The evolutionary relationships of Diprotodontia and improving the accuracy of phylogenetic inference from morphological data

Figures & data

Figure 1. Family-level phylogeny of diprotodontian marsupials. A, The favoured molecular tree in phylogenetic analyses of MtNuc₂₀₆₅₄. The consensus of recent molecular studies collapses the branch indicated by the asterisk. Maximum likelihood bootstrap support is shown at nodes when less than 100%. All nodes received 100% Bayesian posterior probability. B, Algorithmic morphology tree favoured under MP and ML analyses of morph₃₅₂. C, Tree inferred under the optimal mixture (see Fig. 2) of molecular phylogenetic (sim₃₅₂) and ecological (size/diet) signals. Ancestral diet was reconstructed under ordered MP (herbivorous; dark green/dark tone, plant-dominated omnivorous; light green/light tone, broadly omnivorous; orange/intermediate tone, nectivorous; dashed). Circles indicate average adult mass (open; 0–50 g, 1 closed; 50–200 g, 2 closed; 200–800 g, 3 closed; 800 g–3 kg, 4 closed; 3–12 kg, 5 closed; >12 kg). Half circles indicate variation between species (e.g., 3, 4 for Phalangeridae). Diet and size states are assigned according to the attributes of the species included in the studies from which the morph₃₅₂ dataset is derived.

Table 1. Likelihood disadvantage of diprotodontian phylogenies from alternative data sources.

Data source/method	Likelihood disadvantage (ΔlnL)
Molecular studies (summary trees)
a. DNA–DNA hybridization	121.9
b. Albumin microcomplement fixation	182.4
c. Mitochondrial genes	84.4
d. Nuclear genes	96.0
Morphological studies (summary trees)
e. Informal-comparative morphology	71.7
f. algorithmic morphology	690.1
Alternative algorithmic morphology analyses of morph352
g. Maximum parsimony on morph352	594.6
h. Maximum-likelihood on morph352	594.6
i. Bayesian inference on morph352	617.5

The difference in log likelihood (ΔlnL) on MtNuc₂₀₆₅₄, between the molecular consensus (Fig 1 A; −lnL = 121,316.3) and summary trees for alternative data sources and analyses of morph₃₅₂.

Figure 2. Maximum parsimony treelength disadvantage. Percentage additional treelength required for the diprotodontian molecular consensus (open circles) and for the algorithmic morphology tree (closed circles), relative to the treelength of the MP topology, for each mixture of phylogenetic (sim₃₅₂) and ecological (size/diet) characters. Optimal fit to the algorithmic morphology tree occurs with the ecological characters multiplied out to contribute 2.9% of the data. Fit to the molecular consensus tree continues to deteriorate (25.1% treelength disadvantage at 16% ecological contribution).

Table 2. Reverse engineered phylogeny (REP) scores for alternative diprotodontian phylogeny hypotheses, (a) the favoured tree on the morphological character matrix, morph₃₅₂ (Fig. 1B), (b) the favoured tree on the molecular matrix, MtNuc₂₀₆₅₄ (Fig. 1A), and the two other topologies that are consistent with the molecular consensus, which includes a basal trichotomy among phalangeroids, (c) grouping phalangeroids + petauroids (possum monophyly) and (d) grouping macropods and petauroids. The REP score is the morph₃₅₂ MP score minus the size and diet signal correction (size & diet MP score) × 10.2, where 10.2 is the optimal character contribution to apparent phylogenetic signal (2.9% of the 352 characters; see Fig. 2).

Topology	morph352 MP score	Size & diet MP score	REP score
a. Morphology tree	723	14	651.6
Molecular trees
b. macropods + phalangeroids	773	26	640.4
c. phalangeroids + petauroids	763	26	630.4
d. macropods + petauroids	773	26	640.4

The best score in each column is indicated in bold.

Figure 3. Comparison of A, the morph₃₅₂ tree and C, the MtNuc₂₀₆₅₄ molecular tree, respectively, with the diprotodontian phylogenies reconstructed from Bayesian inference of the Bmorph₁₈₀ dataset B, without including fossil taxa and D, with fossil taxa included. Node support values on the Bmorph₁₈₀ trees are Bayesian posterior probabilities.