Monocotyledons - with ca. 65,000 species, 91 families, and 12 orders, and including such groups as grasses, sedges, bromeliads, palms, gingers, orchids, irises, lilies, yams, pondweeds, and aroids - are the most diverse, morphologically varied, ecologically successful, and economically important of the early-divergent clades of angiosperms. Since their origin in the early Cretaceous, monocots have radiated into almost every habitat on earth. Today, they are dominant in many terrestrial and aquatic ecosystems, display kaleidoscopic variation in vegetative and floral morphology, and comprise nearly 25% of all species and families of flowering plants. Understanding their origin, phylogeny, and patterns of morphological divergence, geographic diversification, and ecological radiation represents a major challenge for evolutionary biologists.

We propose to develop a fully resolved, strongly supported, highly inclusive phylogeny for the monocots using multi-gene and genomics approaches, focusing on 13 problematic nodes/regions and including many highly reduced, mycoheterotrophic taxa that often confound molecular and morphological analyses. We will sequence the plastid genome and all mitochondrial genes of 601 taxa; two single-copy nuclear genes in a nested subset of 175 taxa; and the entire transcriptome of young leaves in a further nested subset of 50 taxa. The broadest sampling will include representatives of all monocot families and subfamilies. We will analyze these data using parsimony, Bayesian, and maximum-likelihood methods, drawing on the extraordinary power of the new CIPRES computer cluster and software. We will score more than 223 morphological/anatomical/chemical characters in 601 extant focal taxa, 75 fossil monocots, and 28 non-monocot outgroups, and lodge our data in MorphBank, providing the basis for identifying morphological synapomorphies, diagnosing clades, analyzing character evolution, and incorporating fossils into phylogenetic analyses. Close coordination of our efforts with the ongoing angiosperm AToL project will allow study of a much wider range of monocot taxa and characters; together, our efforts should provide a comprehensive phylogeny for the angiosperms, the second largest terrestrial branch of the Tree of Life.

A fully resolved monocot tree will provide the foundation for studies in many fields of comparative biology, including physiology, ecology, biogeography, and genomics. We will provide web access to phylogenies and databases, together with informatics tools to permit overlays of characters and identification of synapomorphies, as well as voucher information, digitized images of scanned leaves, and a visual glossary of over 180 phenotypic characters. We will emphasize interdisciplinary training of post-doctoral fellows, graduate students, and undergraduates, with a focus on women and minorities, and contribute to the career development of five new faculty PI's. We will update and greatly expand monocot pages for the Tree of Life Web Project, create "TreeHouses" for K-12 students, and forward pre-publication findings to the Angiosperm Phylogeny website. A traveling exhibit on monocot phylogeny and evolution will be displayed in New York City, Ithaca, Athens (GA), Gainesville, Chicago, Denver, and San Francisco; computer graphics associated with this exhibit will be distributed to all institutions involved in the study. A children's garden of monocots will be developed at the New York Botanical Garden. Posters illustrating monocot diversity, phylogeny, and evolution will be designed and made available on CD for local printing and web viewing in classrooms around the country. PI's will provide additional outreach through talks at local public high schools.

• Nested sets of 601, 175, and 50 taxa to be sequenced for organellar genomes, single-copy nuclear genes, and transcriptomes, respectively, with notes on which taxa pertain to each of the problematic nodes under study (see Fig. 1) (pdf)
• Morphological/anatomical/chemical characters and character states to be scored for 601 extant monocots, 75 monocot fossils and 28 non-monocot outgroups (pdf)
• Outgroup taxa to be sequenced for DNA regions where coverage is not provided by the Angiosperm AToL team (pdf)
• Flow diagram showing relationships among main web pages (pdf)

Photographs (see above) illustrate representatives of the twelve orders of monocotyledons. Shown from left to right are: Poales (Elegia, Restionaceae); Commelinales (Pontederia, Pontederiaceae); Zingiberales (Heliconia, Heliconiaceae); Arecales (Johannessteijsmannia, Arecaceae); Dasypogonales (Dasypogon, Dasypogonaceae); Asparagales (Corybas, Orchidaceae); Liliales (Lilium, Liliaceae); Pandanales (Pandanus, Pandanaceae); Dioscoreales (Tacca, Dioscoreaceae); Petrosaviales (Japonolirion, Petrosaviaceae); Alismatales (Amorphophallus, Araceae); and Acorales (Acorus, Acoraceae).

Fig. 1 –Strict consensus of 16 MP trees for 7-gene data set of Chase et al. (2006). Brackets highlight monocot orders; basal angiosperm outgroups are at the base of the tree; bootstrap support for each node is color-coded. Hollow dots indicate non-green, mycoheterotrophic (MHT) taxa. Numbers indicate 13 problematic nodes/regions.