Progress 09/01/03 to 08/31/08
Outputs
OUTPUTS: This phylogenetic analysis of the grass family (Poaceae), with a focus on the critical tribe Poeae, within subfamily Pooideae, was initiated in 2003, and work has proceeded apace. Five plastid-encoded genes and one nuclear-encoded gene have been sequenced from more than 150 representative taxa, and a well-resolved phylogenetic hypothesis based on the plastid genome. Most taxa in the analysis are drawn from subfamily Pooideae, and about half of these are from the tribe Poeae, which includes the fescues, bluegrasses, oats, timothy, and many other grasses of economic importance. Within Pooideae, relationships among tribes are as follows: The Poeae/Aveneae complex is sister of a clade that consists of Bromeae and Triticeae; Brachypodieae is sister of this clade; and the remaining tribes diverge from this large alliance in the following order: Diarrheneae; Meliceae; a complex group consisting of Phaenosperma, Duthiea, and other genera; Stipeae; Lygeeae plus Nardeae; and Brachyelytreae. Simultaneous analysis of morphological characters and the plastid-encoded genes highlights considerable incongruence between these two character sets among taxa of the Poeae/Aveneae complex, and a similar situation exists with respect to the plastid and nuclear genes. These results signify past hybridization among the taxa of this complex, indicating that the traditional division of the group into two tribes is artificial. The Poeae/Aveneae alliance includes many more species than the closely related tribe Triticeae, a polyploid complex that includes wheat, barley, rye, and about 300 other taxa. Details concerning patterns of hybridization among these taxa continue to be investigated. In the meantime, a comprehensive taxonomic system for the group, with 135 genera accommodated in 22 subtribes, within a single tribe, has been proposed to replace the traditional taxonomic system. Six of the subtribes have Aveneae-type plastid genomes, and this group includes Aveninae and Phalaridinae, as expected, but also Brizinae and Torreyochloinae, which lie within tribe Poeae in traditional systems. Similarly, the group with Poeae-type plastid genomes includes Loliinae and Poinae, as might have been expected, but also Alopecurinae and Airinae. Related studies have involved the analysis of relationships among monocots, with a focus on the complex order Poales (which includes the grasses), aimed at clarifying the ancestral characteristics and phylogenetic placement of the grass family and its closest relatives. PARTICIPANTS: Robert Soreng, Ph.D., grass systematist at the Smithsonian Institution (National Museum of Natural History), was an active participant in this research. He provided plant collections used in the study, and expertise concerning the structural features and taxonomy of the group. TARGET AUDIENCES: The principal target audience for this work is the systematics and ecology community, particularly those investigators and students who study grasses and grasslands. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The grass family is includes numerous species of critical economic importance, ranging from species that yield food for human consumption (rice, wheat, maize, oats, sugarcane, etc.), and range and pasture grasses that are consumed by domesticated animals (fescues, timothy, etc.). Grasses also are important elements of erosion management, and the group includes many noxious weeds as well as the bamboos and plants that serve many other purposes. A robust phylogeny of the family contributes to the work of scientists in all of these fields by highlighting relationships among taxa of economic importance (positive and negative) and other lesser-known taxa, and thereby provides opportunities for breeding, plant introductions, and related actions. Grasses also include model taxa used in studies of genetics, physiology, and development, and a clarification of relationships among these taxa and other grasses with different features contributes to our understanding of the origins and phylogenetic distributions of critical genetic and organismal charateristics.
Publications
- No publications reported this period
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Progress 10/01/06 to 09/30/07
Outputs
OUTPUTS: The goals of this project are to examine phylogenetic relationships among the grasses (the plant family Poaceae), a group that includes around 10,000 species, among which are numerous crop species (maize, wheat, rice, barley, etc.), forage species (bluegrasses, fescues, timothy, stipas, etc.) weed species (bromegrasses, crabgrass, etc.) and other groups (such as the bamboos), which are dominants in many natural and human-influenced habitats, and are variously for home construction, biofuels, etc. This study focuses on the critical tribe Poeae, within subfamily Pooideae. Five plastid-encoded genes and one nuclear-encoded gene have been sequenced from more than 150 representative taxa, and a well-resolved phylogenetic hypothesis based on the plastid genome has been generated. A synthesis of these molecular trees, along with morphological data for the group, has resulted in a new classification for the grasses, and in particular, of the subfamily Pooideae and tribe Poeae. More
than 850 DNA sequences generated in the course of this study have been or soon will be submitted to GenBank, where they will be available for study by other investigators. The classification, which is comprehensive for recognized genera of the Pooideae, is available on the internet, and it continues to be improved as the study proceeds. Numerous digital photographs of the taxa and critical characteristics of these grasses have been generated, and these will be added to the website, so that it can be used as a reference for identification, along with published descriptions and floristic treatments. The development of a robust phylogeny of the family, along with these internet resources, contributes to the work of scientists in all of these fields by highlighting relationships among taxa of positive and negative economic importance, and other lesser-known taxa, and thereby provides opportunities for breeding, plant introductions, and related actions. Grasses also include model taxa used
in studies of genetics, physiology, and development, and a clarification of relationships among these taxa and other grasses with different features contributes to our understanding of the origins and phylogenetic distributions of critical genetic and organismal charateristics. These studies also include analyses of monocot groups related to the grasses, and thus provide similar information with regard to sedges, lilies, palms, and other monocot groups.
PARTICIPANTS: Robert J. Soreng, an associate at the Smithsonian Institution, NMNH, is a collaborator on these studies of grasses. In particular, he played a critical role in the collection of plant matrials for study, and in the examination and scoring of morphological features of these taxa.
Impacts
The analyses have helped to clarify phylogenetic relationships and patterns of morphological and molecular evolution in the grasses, specifically within subfamily Pooideae and tribe Poeae. One curious aspect of the plastid DNA of grasses is that two genes that lie at opposite ends of the small single copy (SSC) region of the chloroplast genome, adjacent to the two inverted repeat (IR) regions, sometimes have portions extending into the IR region. The margins of these regions migrate, through time, as the portion of the genome that is duplicated (i.e., that lies in the IR region) increases and decreases. One result of the project was a survey for these characters across the grasses, and several variant forms of these structural features have been described and examined in a phylogenetic context. The results indicate that a portion of ndhH, generally ranging from 150 to 200 nucleotides in length, at the 5' end of the gene, was situated within the IR region in the first
grasses, and as such, there is a duplicate copy of this gene fragment lying in the other IR region, downstream from ndhF. This general state persists in most major grass lineages, in variously modified forms, but within most of the PACCAD the length of the duplicated portion of ndhH is reduced to just 1 or a few nucleotides. Within the PACCAD clade, a 10 to 30 nucleotide portion at the 3' end of ndhF extends into the IR region, and thus is repeated upstream from ndhH in the other IR copy. There are minor variants in all of these states, with the genes extending various numbers of nucleotides into the IR region in close relatives, as the boundaries of the genes and genome regions migrate. In addition to the major shift that occurs in the PACCAD clade, three additional migrations of a portion of ndhF into the IR region are observed in other taxa, and there are five additional shifts of a portion of ndhH into and out of the IR region. The locations of portions of these two genes,
relative to the IR/SSC boundaries, also are associated with shifts in evolutionary rates. Substantial shifts in evolutionary rates of the gene portions that have migrated into and out of the IR region were documented in the course of these studies. The phylogenetic analysis based on five plastid-encoded genes, plus a small portion of a sixth, has provided strong support for a highly resolved phylogenetic structure. The results support the recognition of 12 tribes within the Pooideae, with the largest, Poeae s.l. (corresponding to the Poeae/Aveneae complex), subdivided into 21 subtribes. The subtribes are provisional, and represent our attempts to reconcile phylogenetic relationships among taxa that have been sampled with basic knowledge of the morphology of taxa that have not been sampled. Also, it is becoming evident that hybridization may have occurred between members of different subtribes, and even between elements of different tribes of the subfamily. These analyses, in
combination with parallel analyses of morphology and the nuclear-encoded gene GBSSI (waxy), support the conclusion that major elements of Poeae/Aveneae complex have arisen as a result of hybridization.
Publications
- Davis, J.I. 2007. Torreyochloa. Pp. 607-609 in Flora of North America, vol. 24, eds. M.E Barkworth, K.M. Capels, S. Long, L.K. Anderton, and M.B. Piep. Oxford Univ. Press, New York.
- Davis, J.I. and L.M. Consaul. 2007. Puccinellia. Pp. 459-477 in Flora of North America, vol. 24, eds. M.E Barkworth, K.M. Capels, S. Long, L.K. Anderton, and M.B. Piep. Oxford Univ. Press, New York.
- Davis, J.I. and R.J. Soreng. 2007. A phylogenetic analysis of the grasses (Poaceae), with attention to subfamily Pooideae and structural features of the plastid and nuclear genomes, including an intron loss in GBSSI. Aliso 23:325-338.
- Duvall, M.R., J.I. Davis, L.G. Clark, J.D. Noll, D.H. Goldman, and J.G. Sanchez-Ken. 2007. Phylogeny of the grasses (Poaceae) revisited. Aliso 23:237-247.
- Fay, M.F., Chase, M.W., Ronsted, N., Devey, D.S., Pillon, Y., Pires, J.C., Petersen, G., Seberg, O., and Davis, J.I. 2006. Phylogenetics of Liliales: summarized evidence from combined analyses of five plastid and one mitochondrial loci. Aliso 22:559-565.
- Petersen G., Seberg, O., Davis, J.I., Goldman, D.H., Stevenson, D.W., Campbell, L.M., Michelangeli, F.A., Specht, C.D., Chase, M.W., Fay, M.F., Pires, J.C., Freudenstein, J.V., Hardy, C.R., and Simmons, M.P. 2006. Mitochondrial data in monocot phylogenetics. Aliso 22:52-62.
- Pires, J.C., Maureira, I.J., Givnish, T.J., Sytsma, K.J., Seberg, O., Petersen, G., Davis, J.I., Stevenson, D.W., Rudall, P.J., Fay, M.F., and Chase, M.W. 2006. Phylogeny, genome size, and chromosome evolution of Asparagales. Aliso 22:287-304.
- Rudall P.J., D.D. Sokoloff, M.V. Remizowa, J.G. Conran, J.I. Davis, T.D. Macfarlane, and D.W. Stevenson. 2007. Morphology of Hydatellaceae, an anomalous aquatic family recently recognized as an early-divergent angiosperm lineage. Amer. J. Bot. 94: 1073-1092.
- Soreng, R.J., J.I. Davis, and M.A. Voionmaa. 2007. A phylogenetic analysis of Poaceae tribe Poeae sensu lato based on morphological characters and sequence data from three plastid-encoded genes: evidence for reticulation, and a new classification for the tribe. Kew Bull. 62:425-454.
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Progress 01/01/06 to 12/31/06
Outputs
This phylogenetic analysis of the grass family (Poaceae), with a focus on the critical tribe Poeae, within subfamily Pooideae, was initiated in 2003, and work has proceeded apace. Five plastid-encoded genes and one nuclear-encoded gene have been sequenced from more than 150 representative taxa, and a well-resolved phylogenetic hypothesis based on the plastid genome. Most taxa in the analysis are drawn from subfamily Pooideae, and about half of these are from the tribe Poeae, which includes the fescues, bluegrasses, oats, timothy, and many other grasses of economic importance. Within Pooideae, relationships among tribes are as follows: The Poeae/Aveneae complex is sister of a clade that consists of Bromeae and Triticeae; Brachypodieae is sister of this clade; and the remaining tribes diverge from this large alliance in the following order: Diarrheneae; Meliceae; a complex group consisting of Phaenosperma, Duthiea, and other genera; Stipeae; Lygeeae plus Nardeae; and
Brachyelytreae. Simultaneous analysis of morphological characters and the plastid-encoded genes highlights considerable incongruence between these two character sets among taxa of the Poeae/Aveneae complex, and a similar situation exists with respect to the plastid and nuclear genes. These results signify past hybridization among the taxa of this complex, indicating that the traditional division of the group into two tribes is artificial. The Poeae/Aveneae alliance includes many more species than the closely related tribe Triticeae, a polyploid complex that includes wheat, barley, rye, and about 300 other taxa. Details concerning patterns of hybridization among these taxa continue to be investigated. In the meantime, a comprehensive taxonomic system for the group, with 135 genera accommodated in 22 subtribes, within a single tribe, has been proposed to replace the traditional taxonomic system. Six of the subtribes have Aveneae-type plastid genomes, and this group includes Aveninae and
Phalaridinae, as expected, but also Brizinae and Torreyochloinae, which lie within tribe Poeae in traditional systems. Similarly, the group with Poeae-type plastid genomes includes Loliinae and Poinae, as might have been expected, but also Alopecurinae and Airinae. Related studies have involved the analysis of relationships among monocots, with a focus on the complex order Poales (which includes the grasses), aimed at clarifying the ancestral characteristics and phylogenetic placement of the grass family and its closest relatives.
Impacts
The grass family is includes numerous species of critical economic importance, ranging from species that yield food for human consumption (rice, wheat, maize, oats, sugarcane, etc.), and range and pasture grasses that are consumed by domesticated animals (fescues, timothy, etc.). Grasses also are important elements of erosion management, and the group includes many noxious weeds as well as the bamboos and plants that serve many other purposes. A robust phylogeny of the family contributes to the work of scientists in all of these fields by highlighting relationships among taxa of economic importance (positive and negative) and other lesser-known taxa, and thereby provides opportunities for breeding, plant introductions, and related actions. Grasses also include model taxa used in studies of genetics, physiology, and development, and a clarification of relationships among these taxa and other grasses with different features contributes to our understanding of the
origins and phylogenetic distributions of critical genetic and organismal charateristics.
Publications
- Chase, M.W., Fay, M.F., Devey, D.S., Maurin, O., Roensted, N., Davies, T.J., Pillon, Y., Petersen, G., Seberg,, O., Tamura, M.N., Asmussen, C.B., Hilu, K., Borsch, T., Davis, J.I., Stevenson, D.W., Pires, J.C., Givnish, T.J., Sytsma, K.J., McPherson, M.A., Graham, S.W., and Rai, H.S. 2006. Multigene analyses of monocot relationships: a summary. Aliso 22:63-75.
- Davis, J.I., Petersen, G., Seberg, O., Stevenson, D.W., Hardy, C.R., Simmons, M.P., Michelangeli, F.A., Goldman, D.H., Campbell, L.M., Specht, C.D., and Cohen, J.I. 2006. Are mitochondrial genes useful for the analysis of monocot relationships? Taxon 55:857-870.
- Petersen, G., Seberg, O., Davis, J.I., and Stevenson, D.W. 2006. RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes. Taxon 55:871-886.
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Progress 01/01/05 to 12/31/05
Outputs
This phylogenetic analysis of the grass family (Poaceae), with a focus on the critical tribe Poeae, within subfamily Pooideae, was initiated in 2003, and work has proceeded apace. Five plastid-encoded genes have been sequenced from more than 150 representative taxa, and a well-resolved phylogenetic hypothesis based on this genome has been generated. Most taxa in the analysis are drawn from subfamily Pooideae, and about half of these are from the tribe Poeae, which includes the fescues, bluegrasses, oats, timothy, and many other grasses of economic importance. Within Pooideae, relationships among tribes are as follows: The Poeae/Aveneae complex is sister of a clade that consists of Bromeae and Triticeae; Brachypodieae is sister of this clade; and the remaining tribes diverge from this large alliance in the following order: Diarrheneae; Meliceae; a complex group consisting of Phaenosperma, Duthiea, and other genera; Stipeae; Lygeeae plus Nardeae; and Brachyelytreae.
Bambusoideae and Ehrhartoideae are placed as the closest relatives of Pooideae. Within Pooideae, the present results support a phylogenetic structure in which elements of the traditionally recognized tribes Poeae and Aveneae are intermixed to a degree that was previously unanticipated. This pattern suggest that the Poeae sens. lato is a large polyploid complex, or a group of smaller ones, resulting from successful hybridization among highly disparate elements. The Poeae/Aveneae alliance includes many more species than the closely related tribe Triticeae, a polyploid complex that includes wheat, barley, rye, and about 300 other taxa. The possibility that the Poeae/Aveneae complex is a major polyploid complex is being investigated by the incorporation of nuclear genes and morphological characters into the overall analysis. Related portions of this overall work involve the study of morphological diversity and phylogenetic structure among other monocots, which are the closest relatives of
the grass family, using morphology and genes of the plastid, mitochondrial, and nuclear genomes.
Impacts
The grass family is includes numerous species of critical economic importance, ranging from species that yield food for human consumption (rice, wheat, maize, oats, sugarcane, etc.), and range and pasture grasses that are consumed by domesticated animals (fescues, timothy, etc.). Grasses also are important elements of erosion management, and the group includes many noxious weeds as well as the bamboos and plants that serve many other purposes. A robust phylogeny of the family contributes to the work of scientists in all of these fields by highlighting relationships among taxa of economic importance (positive and negative) and other lesser-known taxa, and thereby provides opportunities for breeding, plant introductions, and related actions. Grasses also include model taxa used in studies of genetics, physiology, and development, and a clarification of relationships among these taxa and other grasses with different features contributes to our understanding of the
origins and phylogenetic distributions of critical genetic and organismal charateristics.
Publications
- Petersen G., O. Seberg, J.I. Davis, D. Goldman, D.W. Stevenson, L.M. Campbell, F.A. Michelangeli, C.D. Specht, M.W. Chase, M.F. Fay, J.C. Pires, J.V. Freudenstein, C.R. Hardy, and M.P. Simmons. 2006. Mitochondrial data in monocot phylogenetics. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
- Pires, J.C., I.J. Maureira, T.J. Givnish, K.J. Sytsma, O. Seberg, G. Petersen, J.I. Davis, D.W. Stevenson, P.J. Rudall, M.F. Fay, and M.W. Chase. 2006. Phylogeny, genome size, and chromosome evolution of Asparagales. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
- Davis, J.I., K.C. Nixon, and D.P. Little. 2005. The limits of conventional cladistic analysis. Pp. 119-147 in Parsimony, Phylogeny, and Genomics, ed. V. Albert. Oxford Univ. Press, New York.
- Chase, M.W., M.F. Fay, D. Devey, N. Ronsted, J. Davies, Y. Pillon, G. Petersen, O. Seberg, C.B. Asmussen, K. Hilu, T. Borsch, J.I. Davis, D.W. Stevenson, J.C. Pires, T.J. Givnish, K.J. Sytsma , and S.W. Graham. 2006. Multi-gene analyses of monocot relationships: a summary. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
- Fay, M.F., M.W. Chase, N. Ronsted, D.S. Devey, Y. Pillon, J.C. Pires, G. Petersen, O. Seberg, and J.I. Davis. 2006. Phylogenetics of Liliales: summarized evidence from combined analyses of five plastid and one mitochondrial loci. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
- Chase, M.W., M.F. Fay, D. Devey, N. Ronsted, J. Davies, Y. Pillon, G. Petersen, O. Seberg, C.B. Asmussen, K. Hilu, T. Borsch, J.I. Davis, D.W. Stevenson, J.C. Pires, T.J. Givnish, K.J. Sytsma , and S.W. Graham. 2006. Multi-gene analyses of monocot relationships: a summary. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
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Progress 01/01/04 to 12/31/04
Outputs
This phylogenetic analysis of the grass family (Poaceae), with a focus on the critical tribe Poeae, within subfamily Pooideae, was initiated in 2003, and work proceeded apace. Four plastid-encoded genes have been sequenced from more than 140 representative taxa, and a well-resolved phylogenetic hypothesis based on this genome has been generated. About half of the taxa in the analysis are drawn from the tribe Poeae, which includes the fescues, bluegrasses, oats, timothy, and many other grasses of economic importance. Present results continue to support the hypothesis that taxa of the traditional tribes Poeae and Aveneae are phylogenetically intermixed, and that the traditional groupings therefore are artificial. Several major clades have been identified, and a majority of these include representatives of both of the traditional groupings, so the transfer of a limited number of taxa would not reconcile the existing system with the relationships that are being
discovered. This pattern raises the possibility that Poeae sens. lato may be a large polyploid complex, or a group of smaller ones, which would include many more taxa of hybrid origin than the well-known tribe Triticeae, which includes wheat, barley, rye, and about 300 other taxa, and is a major constituent of the sister group of Poeae sens. lat. This possibility is currently being investigated by the incorporation of nuclear genes and morphological characters into the overall analysis. Within Pooideae, relationships among tribes, as currently resolved, are as follows: The Poeae/Aveneae complex is sister of a clade that consists of Bromeae and Triticeae; Brachypodieae is sister of this clade, and Diarrheneae and Meliceae are the next two lineages to diverge from this large alliance. The earlier-diverging lineages within the subfamily are Brachyelytreae, Nardeae, Lygeeae, and Stipeae.
Impacts
The grass family is includes numerous species of critical economic importance, ranging from species that yield food for human consumption (rice, wheat, maize, oats, sugarcane, etc.), and range and pasture grasses that are consumed by domesticated animals (fescues, timothy, etc.). Grasses also are important elements of erosion management, and the group includes many noxious weeds as well as the bamboos and plants that serve many other purposes. A robust phylogeny of the family contributes to the work of scientists in all of these fields by highlighting relationships among taxa of economic importance (positive and negative) and other lesser-known taxa, and thereby provides opportunities for breeding, plant introductions, and related actions. Grasses also include model taxa used in studies of genetics, physiology, and development, and a clarification of relationships among these taxa and other grasses with different features contributes to our understanding of the
origins and phylogenetic distributions of critical genetic and organismal charateristics.
Publications
- Davis, J.I. and Soreng, R.J. 2005. A phylogenetic analysis of the grasses (Poaceae), with attention to subfamily Pooideae and structural features of the plastid and nuclear genomes, including an intron loss in GBSSI. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
- Duvall, M.R., Davis, J.I., Clark, L.G., Noll, J.D., Goldman, D.H. and Sanchez-Ken, J.G. 2005. Phylogeny of the grasses (Poaceae) revisited. Monocots III / Grasses IV: Systematics and Evolution. Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons.
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