-likelihood Model Fitting with Single-gene Datasets
BRCA1 vWF IRBP DMP1 RAG1 a
Model
Parameter estimates:
GTR + C TVMef + I + C GTR + I + C GTR + C GTR + I + C
pA 0.37 0.25 0.25 0.37 0.31
pC 0.19 0.25 0.26 0.18 0.23
pG 0.21 0.25 0.27 0.26 0.24
pT 0.23 0.25 0.22 0.18 0.22
rAC 0.91 2.03 1.96 1.12 3.03
rAG 4.75 7.01 5.88 2.64 4.59
rAT 0.76 1.26 1.46 0.39 0.77
rCG 1.05 1.07 1.13 0.77 1.73
rCT 5.52 7.01 7.43 6.74 7.22
a 1.48 0.83 0.81 0.69 0.41
pinv 0.00 0.19 0.32 0.00 0.52
Ln-likelihood b
215078.42 26648.62 26817.82 25943.66 26343.58
a First and second codon positions only.
b Of best tree.
thy features of this topology (fig. 27), didelphid
monophyly is only weakly supported, as
are most patterns of intergeneric relationships.
In fact, only six genera and intergeneric
clades are strongly supported (with bootstrap
values .75%) by parsimony analysis of these
data: (1) a group containing Lestodelphys and
Thylamys; (2) a group that includes Caluromys
and Caluromysiops; (3) the genus
Didelphis; (4) a group that includes Lutreolina,
Philander, and Didelphis; (5) a group
that includes the latter three genera plus
Chironectes; and (6) the genus Monodelphis.
However, several other groups (e.g., the
genus Thylamys, the genus Marmosops, the
genus Caluromys, the genus Philander, and
Philander + Didelphis) receive moderate
bootstrap support.
Bayesian analysis of these nonmolecular
data (implementing the Mkv model of Lewis,
2001) provides strong support (posterior
probabilities .95%) for most of the same
clades that are strongly supported by parsimony,
with the notable exception of (4)
among those listed above. In addition, there
is strong Bayesian support for the monophy-
TABLE 12
Results of Parsimony Analyses of Datasets with Nonmolecular Characters
Nonmolecular data a
Combined data b
w/ Chacodelphys w/o Chacodelphys w/ Chacodelphys w/o Chacodelphys
Ingroup taxa 44 43 44 43
Outgroup taxa 7 7 7 7
Total characters 129 129 7449 7449
Informative characters 114 114 2073 2073
Minimum-length trees 1068 21,803 12 12
Length of best trees 362 356 5960 5954
Consistency Index 0.508 0.517 0.638 0.639
Retention Index 0.788 0.793 0.777 0.777
Resolved nodes (%) c
37 (77.1) 27 (57.4) 44 (91.7) 43 (91.5)
a Morphological and karyotypic characters.
b Nonmolecular data plus concatenated sequences from five loci.
c In strict consensus of minimum-length trees.