Progress 04/01/98 to 03/31/03
Outputs
A major paper is in press, reporting on phylogenetic relationships among 218 species that represent every major lineage of the monocots, as well as related dicots. The analysis is based on nucleotide sequence variation in one gene of the mitochondrial genome (atpA) and one of the chloroplast genome (rbcL). Because the data set includes a mitochondrial gene, it is not exclusively dependent upon genes of the chloroplast genome, which are often lacking or highly modified in nonphotosynthetic plants. Therefore, the data set includes several nonphotosynthetic plants, including three representatives of the enigmatic family Triuridaceae, and provides a placement for them among other monocots. We also examined the distribution of three inversions in the plastid genome, and several other structural mutations in the chloroplast and nuclear genomes. Among significant discoveries are the presence in the Australian family Ecdeiocoleaceae of an inversion in the plastid genome that
previously was believed to occur only in the grasses (Poaceae) and the related family Joinvilleaceae. On the basis of additional evidence, Ecdeiocoleaceae may be a stronger candidate as sister of the grass family than Joinvilleaceae. Also, we have discovered an apparently diagnostic intron loss in the gene GBSSI in grass tribes Poeae and Aveneae (which include many economically important taxa such as oats, bluegrasses, and fescues, and which together constitute the sister of the economically crucial tribe Triticeae, which includes wheat and its relatives). The overall phylogenetic structure that emerges for the monocots is one in which the generally aquatic group of Alismatid families, along with Araceae and Acorus, are sister of a lineage that includes all other monocots, within which a series of 'Lilioid' monocots diverge (Liliales, Asparagales, Pandanales, and Dioscoreales) from a line that includes the commelinids, which includes all other monocots. Within the commelinids, which
has been the main focus of our inquiries, the palms (Arecaceae) and the Dasypogonaceae are early-diverging elements from a line that includes the Zingiberales, Commelinales, Rapateaceae, Bromeliales, Cyperales, Poales, and a series of small families that traditionally have been difficult to place. Within the Poales, continuing studies of the grasses (Poaceae) have resulted in a comprehensive phylogeny for the family, and in a clarification of relationships among the various families of the overall group. There is a growing body of evidence in support of a southern hemisphere origin of Poales, where Restionaceae sens. lat. has diversified, particularly in Australia and southern Africa, while Poaceae (the grasses), initially inhabiting the forest understory, diversified as three major lineages: the bamboos (which have largely remained in tropical and subtropical forested environments), the PACCAD clade (which have moved into arid and semi-arid regions, and which include all C4 lineages
within the family), and the Pooideae, which principally inhabit temperate and boreal regions.
Impacts
A comprehensive phylogeny of the monocots, as well as one of the economically crucial family Poaceae, and its closest relatives, will inform studies in economic botany, comparative genomics, plant breeding, rangeland management, and other areas that rely on an understanding of evolutionary relationships in these groups. Clarification of the origin of the grass family and its closest relatives has important implications concerning the origin of the various unique features of grasses. All of this work, as a collaborative effort by myself and Dennis Stevenson (New York Botanical Garden) has employed several students and postdoctoral associates, and thus has contributed to human resource development.
Publications
- Michelangeli, F.A., Davis, J.I., and Stevenson, D.W. 2003. Phylogenetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from the mitochondrial and plastid genomes. Amer. J. Bot. 90:93-106.
- Davis, J.I., Stevenson, D.W., Petersen, G., Seberg, O., Campbell, L.M., Freudenstein, J.V., Goldman, D.H., Hardy, C.R., Michelangeli, F.A., Simmons, M.P., Specht, C.D., Vergara-Silva, F., and Gandolfo, M.A. 2004. A phylogeny of the monocots, as inferred from rbcL and atpA sequence variation, and a comparison of methods for calculating jackknife and bootstrap values. Syst. Bot.
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Progress 01/01/02 to 12/31/02
Outputs
During the past year a major manuscript was completed, summarizing phylogenetic relationships among 218 species representing every major lineage of the monocots, as well as related dicots. The analysis is based on one gene of the mitochondrial genome (atpA) and one of the chloroplast genome (rbcL). Because the data set is not based exclusively on genes of the chloroplast genome, which are often lacking or highly modified in nonphotosynthetic plants, the data set includes several such plants and provides a phylogenetic placement for them. We have also examined the distribution of three inversions in the chloroplast genome, initially considered specific to the grasses. In an earlier study with J. Doyle we demonstrated that the grass family is the only lineage with all three, while one other family, Joinvilleaceae has two, and Restionaceae has one, thus supporting a phylogenetic structure in which Joinvillea is sister of the grasses. We have determined that another small
plant family, Ecdeiocoleaceae, also has two of the inversions, and thus is as strong a candidate as Joinvilleaceae as the closest relative of the grasses. This particular character, as compelling as it is, cannot be regarded as definitive, but the same relationship also is supported by our overall phylogenetic analysis of atpA, rbcL, and a suite of structural characters. The overall phylogenetic structure that emerges from these studies is one in which the generally aquatic group of Alismatid families, along with Araceae and Acorus, are sister of a lineage that includes all other monocots, within which a series of "Lilioid" monocots diverge (Liliales, Asparagales, Pandanales, and Dioscoreales) from a major lineage, the Commelinids, which includes all other monocots. Within the Commelinids, which is the main focus of our inquiries regarding the grass family, the palms (Arecaceae) and the Dasypogonaceae are early-diverging elements. Among the remaining groups within this clade are the
Zingiberales/Commelinales, Rapateaceae, Bromeliales, Cyperales, Poales, and a series of small families that traditionally have been difficult to place. Within the Poales, continuing studies of the grasses (Poaceae) have resulted in a comprehensive phylogeny for the family, and in a clarification of relationships among the various families of the overall group. There is a growing body of evidence in support of a southern hemisphere origin of Poales, where Restionaceae sens. lat. has diversified, particularly in Australia and southern Africa, while Poaceae (the grasses), initially inhabiting the forest understory, diversified as three major lineages: the bamboos (which have largely remained in tropical and subtropical forested environments), the PACCAD clade (which have moved into arid and semi-arid regions, and which include all C4 lineages within the family), and the Pooideae, which principally inhabit temperate and boreal regions.
Impacts
A comprehensive phylogeny of the monocots, as well as one of the economically crucial family Poaceae, and its closest relatives, will inform studies in economic botany, genomics, plant breeding, rangeland management, and other areas that rely on an understanding of evolutionary relationships in these groups. Clarification of the origin of the grass family, and its closest relatives, has important implications concerning the origin of the various unique features of grasses. All of this work, as a collaborative effort by myself and Dennis Stevenson (New York Botanical Garden) has employed several students and postdoctoral associates, and thus has contributed to human resource development.
Publications
- Michelangeli, F.A., J.I. Davis, and D.W. Stevenson. 2003. Phylogenetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from the mitochondrial and plastid genomes. Amer. J. Bot. 90:93-106.
- Davis, J.I., D. W. Stevenson, G. Petersen, O. Seberg, L.M. Campbell, J.V. Freudenstein, D.H. Goldman, C.R. Hardy, F.A. Michelangeli, M.P. Simmons, and C.D. Specht. 2003. A phylogeny of the monocots, as inferred from rbcL and atpA sequence variation. In press, Systematic Botany.
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Progress 01/01/01 to 12/31/01
Outputs
During the past year the working data set for the monocots has expanded to over 250 taxa, each of which is scored for the plastid-encoded gene rbcL, two mitochondrion-encoded genes (atpA and cob), and 150 structural characters (representing variation in morphological, anatomical, embryological, developmental, biochemical, and palynological features). In addition to a broad representation of monocots, the taxon sample includes representative Magnoliid and tricolpate dicots, plus several gymnosperms, as outgroups. We have also examined the distribution of three inversions in the chloroplast genome, initially considered specific to the grasses. In an earlier study with J. Doyle we demonstrated that the grass family is the only lineage with all three, but that Joinvilleaceae has two, and Restionaceae has one, thus supporting a phylogenetic structure in which Joinvillea is sister of the grasses. We have recently determined that another group also has two of the inversions,
and thus is equally well supported as sister of the grasses. This discovery is further substantiated by relationships supported by the overall phylogenetic analysis. The overall phylogenetic structure that is emerging is one in which Alismatids, Arales, and Acorus are sister of a lineage that includes all other monocots, and in which there is a pectinate arrangement of five additional lineages, these being Liliales, Asparagales, Pandanales, Dioscoreales, and Commelinids. Within the latter group, which is the main focus of the analysis, the palms, possibly along with Dasypogonaceae, are sister of the remaining elements of the clade, with the other major lineages being Zingiberales/Commelinales, Rapateaceae, Bromeliales, Cyperales, and Poales. Within the last of these groups, continuing studies of the grasses (Poaceae) have resulted in a comprehensive phylogeny for the family, and in a clarification of relationships among the various families of the Poales. There is a growing body of
evidence in support of a southern hemisphere origin of Poales, where Restionaceae sens. lat. has diversified, particularly in Australia and southern Africa, while Poaceae (the grasses), initially inhabiting the forest understory, diversified as three major lineages: the bamboos (which have largely remained in tropical and subtropical forested environments), the PACCAD clade (which have moved into arid and semi-arid regions, and which include all C4 lineages within the family), and the Pooideae, which principally inhabit temperate and boreal regions.
Impacts
A comprehensive phylogeny of the monocots, as well as one of the economically crucial family Poaceae, will inform studies in economic botany, genomics, plant breeding, rangeland management, and other areas that rely on an understanding of evolutionary relationships in these groups. Clarification of the origin of the grass family, and its closest relatives, has important implications concerning the origin of the various unique features of grasses. All of this work, as a collaborative effort by myself and Dennis Stevenson (New York Botanical Garden) has employed several students and postdoctoral associates, and thus has contributed to human resource development.
Publications
- Grass Phylogeny Working Group (N.P. Barker, L.G. Clark, J.I. Davis, M.R. Duvall, G.F. Guala, C. Hsaio, E.A. Kellogg, H.P. Linder, R. Mason-Gamer, S. Mathews, M. Simmons, R. Soreng, and R.E. Spangler). 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Ann. Mo. Bot. Gard. 88:373-457.
- Hardy, C.R. 2001. Systematics of Cochliostema, Geogenanthus, and an undescribed genus in the Spiderwort family, Commelinaceae. Ph.D. Dissertation, Cornell University, Ithaca, NY, USA.
- Flores, H. and J.I. Davis. 2001. A cladistic analysis of Atripliceae (Chenopodiaceae) based on morphological data. J. Torrey Bot. Soc. 128:297-319.
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Progress 01/01/00 to 12/31/00
Outputs
During the past year our working data set for the monocots has expanded to over 200 taxa, each of which is scored for the plastid-encoded gene rbcL, two mitochondrion-encoded genes (atpA and cob), and 150 structural characters (representing variation in morphological, anatomical, embryological, developmental, biochemical, and palynological features). In addition to a broad representation of monocots, the taxon sample includes representative Magnoliid and tricolpate dicots, plus several gymnosperms, as outgroups. The overall phylogenetic structure for the monocots that is emerging is one in which Alismatids, Arales, and Acorus are sister of a lineage that includes all other monocots, and in which there is a pectinate arrangement of five additional lineages, these being Liliales, Asparagales, Pandanales, Dioscoreales, and Commelinids. Within the latter group, which is the main focus of the analysis, the palms are sister of the remaining elements of the clade, with the
other major lineages being the Dasypogonaceae, the Zingiberales/Commelinales, Rapateaceae, Bromeliales, Cyperales, and Poales. Within the last of these groups, continuing studies of the grasses (Poaceae) have resulted in a comprehensive phylogeny for the family, and in a clarification of relationships among the various families of the Poales. There is a growing body of evidence in support of a southern hemisphere origin of Poales, where Restionaceae sens. lat. has diversified, particularly in Australia and southern Africa, while Poaceae (the grasses), initially inhabiting the forest understory, diversified as three major lineages: the bamboos (which have largely remained in tropical and subtropical forested environments), the PACCAD clade (which have moved into arid and semi-arid regions, and which include all C4 lineages within the family), and the Pooideae, which principally inhabit temperate and boreal regions.
Impacts
A comprehensive phylogeny of the monocots, as well as one of the economically crucial family Poaceae, will inform studies in economic botany, genomics, plant breeding, rangeland management, and other areas that rely on an understanding of evolutionary relationships in these groups. This work, as a collaborative effort by myself and Dennis Stevenson (New York Botanical Garden) has employed several students and postdoctoral associates, and thus has contributed to their training.
Publications
- Stevenson, D.W., J.I. Davis, J.V. Freudenstein, C.R. Hardy, M.P. Simmons, and C.D. Specht. 2000. A phylogenetic analysis of the monocotyledons based on morphological and molecular character sets, with comments onthe placement of Acorus and Hydatellaceae. Pp. 17-24 in Monocots - Systematics and Evolution - Vol. 1 of Proceedings of the Second International Conference on the Comparative Biology of the Monocots, Sydney, September 1998, eds K.L. Wilson and D.A. Morrison. CSIRO, Melbourne.
- Grass Phylogeny Working Group (N.P. Barker, L.G. Clark, J.I. Davis, M.R. Duvall, G.F. Guala, C. Hsaio, E.A. Kellogg, H.P. Linder, R. Mason-Gamer, S. Mathews, R. Soreng, and R. Spangler. 2000. A phylogeny of the grass family (Poaceae), as inferred from eight character sets. Pp. 3-7 in Grasses - Systematics and Evolution - Vol. 2 of Proceedings of the Second International Conference on the Comparative Biology of the Monocots, Sydney, September 1998, eds S.W.L. Jacobs and J. Everett. CSIRO, Melbourne.
- Soreng, R.J. and J.I. Davis. 2000. Phylogenetic structure in Poaceae subfamily Pooideae as inferred from molecular and morphological characters: misclassification versus reticulation. Pp. 61-74 in Grasses - Systematics and Evolution - Vol. 2 of Proceedings of the Second International Conference on the Comparative Biology of the Monocots, Sydney, September 1998, eds. S.W.L. Jacobs and J. Everett. CSIRO, Melbourne.
- Grass Phylogeny Working Group (N.P. Barker, L.G. Clark, J.I. Davis, M.R. Duvall, G.F. Guala, C. Hsaio, E.A. Kellogg, H.P. Linder, R. Mason-Gamer, S. Mathews, M. Simmons, R. Soreng, and R.E. Spangler. 2000 in press. Phylogeny and subfamilial classification of the grasses (Poaceae). Ann. Mo. Bot. Gard.
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Progress 01/01/99 to 12/31/99
Outputs
During the past year our working data set for the monocots was expanded from the 53 representative taxa previously scored for four character sets (morphology, mapped chloroplast DNA restriction sites, and nucleotide sequences of the plastid-encoded gene rbcL and the mitochondrion-encoded gene atpA) to over 200 taxa that are scored for up to five character sets each (the four that are named above plus an additional mitochondrion-encoded gene, cob). The taxon sample has been broadened to include representative Magnoliid and tricolpate dicots, plus several gymnosperms. Preliminary findings indicate that these data, particularly by inclusion of the slowly evolving mitochondrial genes atpA and cob, are useful in the analysis of the deepest relationships within the seed plants. Analysis of this matrix supports the conclusion that the deepest branch within the monocots is not between Acorus and all other monocots (as suggested by other analyses) but between a clade that
includes all sampled elements of Alismatales, Najadales, and Arales, and Acorus, and a second clade that includes all other monocots. Within the latter group a series of lineages diverge in sequence (Dioscoreales, Asparagales, Liliales, Pandanales) from the Commelinid clade, which includes Arecales, Zingiberales, Commelinales, Typhales, Bromeliales, Poales, Cyperales, and additional groups such as Dasypogonaceae, Rapateaceae, Eriocaulaceae, and Xyridaceae. Continuing studies of the grasses (Poaceae) have resulted in a clarification of relationships within Pooideae, the major group of C3 grasses of Earth's temperate regions.
Impacts
(N/A)
Publications
- Davis, J.I. 1999. Monophyly, populations, and species. Pp. 139-170 in: Molecular systematics and plant evolution, eds. P.M. Hollingsworth, R.M. Bateman, and R.J. Gornall. Taylor & Francis, London.
- Zink, R.M. and J.I. Davis. 1999. New perspectives on the nature of species. Pp. 1505-1518 in: Proceedings of the 22nd International Ornithological Congress, Durban, eds. N.J. Adams and R.H. Slotow. BirdLife South Africa, Johannesburg [published on compact disc].
- Grass Phylogeny Working Group (N. Barker, L. Clark, J. Davis, M. Duvall, G. Guala, C. Hsiao, E. Kellogg, R. Mason-Gamer, S. Mathews, R. Soreng, and R. Spangler). 1999 in press. A phylogeny of the grass family (Poaceae), as inferred from eight character sets. Symposium volume from Monocots II, Sydney, Australia.
- Soreng, R.J. and J.I. Davis. 1999 in press. A cladistic analysis of Poaceae subfamily Pooideae. Symposium volume from Monocots II, Sydney, Australia.
- Stevenson, D.W., J.I. Davis, J.V. Freudenstein, C.R. Hardy, M.P. Simmons, and C.D. Specht. 1999 in press. A phylogenetic analysis of the monocotyledons based on morphological and molecular character sets, with comments on the placement of Acorus and Hydatellaceae. Symposium volume from Monocots II, Sydney, Australia.
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Progress 01/01/98 to 12/31/98
Outputs
During the past year our working data set for the monocots was expanded to include 53 representative taxa scored for four character sets (morphology, mapped chloroplast DNA restriction sites, and nucleotide sequences of the plastid-encoded gene rbcL and the mitochondrion-encoded gene atpA). The taxon set includes representatives of 20 of the 23 orders recognized in the comprehensive treatment of monocots by Dahlgren et al (1985). Analysis of this matrix supports conclusion that the deepest branch within the monocots is between a clade that includes all sampled elements of Alismatales, Najadales, and Arales (including Acorus, which is resolved as more closely related to Alismatales and Najadales than to the other sampled elements of Arales), and a second clade that includes all other monocots. Within the latter group, a lineage consisting of two elements of Dioscoreales (Dioscorea and Tacca) is resolved as the sister of all remaining monocots. The remaining monocots
fall into three major clades, relationships among which are unresolved. The first of these three clades comprises Melanthiales, two additional elements of Dioscoreales (Trillium and Smilax), and Alstroemeria (of Liliales). The second clade consists of two major subclades, the first of which includes Velloziales, Cyclanthales, and Pandanales, and the second of which includes Asparagales plus Sisyrinchium (of Liliales). The third major clade includes all remaining elements of the monocots; within this clade, Arecales are sister of a clade that comprises two main subclades, the first of which includes Zingiberales, Haemodorales, Philydrales, Pontederiales, and Commelinaceae (of Commelinales), the second of which includes Bromeliales, Rapateaceae (of Commelinales), Typhales, Eriocaulales, Cyperales, and Poales. As interpreted with respect to this phylogeny, a petaloid perianth is plesiomorphically present in the monocots, lost at least seven times, and never regained. Several other
characters also are homoplasious in most-parsimonious trees, but useful as synapomorphies in particular regions of the phylogeny; this group includes reticulate leaf venation, epicuticular waxes, simultaneous microsporogenesis, porate pollen, apocarpy, and orthotropous ovules.
Impacts
(N/A)
Publications
- avis, J.I., M.P. Simmons, D.W. Stevenson, and J.F. Wendel. 1998. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atpA sequences. Syst. Biol. 47:282-310.
- Doyle, J.J. and J.I. Davis. 1998. Homology in molecular phylogenetics: a parsimony perspective. Pp. 101-131 in: Molecular systematics of plants II, eds. D.E. Soltis, P.S. Soltis, and J.J Doyle. Kluwer,
- Soreng, R.J. and J.I. Davis. 1998. Phylogenetics and character evolution in the grass family (Poaceae): Simultaneous analysis of morphological and chloroplast DNA restriction site character sets. Bot. Rev. 64:1-85.
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