Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa?

The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because fossil taxa often interdigitate among living taxa on the Tree of Life, molecular data may indirectly enhance phylogenetic accuracy for fossil taxa in the context of a combined analysis of morphological and molecular data for living and fossil taxa. Here, I use simulations to assess accuracy for fossil taxa in a mixed analysis of living and fossil taxa, before and after addition of molecular data to the living taxa. The results show conditions where the accuracy for fossil taxa is greatly increased by adding molecular data, sometimes by as much as 100%. In other cases, the increase is negligible, such as when fossil taxa greatly outnumber living taxa in the analysis. However, there were few cases where accuracy was significantly decreased by the addition of the molecular data, suggesting that this practice may range from highly beneficial to mostly harmless. Overall, the results suggest that improvements in molecular phylogenetics can potentially benefit phylogeny reconstruction for fossil taxa.