Wilkinson support calculated with exact probabilities: An example using Floricaula/LEAFY amino acid sequences that compares three hypotheses involving gene gain/loss in seed plants

This paper describes a method for quantifying the extent to which a charact er supports a hypothesized monophyletic group. The basic idea was first pro posed by Wilkinson in 1998; hence, we call it Wilkinson support. A characte r provides Wilkinson support if it could have changed state on the branch l eading to the hypothesized monophyletic group without requiring any extra s teps in an evolutionary tree. We describe a method to determine the exact p robability that a character would provide Wilkinson support for a random gr oup of the same size as the hypothesized monophyletic group. A character's weight is defined as the negative natural log of this probability. The sum over all characters of these weights in a data set is a measure of total we ighted support. We exemplify this method using 30 Floricaula/LEAFY amino ac id sequences. One copy of this gene occurs in angiosperms, but two copies o ccur in the other four seed plant groups. Angiosperms could have been primi tively single-copy or could have lost either of the two paralogs. These pos sibilities correspond to three hypotheses of monophyly. We use total weight ed Wilkinson support to evaluate these three hypotheses, and all three are shown to be significantly different from random as individual hypothesized monophyletic groups. Comparing these three hypotheses for total weighted su pport reveals that one has much more support than do the other two. This hy pothesis favors the "mostly-male" theory of flowering-plant origins.