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.

Congruence, fossils and the evolutionary tree of rodents and lagomorphs

“…The correlation between increased congruence and increased sampling of taxa known for morphology was highly significant both for fossils and hypothetical ancestors. In agreement with Beck & Baillie [16], addition of hypothetical ancestors was particularly effective and exhibited increased congruence with a higher slope (i.e. more congruence per added taxon) compared to fossils (figure 6).…”

“…Beck & Baillie [16] used a novel method to incorporate data from living taxa in studies of fossils where genomic data are generally unavailable. Using the topology from Meredith et al .…”

“…[25]. Ancestors inferred using maximum parsimony (MP) were ‘somewhat more successful in recovering’ [16] well-corroborated clades compared to likelihood-inferred ancestors. They assumed the phylogeny of Meredith et al .…”

“…Their study was not a test of evolution per se , or a test of the topology proposed by Meredith et al [25], but it did provide a means by which to increase congruence of topologies derived from fossils with topologies based on living taxa sampled for DNA. The method of Beck & Baillie[16] thus provides a means to include the phylogenetic information from modern taxa in an analysis of fossils, without directly having to sample non-fossilizable data, such as DNA.…”

“…By ‘well-corroborated’, we mean that one or an extremely small number of mutually consistent topologies, out of an astronomically huge number of possibilities, result from phylogenetic optimality criteria applied to these datasets. Secondly, we measure the phylogenetic impact of fossils, extant taxa and hypothetical ancestors [16] on congruence with this well-corroborated topology of extant taxa. We hypothesize that if evolution left a historical signal in bones and teeth, then ever-increasing samples from our dataset should converge on the well-corroborated species tree of mammals in general and Glires in particular.…”