PALEONTOLOGICALLY INFORMED SUPERMATRICES: FOSSILS AND PHYLOGENETICS IN THE AGE OF GENOMICS

The important role that fossils once played in the process of phylogeny reconstruction has been diminished over the last half-century by the advent of cladistic methodologies and the ever-increasing reliance upon molecular sequence data for generating phylogenetic hypotheses. Nevertheless, extinct taxa (represented by fossils) offer unique data relevant to reconstructing the tree of life, including extinct morphologies and temporal information. One way to directly incorporate both extinct and extant taxa into the process of phylogeny reconstruction is through construction and simultaneous analysis of robust total evidence supermatrices that include morphological and molecular sequence data and both extinct and extant terminal taxa. In such supermatrices, fossil taxa are typically coded for only a portion of the morphological dataset (those characters that are preserved and/or interpretable) and completely lack molecular sequence data. Although fossils may bear large numbers of missing data (in some cases, over 99% of all characters are scored as missing for extinct terminals), over 30 studies have demonstrated the utility of a supermatrix approach for reconstructing the phylogenetic positions of extinct taxa among their extant relatives and, in some cases, for addressing questions pertaining to the timing and sequence of morphological character evolution and the evolutionary histories of particular clades. We demonstrate the potential of this methodology using a supermatrix constructed from previously published morphological and molecular sequence data from the Chiroptera (bats). Incorporation of fossil taxa into robust datasets derived from extant taxa has the potential to once again bring fossils to the forefront of the process of phylogeny reconstruction and may also present new avenues to test hypotheses concerning the evolutionary histories of particular clades.