A higher-level MRP supertree of placental mammals

Abstract

Background: The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP supertree that favoured 'outdated' hypotheses (notably, monophyly of both Artiodactyla and Lipotyphla) has been heavily criticised for including low-quality and redundant data. We apply a stringent data selection protocol designed to minimise these problems to a much-expanded data set of morphological, molecular and combined source trees, to produce a supertree that includes every family of extant placental mammals.

Results: The supertree is well-resolved and supports both polyphyly of Lipotyphla and paraphyly of Artiodactyla with respect to Cetacea. The existence of four 'superorders'--Afrotheria, Xenarthra, Laurasiatheria and Euarchontoglires--is also supported. The topology is highly congruent with recent (molecular) phylogenetic analyses of placental mammals, but is considerably more comprehensive, being the first phylogeny to include all 113 extant families without making a priori assumptions of suprafamilial monophyly. Subsidiary analyses reveal that the data selection protocol played a key role in the major changes relative to a previously published higher-level supertree of placentals.

Conclusion: The supertree should provide a useful framework for hypothesis testing in phylogenetic comparative biology, and supports the idea that biogeography has played a crucial role in the evolution of placental mammals. Our results demonstrate the importance of minimising poor and redundant data when constructing supertrees.

Figure 1

Supertree of extant placentals (50% majority rule consensus of 17 most parsimonious trees – length = 8150.935), following application of the protocol of Bininda-Emonds et al. [32] to the complete set of references. Asterisks indicate which branches collapse in the strict consensus. Numbers above branches represent reduced qualitative support (rQS; [26,39]) values. The orders are indicated by brackets and the first three letters of their names following Table 1, with the additional fossil order Bibymalagasia indicated by BIB. Whippomorpha and the four superorders are also indicated.

Figure 2

Supertree of extant placentals (50% majority rule consensus of 5540 most parsimonious trees – length = 4262.625), following application of the protocol of Bininda-Emonds et al. [32] to only those references used by Liu et al. [29]. Asterisks indicate which branches collapse in the strict consensus. Numbers above branches represent rQS values, and numbers below represent decay indices. The orders and Whippomorpha are indicated and bracketed as in Figure 1, as are the two superorders (Xenarthra and Afrotheria) recovered as monophyletic in this analysis.