Comparing the stratigraphic record to estimates of phylogeny

The age of first occurrence of taxa remains an underutilized source of information in phylogenetic analysis. In this paper I develop a method whereby one can measure the fit of the stratigraphic record to an estimated phylogenetic tree. The method works as follows: (1) each of the internal nodes excluding the root node of a phylogenetic tree is visited, (2) the oldest age of first occurrence for the taxa above the node is compared to the oldest age of first occurrence for the sister node, and (3) if the age above the node is the same age or younger than the age below the node, then the node is stratigraphically consistent. A measure of the total fit of the stratigraphic record to the tree is the proportion of nodes that are stratigraphically consistent (expressed as the stratigraphic consistency index, SCI). This measure of stratigraphic fit is sensitive to errors in phylogenetic estimation as well as to missing lineages (or parts of lineages). The significance of the fit of the stratigraphic record to the tree can be determined through a permutation approach that generates the null distribution for SCI under the hypothesis that the stratigraphic fit is no better than would be expected at random. The method is applied to several studies taken from the literature. Almost all published trees had significant SCI values, meaning the trees fit the stratigraphic record quite well. Applications of stratigraphic consistency for determining the confidence that should be placed in a phylogenetic estimate, for determining the root of a tree, and as a modified optimality criterion for estimating phylogenetic trees are discussed.