A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Research output: Contribution to journal › Journal article › Research › peer-review

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A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values. / Davis, Jerrold I.; Stevenson, Dennis W.; Petersen, Gitte; Seberg, Ole; Campbell, Lisa M.; Freudenstein, John V.; Goldman, Douglas H.; Hardy, Christopher R.; Michelangeli, Fabian A.; Simmons, Mark P; Specht, Chelsea D.; Vergara-Silva, Francisco; Gandolfo, María.

In: Systematic Botany, Vol. 29, No. 3, 2004, p. 467-510.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Davis, JI, Stevenson, DW, Petersen, G, Seberg, O, Campbell, LM, Freudenstein, JV, Goldman, DH, Hardy, CR, Michelangeli, FA, Simmons, MP, Specht, CD, Vergara-Silva, F & Gandolfo, M 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', Systematic Botany, vol. 29, no. 3, pp. 467-510. https://doi.org/10.1600/0363644041744365

APA

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., & Gandolfo, M. (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. Systematic Botany, 29(3), 467-510. https://doi.org/10.1600/0363644041744365

Vancouver

Davis JI, Stevenson DW, Petersen G, Seberg O, Campbell LM, Freudenstein JV et al. A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values. Systematic Botany. 2004;29(3):467-510. https://doi.org/10.1600/0363644041744365

Author

Davis, Jerrold I. ; Stevenson, Dennis W. ; Petersen, Gitte ; Seberg, Ole ; Campbell, Lisa M. ; Freudenstein, John V. ; Goldman, Douglas H. ; Hardy, Christopher R. ; Michelangeli, Fabian A. ; Simmons, Mark P ; Specht, Chelsea D. ; Vergara-Silva, Francisco ; Gandolfo, María. / A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values. In: Systematic Botany. 2004 ; Vol. 29, No. 3. pp. 467-510.

Bibtex

@article{c98457e074c311dbbee902004c4f4f50,
title = "A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values",
abstract = "A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.",
author = "Davis, {Jerrold I.} and Stevenson, {Dennis W.} and Gitte Petersen and Ole Seberg and Campbell, {Lisa M.} and Freudenstein, {John V.} and Goldman, {Douglas H.} and Hardy, {Christopher R.} and Michelangeli, {Fabian A.} and Simmons, {Mark P} and Specht, {Chelsea D.} and Francisco Vergara-Silva and Mar{\'i}a Gandolfo",
year = "2004",
doi = "10.1600/0363644041744365",
language = "English",
volume = "29",
pages = "467--510",
journal = "Systematic Botany",
issn = "0363-6445",
publisher = "American Society of Plant Taxonomists",
number = "3",

}

RIS

TY - JOUR

T1 - A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

AU - Davis, Jerrold I.

AU - Stevenson, Dennis W.

AU - Petersen, Gitte

AU - Seberg, Ole

AU - Campbell, Lisa M.

AU - Freudenstein, John V.

AU - Goldman, Douglas H.

AU - Hardy, Christopher R.

AU - Michelangeli, Fabian A.

AU - Simmons, Mark P

AU - Specht, Chelsea D.

AU - Vergara-Silva, Francisco

AU - Gandolfo, María

PY - 2004

Y1 - 2004

N2 - A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

AB - A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

U2 - 10.1600/0363644041744365

DO - 10.1600/0363644041744365

M3 - Journal article

VL - 29

SP - 467

EP - 510

JO - Systematic Botany

JF - Systematic Botany

SN - 0363-6445

IS - 3

ER -

ID: 101723