Monocots (including such groups as grasses, palms, orchids, and philodendrons) include more than 65,000 species of flowering plants, occur in almost all habitats, and provide the great majority of the human diet. A definitive family tree for this group will be developed and used to understand the broad-scale evolution of monocots over geologic time. A total of 23 genes in 601 species, whole chloroplast genomes in 175 species, and all genes expressed in 50 species will be sequenced and used to reconstruct the evolutionary history of this group. Additionally, phenotypic data from living and fossil species will be collected, and all data will be analyzed integratively to provide a comprehensive understanding of monocot evolution.
The resulting family tree will provide the foundation for many new studies in physiology, ecology, biogeography, and genomics of flowering plants. Web access to all data and results will be provided to researchers and K-12 teachers and students. Several post-doctoral fellows, graduate students, and undergraduates will be trained, and four young faculty will be supported. A museum exhibit on the evolution of flowering plants will be produced for high-profile venues in New York, Chicago, Denver, and Berkeley, and a children's monocot garden exhibit will be developed at the New York Botanical Garden. Posters illustrating monocot diversity and evolution will be distributed to colleges, and staff will give talks at public high schools.
This project was part of a broader collaborative study aimed at clarifying broad-scale relationships among the monocots, the economically most important important lineage of flowering plants and a source of most of the human diet, including such diverse groups as the grasses, sedges, palms, gingers, bananas, onions, orchids, aroids, and seagrasses. We succeeded in using powerful new sources of data obtained through next-generation DNA sequencing to resolve relationships among families in five of the twelve monocot orders, and in the large family Orchidaceae that comprises about 40% of all monocots and roughly 8% of all land plant species. Using sequences of entire chloroplast DNA complement (plastome) of over 100 monocots representing several dozen families, we identified the closest relatives of the economically paramount grass family and resolved relationships among all families in its order Poales (which contains the grasses, sedges, and 13 other lineages). We showed that wind pollination in the order Poales has arisen five times independently, and characterized some additional factors promoting wind pollination and its frequent evolution in this order. We demonstrated that the bromeliad family – whose affinities have long been obscure based on both morphology and DNA sequences – are sister to the remainder of the order Poales, and with its ancestor having diverged from the others roughly 100 million years ago. Within the bromeliads, we and our international collaborators produced a new phylogeny showing that the present-day genera and subfamilies began diverging from each other only 23 million years ago. Our data support a deductive model for bromeliad evolution, helping account for the sequences in which several key traits (epiphytism, the tank habit, avian pollination, life in montane habitats) evolved and in which several biogeographic areas in the New World Tropics were colonized. We found that the net rates of species diversification in bromeliads were most closely tied to life in geographically extensive cordilleras (the Andes and the Serra do Mar in Brazil), to the evolution of epiphytism and the tank habit, and to adaptation to hummingbird pollination. We produced the first fully resolved, strongly supported family tree (or phylogeny) for the orchids based on over 60,000 aligned bases from the coding regions of the chloroplast genome. Our phylogeny implies that this highly diverse group first arose about 100 million years ago in Australia, dispersed to South America, from there independently to found lineages in Africa, North America, and Asia, and from Asia subsequently back to the Americas. Rates of net species diversification first accelerated not at the base of the orchid family, but with the ancestor of the sister subfamilies Orchidoideae and Epidendroideae, comprised primarily of temperate ground-dwelling orchids and tropical epiphytic species, respectively. Subsequently, there was an even greater acceleration of diversification in several tribes of the epidendroids. Species diversification appear to be stimulated by the acquisition of pollinia (packages of pollen moved en masse from one flower to the next by pollinators), of the epiphytic habit, and of some reproductive traits in some of the epidroids (e.g., deceit of pollinators). New insights into relationships in four other orders of monocots were also obtained via the use of DNA sequences for whole chloroplast genomes, as well as into relationships among various groups that have lost the power of photosynthesis and parasitize soil fungi and the green plants that feed them with sugars. Our work on the theoretical behavior of comparative methods on very large trees is promoting the utility and appropriate usage of these comparative methods is systematics research. This contribution will be of interest far beyond monocots, and especially to other projects that are clarifying our view of the overall Tree of Life. Research on the statistical analysis of very large data sets used to infer family trees have uncovered similarities with the theory of spatial statistics. As a consequence, progress in comparative methods is gaining interest from the spatial statistics community. This project resulted in the training of one post-doctoral associate, three PhD students, two Master's students, and three undergraduates in various aspects of next-generation sequencing, the derivation of family trees (phylogenies) from DNA sequence data, and the use of such phylogenies to reconstruct the past, including the historical pattern of movement of different plant groups across the globe, the acquisition of particular traits and apparent adaptations in particular environments, and the acceleration of net rates of speciation by certain environmental conditions and plant traits. Over 100 chloroplast genomes or parts thereof have been or soon will be uploaded to GenBank, forming an invaluable permanent resource with which to infer patterns of relationships, phenotypic evolution, geographic spread, and species diversification in the monocots.
