Reconstructing the Tree of Life: Are molecular phylogenies really better than morphological ones?

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The phenomenon of evolutionary convergence has intriguing implications for the extent to whichevolution may be predictable (https://theconversation.com/what-do-aliens-look-like-the-clue-is-inevolution-63899).However, it often makes it difficult to reconstruct evolutionary relationships withaccuracy. In particular, it is often assumed that convergence is a problem that particularly bedevilsmorphological phylogenies, making them less accurate(http://www.42evolution.org/videos/researcher/professor-matthew-wills/), but is this really thecase?It is increasingly easy to generate phylogenetic trees from molecular data, with analyses routinelyconcatenating sequences from many tens or hundreds of genes. Despite their data-richunderpinnings, new molecular trees often contain surprises, and frequently imply relationships thatare at odds with established and traditional hypotheses derived from morphological data. One suchexample is the phylogeny of mammal orders: the 'new mammal phylogeny' overturns many'traditional' groups (Fig. 1). Another example is the arthropods. How are we to view these conflicts?Should we necessarily conclude that the new molecular trees are likely to be the correct ones; swayedby the mass of molecular data and greater complexity of analytical models? To do so implies that manydecades of comparative anatomy and morphological scholarship have yielded data that are - at best- simply more noisy and error prone than the data from molecules. At worst, it may indicate thatconvergence within morphological data implies relationships that are positively misleading.Since phylogeny cannot be known with certainty, there can be no objective test of accuracy. However,it is possible to assess the congruence of competing trees with independent sources of data onevolutionary history. Firstly, where the stratigraphic first occurrence dates of terminals (species,genera and higher taxa) are known with reasonable accuracy, the extent of implied ghosts lineages(relative to theoretical limits) offers an index of the 'goodness of fit' to the fossil record. Secondly, thebiogeographical or palaeobiogeographical distributions of many groups contain a residualevolutionary signal, and this can also be tested for its fit to competing trees. While neither stratigraphynor biogeography necessarily offers foolproof discrimination in any particular case, their applicationto a large statistical sample of cases - different major clades, different taxonomic levels, different agesof radiations - allows for some level of generality. The project will also identify which clades underwhich circumstances are most prone to morphological convergence, and therefore most suitablyanalysed with molecular data.The student will acquire an interdisciplinary and transferrable skill set: bioinformatics, phylogenetics,statistics and palaeontology.