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Hardy, C R; Moline, P; Linder, H P (2008). A phylogeny for the African Restionaceae and new perspectives on morphology's role in generating complete species phylogenies for large clades. International Journal of Plant Sciences, 169(3):377-390. Postprint available at: http://www.zora.uzh.ch University of Zurich Posted at the Zurich Open Repository and Archive, University of Zurich. Zurich Open Repository and Archive http://www.zora.uzh.ch Originally published at: International Journal of Plant Sciences 2008, 169(3):377-390. Winterthurerstr. 190 CH-8057 Zurich http://www.zora.uzh.ch Year: 2008 A phylogeny for the African Restionaceae and new perspectives on morphology's role in generating complete species phylogenies for large clades Hardy, C R; Moline, P ; Linder, H P Hardy, C R; Moline, P; Linder, H P (2008). A phylogeny for the African Restionaceae and new perspectives on morphology's role in generating complete species phylogenies for large clades. International Journal of Plant Sciences, 169(3):377-390. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: International Journal of Plant Sciences 2008, 169(3):377-390. A phylogeny for the African Restionaceae and new perspectives on morphology's role in generating complete species phylogenies for large clades 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. Int. J. Plant Sci. 169(3):377–390. 2008. Ó 2008 by The University of Chicago. All rights reserved. 1058-5893/2008/16903-0006$15.00 DOI: 10.1086/526467 A PHYLOGENY FOR THE AFRICAN RESTIONACEAE AND NEW PERSPECTIVES ON MORPHOLOGY’S ROLE IN GENERATING COMPLETE SPECIES PHYLOGENIES FOR LARGE CLADES Christopher R. Hardy,1,*,y Philip Moline,* and H. Peter Linder* *Institute for Systematic Botany, 8008 Zurich, Switzerland; and yBiology Department, James C. Parks Herbarium, Millersville University, Millersville, Pennsylvania 17551, U.S.A. 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 parsimony- informative 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) morpholog- ical 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. Keywords: African Restionaceae, Bayesian, Cape floristic region, continuous characters, interactive keys, morphological characters, simultaneous analysis. Online enhancements: appendixes. Introduction relevant species, and (3) the detection of sufficient sequence var- iation to resolve relationships among closely related species. Species-level (i.e., complete and resolved) phylogenies are These problems are particularly acute in studies of large spe- needed for the rigorous execution of many taxonomic/evolu- cies radiations (Nyffeler 2002; Bateman et al. 2003; Salz- tionary investigations, among which are the circumscription burger and Meyer 2004) because of the large number of closely of taxa, assessment of variation in speciation rates, detailed related species and potentially short (i.e., difficult to resolve) historical biogeographical studies, ancestor reconstruction, and branch lengths. Ironically, it is in such difficult groups where the testing of adaptational hypotheses (e.g., Guyer and Slowin- many of the questions that require species-level phylogenies have ski 1993; Nee and Barraclough 1996; Barraclough et al. 1998; been applied, since these groups are seen by many as models Barraclough and Nee 2001; Nee 2001; Salisbury and Kim for understanding the diversification process itself. 2001; Zwickl and Hillis 2002; Linder et al. 2003, 2005). How- We searched for solutions to these problems in a study of ever, species-level phylogenetics is often hindered by problems the African Restionaceae (i.e., Cape reeds). This is the third- associated with (1) the accurate identification of species such largest clade (350 species; Linder 2003) and an ecologically dom- that the terminals in the resulting cladograms are accurately inant component (Taylor 1978) of the species-rich Cape flora labeled, (2) the collection of suitable DNA material for every of southern Africa. Although the African Restionaceae are taxonomically well known (Pillans 1942, 1945, 1952; Linder 1 Author for correspondence; e-mail: christopher.hardy@millersville 1985, 1986, 1991; Linder et al. 1998) and a large descriptive .edu. morphological and ecological database is currently available in Manuscript received April 2007; revised manuscript received July 2007. the form of an interactive key (Linder 2004), the remaining 377 378 INTERNATIONAL JOURNAL OF PLANT SCIENCES impediment to an understanding of the origins, patterns, rates Table 1 of diversification, and generic limits within the clade had been Species or Subspecies Lacking DNA Data the lack of a species-level phylogenetic hypothesis. The approach taken here was necessarily integrative, combining a large mo- Species lecular data set with 138 categorical characters and 15 contin- Calopsis sparsa uous (quantitative measurement) characters from the DELTA Elegia altigenaa (Dallwitz et al. 1993) database on which the interactive key Elegia fastigiataa to species is based. This set of characters is especially hetero- Elegia marlothiia geneous and required the use of recently developed programs Ischyrolepis affinis capable of accommodating continuous and multistate charac- Ischyrolepis fraterna ters (Goloboff et al. 2003; Ronquist and Huelsenbeck 2003; Ischyrolepis fuscidula Ischyrolepis gaudichauldiana var. gaudichauldiana Pagel and Meade 2004). Although discussion over the role of Ischyrolepis helenae morphological
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