Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

Abstract

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

Keywords: ancestors; fossil; mammals; morphology; phylogeny.

Figure 1.

Phylogenies of mammals based on (a) molecular and (b) morphological datasets. The topology shown in (a) is modified from fig. 1 of Meredith et al. [4] and is based on an 11 000 amino acid alignment from 26 gene fragments, whereas that in (b) is modified from electronic supplementary material, figure S2A of O'Leary et al. [3] and is based on 4541 morphological characters (fossil taxa have been deleted). Branches are colour coded according to their membership of the superorders Afrotheria, Xenarthra, Laurasiatheria and Euarchontoglires. Node numbers in (a) correspond to the predicted ancestors for those nodes in figure 2.

Figure 2.

Phylogeny of mammals based on maximum parsimony (MP) analysis of a modified version of the morphological dataset of O'Leary et al. [3] and with ‘max preservation’ predicted ancestors (PAs) added. Topology shown is a strict consensus of 64 most parsimonious trees. Ancestral states for the predicted ancestor were reconstructed using MP. Predicted ancestors are shown in bold, with numbers corresponding to the nodes for which they are ancestral, as shown in figure 1a. Fossil taxa are indicated with †. Circles at nodes indicate support, with the top half representing standard bootstrap values and the bottom half ‘transfer bootstrap expectation’ (TBE) values: black indicates greater than or equal to 70% support, grey 50–69% and white less than 50%.