A Phylogeny for the African Restionaceae and New Perspectives on Morphology’s Role in Generating Complete Species Phylogenies for Large Clades

Abstract

Hardy, C R; Moline, P ; Linder, H P Hardy, C R; Moline, P; Linder, H P (2008 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. 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 s...

A generic classification of the Restioneae (Restionaceae), southern Africa

“…Although the morphological and anatomical data are thought to provide phylogenetic signal under the influence of the nuclear genome and therefore independent of the plastid dataset, the relatively large size of the plastid dataset may have had a disproportionate influence on the resulting phylogenetic inferences. However, because the addition of our mor phological data to the plastid data in a combined analysis resulted in increased support (via bootstrap and posterior probabilities) for most clades than did either data set alone (Hardy et al 2008), we are confident that the phylogeny is a good approximation of the species phylogeny.…”

“…All genera and subgenera recognized here, were resolved as (potentially) monophyletic (i.e. as clades) by Hardy et al (2008;summarized in Figures 1-5). Monophyletic taxa contain a closed segment of evo lutionary history; therefore, such taxa can be expected to have a much greater predictive power than taxa that are not monophyletic.…”

“…The first set o f problems was in the Elegia clade, where Chondropetalum lacked synapomorphies. Moline & Linder (2005) Recently, Hardy et al (2008) published an almost com pletely sampled phylogeny o f the African Restionaceae (subfam. Restionoideae), expanding the previously pub lished phylogeny for the nested Elegia group (Moline & Linder 2005) to include a complete species sampling of the entire tribe Restioneae (Figures 1-5).…”

“…The phylogenetic inferences of Hardy et al (2008) were based on both parsimony and Bayesian analysis of a mod erately large dataset consisting of plastid DNA sequences (± 7.3 Kb) and 150 morphological and anatomical charac ters for all 292 species and subspecies of the Restioneae. The robustness of these inferences, how ever, is limited by the inability of Hardy et al (2008) to successfully generate nuclear DNA sequences.…”

“…The robustness of these inferences, how ever, is limited by the inability of Hardy et al (2008) to successfully generate nuclear DNA sequences. As such, the phylogenetic infer ences of Hardy et al (2008) were strongly influenced by evolutionary history of the plastid genome w hich, because of problems associated w ith phenomena such as introgressive hybridization (e.g. chloroplast capture) or lineage sort ing.…”