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, comprise nearly 25% of all species and families of flowering plants, and provide – directly or indirectly – the basis for most of the human diet. 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 domains and including many highly reduced, mycoheterotrophic taxa that often confound molecular and morphological analyses. We will sequence the entire plastid genomes (> 80 genes) of 150 taxa (for a total of 175 monocots and >230 seed plants) to permit powerful analyses based on both gene content and order. We will sequence 23 genes (29.2 unaligned kb) from all three genomes (plastid, mitochondrion, nucleus) as well as entire transcriptomes (ca. 100 single-copy nuclear genes) across nested sets of 601, 175, and 50 taxa, respectively, representing all monocot orders and families and up to 24% of all genera. Our innovative use of transcriptomes and single-copy nuclear genes (PHYC, RPB2) will provide an avalanche of nuclear and create a model system for studies of gene-expression evolution. We will analyze these data using parsimony, Bayesian, and maximum-likelihood methods, drawing on the extraordinary power of the CIPRES computer cluster and software. We will examine the stability of phylogenies obtained via supermatrix simulations involving the deletion of characters and taxa.  We will complete scoring of 223 morphological/anatomical 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 and a visual glossary of 223 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.

• Plastid genomes to be sequenced (pdf)
• Nested sets of 601, 175, and 50 taxa to be sequenced for organellar, ribosomal, and single-copy nuclear genes, as well as transcriptomes, 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.