Abstract
Difficulties with obtaining complete species-level phylogenies include (1) the accurate identification and
sampling of species, (2) obtaining a complete species sampling, and (3) resolving relationships among closely
related species.We addressed these in a study of 317 species and subspecies of the African Restionaceae. Accurate
species identification and collection in the field was facilitated by a morphology-based interactive key to all
species. Despite intensive fieldwork, however, material for DNA extraction could not be obtained for 20 of the
292 species of the focal Restio subclade. Furthermore, the 6831 aligned nucleotides and 1685 parsimonyinformative
sequence characters were insufficient to resolve relationships fully within the clade. A simulation
indicated that an additional 5000–7000 bases may have been needed to achieve supported resolution in the
neighborhood of 95%–100%. Instead of further sequencing, we investigated the phylogenetic utility of the large
set of characters contained within the interactive key data set, exploiting recent advances in parsimony and
Bayesian programs that allow multistate and supermultistate (including continuous for parsimony) morphological
characters. On doing so, parsimony resolution increased 17% to nearly 100%, and overall support increased
in both parsimony (bootstrap) and Bayesian (posterior probability) frameworks. Taxa for which DNA data were
lacking could be placed in fully resolved positions. Experiments using the parsimony ratchet indicated that
placement of these morphology-only taxa may have been completely accurate 30% of the time, to within three
nodes of accuracy 60% of time, and accurate to genus 96% of the time. Accurate placement of morphology-only
taxa through Bayesian analysis may require extensive effort devoted toward exploring tree and parameter space.
We conclude that the increasingly available large morphological data sets associated with interactive keys or
informatics initiatives represent convenient yet potentially powerful tools in overcoming many of the commonly encountered obstacles in molecular-based species-level phylogenetics.
Hardy, C R