Botany

Introduction When on board H.M.S. ‘Beagle,’ as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me...

@book{doi105962bhltitle59991,
    author = "Darwin, Charles and Darwin, Charles and Remnants, Edmonds \\&",
    title = "On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life /",
    year = "1859",
    booktitle = "John Murray eBooks",
    abstract = "Introduction When on board H.M.S. ‘Beagle,’ as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me...",
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@book{doi105962bhltitle82303,
    author = "Darwin, Charles and Murray, John and Clowes, William and Sons and Evans., Bradbury \\&",
    title = "On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life",
    year = "1859",
    url = "https://doi.org/10.5962/bhl.title.82303",
    doi = "10.5962/bhl.title.82303",
    openalex = "W4299541734"
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@article{crossref1870botany,
    title = "Botany",
    year = "1870",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/270557",
    doi = "10.1086/270557",
    number = "3",
    pages = "183-188",
    volume = "4"
}

@article{crossref1874botany,
    title = "Botany",
    year = "1874",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/271273",
    doi = "10.1086/271273",
    number = "2",
    pages = "116-120",
    volume = "8"
}

@article{crossref1879botany,
    title = "Botany",
    year = "1879",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/272411",
    doi = "10.1086/272411",
    number = "9",
    pages = "580-582",
    volume = "13"
}

@article{crossref1880botany,
    title = "BOTANY",
    year = "1880",
    journal = "Science",
    url = "https://doi.org/10.1126/science.os-1.26.306",
    doi = "10.1126/science.os-1.26.306",
    number = "26",
    pages = "306-306",
    volume = "os-1"
}

@article{crossref1889botany,
    title = "Botany",
    year = "1889",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/274993",
    doi = "10.1086/274993",
    number = "272",
    pages = "723-725",
    volume = "23"
}

@article{crossref1890botany,
    title = "Botany",
    year = "1890",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/275129",
    doi = "10.1086/275129",
    number = "281",
    pages = "473-476",
    volume = "24"
}

@misc{clements1920plant9,
    author = "Clements, F. E",
    title = "Plant Succession",
    year = "1920",
    howpublished = "An Analysis of the Development of Vegetation: Washington, D.C., Carnegie Institute, 388 p.; Publication No. 290",
    note = "talkorigins\_source = {true}; raw\_reference = {Clements, F. E., 1920, Plant Succession: An Analysis of the Development of Vegetation: Washington, D.C., Carnegie Institute, 388 p.; Publication No. 290.}"
}

@misc{braunblanquet1932plant5,
    author = "Braun-Blanquet, J",
    title = "Plant Sociology",
    year = "1932",
    howpublished = "The study of plant communities: New York, McGraw-Hill, 439 p.; [Translated and edited by G.D. Fuller and H.C. Conrad]",
    note = "talkorigins\_source = {true}; raw\_reference = {Braun-Blanquet, J., 1932, Plant Sociology: The study of plant communities: New York, McGraw-Hill, 439 p.; [Translated and edited by G.D. Fuller and H.C. Conrad].}"
}

@misc{copeland1936yellowstone11,
    author = "Copeland, J. J",
    title = "Yellowstone thermal myxophyceae",
    year = "1936",
    howpublished = "Annals of the New York Academy of Sciences, v. 36, p. 1-232",
    note = "talkorigins\_source = {true}; raw\_reference = {Copeland, J. J., 1936, Yellowstone thermal myxophyceae: Annals of the New York Academy of Sciences, v. 36, p. 1-232.}"
}

@misc{doctersvanleeuwen1936krakatau15,
    author = "Docters van Leeuwen, W. M",
    title = "Krakatau, 1833 to 1933",
    year = "1936",
    howpublished = "Ann. Jard. Botan. Buitenzorg, v. 56-57, p. 1-506",
    note = "talkorigins\_source = {true}; raw\_reference = {Docters van Leeuwen, W. M., 1936, Krakatau, 1833 to 1933: Ann. Jard. Botan. Buitenzorg, v. 56-57, p. 1-506.}"
}

@misc{seward1938the29,
    author = "Seward, A. C",
    title = "The story of the maidenhair tree",
    year = "1938",
    howpublished = "Science Programs, v. 32, p. 420-440",
    note = "talkorigins\_source = {true}; raw\_reference = {Seward, A. C., 1938, The story of the maidenhair tree: Science Programs, v. 32, p. 420-440.}"
}

@misc{elias1942tertiary17,
    author = "Elias, M. K",
    title = "Tertiary prairie grasses and other herbs from the High Plains, 41 of Geological Society of America, Special Paper",
    year = "1942",
    howpublished = "p. 1-176",
    note = "talkorigins\_source = {true}; raw\_reference = {Elias, M. K., 1942, Tertiary prairie grasses and other herbs from the High Plains, 41 of Geological Society of America, Special Paper: p. 1-176.}"
}

@article{brown1943some6,
    author = "Brown, R. W",
    title = "Some prehistoric trees of the United States",
    year = "1943",
    journal = "Journal of Forestry, v. 41, p. 861-868",
    note = "talkorigins\_source = {true}; raw\_reference = {Brown, R. W., 1943, Some prehistoric trees of the United States: Journal of Forestry, v. 41, p. 861-868.}"
}

@misc{arnold1947introduction2,
    author = "Arnold, C. A",
    title = "Introduction to Paleobotany",
    year = "1947",
    howpublished = "New York, McGraw-Hill, 433 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Arnold, C. A., 1947, Introduction to Paleobotany: New York, McGraw-Hill, 433 p.}"
}

@book{daubenmire1947plants12,
    author = "Daubenmire, R. F",
    title = "Plants and Environment",
    year = "1947",
    publisher = "New York, Wiley, 424 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Daubenmire, R. F., 1947, Plants and Environment: New York, Wiley, 424 p.}"
}

@misc{cheney1948metasequoia8,
    author = "Cheney, R. W",
    title = "Metasequoia discovery",
    year = "1948",
    howpublished = "American Scientist, v. 36, p. 490- 494",
    note = "talkorigins\_source = {true}; raw\_reference = {Cheney, R. W., 1948, Metasequoia discovery: American Scientist, v. 36, p. 490- 494.}"
}

@misc{clements1949dynamics10,
    author = "Clements, F. E",
    title = "Dynamics of Vegetation",
    year = "1949",
    howpublished = "New York, Hafner, 296 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Clements, F. E., 1949, Dynamics of Vegetation: New York, Hafner, 296 p.}"
}

@book{stebbins1949rates30,
    author = "Stebbins, G. L. and Jr",
    title = "Rates of evolution in plants, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution",
    year = "1949",
    publisher = "Princeton, Princeton University Press, p. 229-242; 474 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Stebbins, G. L., Jr., 1949, Rates of evolution in plants, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution: Princeton, Princeton University Press, p. 229-242; 474 p.}"
}

@article{cain1950lifeforms7,
    author = "Cain, S. A",
    title = "Life-forms and phytoclimate",
    year = "1950",
    journal = "Botanical Review, v. 16, p. 1- 32",
    note = "talkorigins\_source = {true}; raw\_reference = {Cain, S. A., 1950, Life-forms and phytoclimate: Botanical Review, v. 16, p. 1- 32.}"
}

@misc{florin1951evolution19,
    author = "Florin, R",
    title = "Evolution in cordiates and conifers",
    year = "1951",
    howpublished = "Acta Horticulture Bergiani, v. 15, p. 285-388",
    note = "talkorigins\_source = {true}; raw\_reference = {Florin, R., 1951, Evolution in cordiates and conifers: Acta Horticulture Bergiani, v. 15, p. 285-388.}"
}

@misc{daubenmire1956climate13,
    author = "Daubenmire, R. F",
    title = "Climate as a determinant of vegetation distribution in eastern Washington and northern Idaho",
    year = "1956",
    howpublished = "Ecological Monographs, v. 26, p. 131-154",
    note = "talkorigins\_source = {true}; raw\_reference = {Daubenmire, R. F., 1956, Climate as a determinant of vegetation distribution in eastern Washington and northern Idaho: Ecological Monographs, v. 26, p. 131-154.}"
}

@book{andrews1961studies1,
    author = "Andrews, H. N. and Jr",
    title = "Studies in Paleobotany",
    year = "1961",
    publisher = "New York, Wiley",
    note = "talkorigins\_source = {true}; raw\_reference = {Andrews, H. N., Jr., 1961, Studies in Paleobotany: New York, Wiley.}"
}

@misc{erhlich1964butterflies18,
    author = "Erhlich, P. R. and Raven, P. H",
    title = "Butterflies and plants",
    year = "1964",
    howpublished = "a study in coevolution: Evolution, v. 18, p. 586-608",
    note = "talkorigins\_source = {true}; raw\_reference = {Erhlich, P. R., and Raven, P. H., 1964, Butterflies and plants: a study in coevolution: Evolution, v. 18, p. 586-608.}"
}

Most plant communities consist of several or many species which compete for light, water, and nutrients. Species in a given community may be ranked by their relative success in competition; productivity seems to be the best measure of their success or importance in the community. Curves of decreasing productivity connect the few most important species (the dominants) with a larger number of species of intermediate importance (whose number primarily determines the community's diversity or richness in species) and a smaller number of rare species. These curves are of varied forms and are believed to express different patterns of competition and niche differentiation in communities. It is probably true of plants, as of animals, that no two species in a stable community occupy the same niche. Evolution of niche differentiation makes possible the occurrence together of many plant species which are partial, rather than direct, competitors. Species tend to evolve also toward habitat differentiation, toward scattering of their centers of maximum population density in relation to environmental gradients, so that few species are competing with one another in their population centers. Evolution of both niche and habitat differentiation permits many species to exist together in communities as partial competitors, with distributions broadly and continuously overlapping, forming the landscape's many intergrading communities.

@article{doi101126science1473655250,
    author = "Whittaker, R. H.",
    title = "Dominance and Diversity in Land Plant Communities",
    year = "1965",
    journal = "Science",
    abstract = "Most plant communities consist of several or many species which compete for light, water, and nutrients. Species in a given community may be ranked by their relative success in competition; productivity seems to be the best measure of their success or importance in the community. Curves of decreasing productivity connect the few most important species (the dominants) with a larger number of species of intermediate importance (whose number primarily determines the community's diversity or richness in species) and a smaller number of rare species. These curves are of varied forms and are believed to express different patterns of competition and niche differentiation in communities. It is probably true of plants, as of animals, that no two species in a stable community occupy the same niche. Evolution of niche differentiation makes possible the occurrence together of many plant species which are partial, rather than direct, competitors. Species tend to evolve also toward habitat differentiation, toward scattering of their centers of maximum population density in relation to environmental gradients, so that few species are competing with one another in their population centers. Evolution of both niche and habitat differentiation permits many species to exist together in communities as partial competitors, with distributions broadly and continuously overlapping, forming the landscape's many intergrading communities.",
    url = "https://doi.org/10.1126/science.147.3655.250",
    doi = "10.1126/science.147.3655.250",
    openalex = "W2035166278",
    references = "beauchamp1932competitive, doi101038163688a0, doi101086282070, doi101086282106, doi101086282286, doi101093biomet3812196, doi101126science13134091292, doi1023071411, doi1023071931600, doi1023071931976, doi1023071932254, doi1023071942268, doi1023071943563, doi1023072407089, doi1023072411924, doi104159harvard9780674865327, doi105962bhltitle4489, openalexw3035987306"
}

@misc{scagel1965an28,
    author = "Scagel, R. F. et al",
    title = "An Evolutionary Survey of the Plant Kingdom",
    year = "1965",
    howpublished = "Belmont, Wadsworth, 658 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Scagel, R. F. et al., 1965, An Evolutionary Survey of the Plant Kingdom: Belmont, Wadsworth, 658 p.}"
}

@misc{daubenmire1968plant14,
    author = "Daubenmire, R. F",
    title = "Plant Communities",
    year = "1968",
    howpublished = "New York, Harper \& Row, 300 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Daubenmire, R. F., 1968, Plant Communities: New York, Harper \& Row, 300 p.}"
}

@misc{mcneilly1968evolutionary27,
    author = "McNeilly, T. and Bradshaw, A. D",
    title = "Evolutionary processes in populations of copper tolerant Agrostis tenuis Sibth",
    year = "1968",
    howpublished = "Evolution, v. 22, p. 108-118",
    note = "talkorigins\_source = {true}; raw\_reference = {McNeilly, T., and Bradshaw, A. D., 1968, Evolutionary processes in populations of copper tolerant Agrostis tenuis Sibth: Evolution, v. 22, p. 108-118.}"
}

@article{crossref1969botany,
    title = "Botany: Roadside Botany",
    year = "1969",
    journal = "Nature",
    url = "https://doi.org/10.1038/2211090a0",
    doi = "10.1038/2211090a0",
    number = "5186",
    pages = "1090-1090",
    volume = "221"
}

@inproceedings{whittaker1969evolution31,
    author = "Whittaker, R. H",
    title = "Evolution of diversity in plant communities",
    year = "1969",
    booktitle = "Brookhaven Symposium on Biology, v. 22, p. 178-196",
    note = "talkorigins\_source = {true}; raw\_reference = {Whittaker, R. H., 1969, Evolution of diversity in plant communities: Brookhaven Symposium on Biology, v. 22, p. 178-196.}"
}

@book{joravsky1970the25,
    author = "Joravsky, D",
    title = "The Lysenko Affair",
    year = "1970",
    publisher = "Cambridge, Mass., Harvard University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Joravsky, D., 1970, The Lysenko Affair: Cambridge, Mass., Harvard University Press.}"
}

@article{gottlieb1973genetic24,
    author = "Gottlieb, L. D",
    title = "Genetic differentiation, sympatric speciation, and the origin of a diploid species of Stephanomeria",
    year = "1973",
    journal = "American Journal of Botany, v. 60, p. 545-553",
    note = "talkorigins\_source = {true}; raw\_reference = {Gottlieb, L. D., 1973, Genetic differentiation, sympatric speciation, and the origin of a diploid species of Stephanomeria: American Journal of Botany, v. 60, p. 545-553.}"
}

@article{crossref1974botany,
    title = "Botany",
    year = "1974",
    journal = "Science News",
    url = "https://doi.org/10.2307/3959424",
    doi = "10.2307/3959424",
    number = "16",
    pages = "252",
    volume = "106"
}

@techreport{mcandrews1976fossil26,
    author = "McAndrews, J. H",
    title = "Fossil history of man's impact on the Canadian flora",
    year = "1976",
    howpublished = "an example from southern Ontario: Canadian Botanical Association Bulletin, v. 9, p. 1-6",
    note = "talkorigins\_source = {true}; raw\_reference = {McAndrews, J. H., 1976, Fossil history of man's impact on the Canadian flora: an example from southern Ontario: Canadian Botanical Association Bulletin, v. 9, p. 1-6.}"
}

It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.

@article{doi101086283244,
    author = "Grime, J. P.",
    title = "Evidence for the Existence of Three Primary Strategies in Plants and Its Relevance to Ecological and Evolutionary Theory",
    year = "1977",
    journal = "The American Naturalist",
    abstract = "It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.",
    url = "https://doi.org/10.1086/283244",
    doi = "10.1086/283244",
    openalex = "W2055424972",
    references = "doi101038242344a0, doi101038250026a0, doi101086282454, doi101086282455, doi1015159781400881376, doi102307213332, doi1023072258728, doi10230725528056, doi1023073241344, doi105962bhltitle59991"
}

@misc{franks1979plants20,
    author = "Franks, J",
    title = "Plants, in Steel, R., and Harvey, A., eds., The Encyclopedia of Prehistoric Life",
    year = "1979",
    howpublished = "New York, McGraw-Hill, p. 163",
    note = "talkorigins\_source = {true}; raw\_reference = {Franks, J., 1979, Plants, in Steel, R., and Harvey, A., eds., The Encyclopedia of Prehistoric Life: New York, McGraw-Hill, p. 163.}"
}

@misc{galston1979the22,
    author = "Galston, A. W. and Slayman, C. L",
    title = "THe Not-So-Secret Life of Plants",
    year = "1979",
    howpublished = "American Scientist, v. 67, p. 337-344",
    note = "talkorigins\_source = {true}; raw\_reference = {Galston, A. W., and Slayman, C. L., 1979, THe Not-So-Secret Life of Plants: American Scientist, v. 67, p. 337-344.}"
}

@book{edwards1980early16,
    author = "Edwards, D",
    title = "Early Land Floras, in Panchen, A. L., ed., The Terrestrial Environment and the Origin of Land Vertebrates",
    year = "1980",
    publisher = "London, Academic Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Edwards, D., 1980, Early Land Floras, in Panchen, A. L., ed., The Terrestrial Environment and the Origin of Land Vertebrates: London, Academic Press.}"
}

@misc{baltscheffsky1981stepwise3,
    author = "Baltscheffsky, H",
    title = "Stepwise molecular evolution of bacterial photosynthetic energy conversion",
    year = "1981",
    howpublished = "BioSystems, v. 14, p. 49-56",
    note = "talkorigins\_source = {true}; raw\_reference = {Baltscheffsky, H., 1981, Stepwise molecular evolution of bacterial photosynthetic energy conversion: BioSystems, v. 14, p. 49-56.}"
}

@misc{bisacre1984the4,
    author = "Bisacre, M. and Carlisle, R. and Robertson, D. and Ruck, J",
    title = "The Illustrated Encyclopedia of Plants",
    year = "1984",
    howpublished = "New York, Exeter Books",
    note = "talkorigins\_source = {true}; raw\_reference = {Bisacre, M., Carlisle, R., Robertson, D., and Ruck, J., 1984, The Illustrated Encyclopedia of Plants: New York, Exeter Books.}"
}

@article{schmid1986origin,
    author = "Schmid, Rudolf and Hara, H.",
    title = "Origin and Evolution of Diversity in Plants and Plant Communities",
    year = "1986",
    journal = "Taxon",
    url = "https://doi.org/10.2307/1221326",
    doi = "10.2307/1221326",
    number = "2",
    openalex = "W2325499884",
    pages = "446",
    volume = "35"
}

@misc{goldberg1988plants23,
    author = "Goldberg, R. B",
    title = "Plants",
    year = "1988",
    howpublished = "Novel Developmental Processes: Science, v. 240, p. 1460-1467",
    note = "talkorigins\_source = {true}; raw\_reference = {Goldberg, R. B., 1988, Plants: Novel Developmental Processes: Science, v. 240, p. 1460-1467.}"
}

@misc{freidman1990double21,
    author = "Freidman, W. E",
    title = "Double fertilization in Ephedra, a nonflowering plant; its bearing on the origin of angiosperms",
    year = "1990",
    howpublished = "Science, v. 247, p. 951",
    note = "talkorigins\_source = {true}; raw\_reference = {Freidman, W. E., 1990, Double fertilization in Ephedra, a nonflowering plant; its bearing on the origin of angiosperms: Science, v. 247, p. 951.}"
}

@article{doi1023073243920,
    author = "Schuster, R. M. and Stewart, Wilson N. and Rothwell, Gar W.",
    title = "Paleobotany and the Evolution of Plants",
    year = "1994",
    journal = "The Bryologist",
    url = "https://doi.org/10.2307/3243920",
    doi = "10.2307/3243920",
    openalex = "W1977838623"
}

Abstract. Much confusion exists in the English‐language literature on plant invasions concerning the terms ‘naturalized’ and ‘invasive’ and their associated concepts. Several authors have used these terms in proposing schemes for conceptualizing the sequence of events from introduction to invasion, but often imprecisely, erroneously or in contradictory ways. This greatly complicates the formulation of robust generalizations in invasion ecology. Based on an extensive and critical survey of the literature we defined a minimum set of key terms related to a graphic scheme which conceptualizes the naturalization/invasion process. Introduction means that the plant (or its propagule) has been transported by humans across a major geographical barrier. Naturalization starts when abiotic and biotic barriers to survival are surmounted and when various barriers to regular reproduction are overcome. Invasion further requires that introduced plants produce reproductive offspring in areas distant from sites of introduction (approximate scales: > 100 m over 6 m/3 years for taxa spreading by roots, rhizomes, stolons or creeping stems). Taxa that can cope with the abiotic environment and biota in the general area may invade disturbed, seminatural communities. Invasion of successionally mature, undisturbed communities usually requires that the alien taxon overcomes a different category of barriers. We propose that the term ‘invasive’ should be used without any inference to environmental or economic impact. Terms like ‘pests’ and ‘weeds’ are suitable labels for the 50–80% of invaders that have harmful effects. About 10% of invasive plants that change the character, condition, form, or nature of ecosystems over substantial areas may be termed ‘transformers’.

@article{doi101046j14724642200000083x,
    author = "Richardson, David M. and Pyšek, Petr and Rejmánek, Marcel and Barbour, Michael G. and Panetta, F. D. and West, Carol J.",
    title = "Naturalization and invasion of alien plants: concepts and definitions",
    year = "2000",
    journal = "Diversity and Distributions",
    abstract = "Abstract. Much confusion exists in the English‐language literature on plant invasions concerning the terms ‘naturalized’ and ‘invasive’ and their associated concepts. Several authors have used these terms in proposing schemes for conceptualizing the sequence of events from introduction to invasion, but often imprecisely, erroneously or in contradictory ways. This greatly complicates the formulation of robust generalizations in invasion ecology. Based on an extensive and critical survey of the literature we defined a minimum set of key terms related to a graphic scheme which conceptualizes the naturalization/invasion process. Introduction means that the plant (or its propagule) has been transported by humans across a major geographical barrier. Naturalization starts when abiotic and biotic barriers to survival are surmounted and when various barriers to regular reproduction are overcome. Invasion further requires that introduced plants produce reproductive offspring in areas distant from sites of introduction (approximate scales: > 100 m over 6 m/3 years for taxa spreading by roots, rhizomes, stolons or creeping stems). Taxa that can cope with the abiotic environment and biota in the general area may invade disturbed, seminatural communities. Invasion of successionally mature, undisturbed communities usually requires that the alien taxon overcomes a different category of barriers. We propose that the term ‘invasive’ should be used without any inference to environmental or economic impact. Terms like ‘pests’ and ‘weeds’ are suitable labels for the 50–80\% of invaders that have harmful effects. About 10\% of invasive plants that change the character, condition, form, or nature of ecosystems over substantial areas may be termed ‘transformers’.",
    url = "https://doi.org/10.1046/j.1472-4642.2000.00083.x",
    doi = "10.1046/j.1472-4642.2000.00083.x",
    openalex = "W2163826476",
    references = "doi1010079781489972149, doi1010079789400958517, doi101046j13652745200000473x, doi101093auk1002507, doi1018900012965819990801522gpopia20co2, doi1023072257385, doi105281zenodo18199125, doi105962bhltitle59991, doi105962bhltitle82303, openalexw1550375751, openalexw2101875448, openalexw2990282461"
}

Summary The concept of plant functional type proposes that species can be grouped according to common responses to the environment and/or common effects on ecosystem processes. However, the knowledge of relationships between traits associated with the response of plants to environmental factors such as resources and disturbances (response traits), and traits that determine effects of plants on ecosystem functions (effect traits), such as biogeochemical cycling or propensity to disturbance, remains rudimentary. We present a framework using concepts and results from community ecology, ecosystem ecology and evolutionary biology to provide this linkage. Ecosystem functioning is the end result of the operation of multiple environmental filters in a hierarchy of scales which, by selecting individuals with appropriate responses, result in assemblages with varying trait composition. Functional linkages and trade‐offs among traits, each of which relates to one or several processes, determine whether or not filtering by different factors gives a match, and whether ecosystem effects can be easily deduced from the knowledge of the filters. To illustrate this framework we analyse a set of key environmental factors and ecosystem processes. While traits associated with response to nutrient gradients strongly overlapped with those determining net primary production, little direct overlap was found between response to fire and flammability. We hypothesize that these patterns reflect general trends. Responses to resource availability would be determined by traits that are also involved in biogeochemical cycling, because both these responses and effects are driven by the trade‐off between acquisition and conservation. On the other hand, regeneration and demographic traits associated with response to disturbance, which are known to have little connection with adult traits involved in plant ecophysiology, would be of little relevance to ecosystem processes. This framework is likely to be broadly applicable, although caution must be exercised to use trait linkages and trade‐offs appropriate to the scale, environmental conditions and evolutionary context. It may direct the selection of plant functional types for vegetation models at a range of scales, and help with the design of experimental studies of relationships between plant diversity and ecosystem properties.

@article{doi101046j13652435200200664x,
    author = "Lavorel, Sandra and Garnier, Éric",
    title = "Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail",
    year = "2002",
    journal = "Functional Ecology",
    abstract = "Summary The concept of plant functional type proposes that species can be grouped according to common responses to the environment and/or common effects on ecosystem processes. However, the knowledge of relationships between traits associated with the response of plants to environmental factors such as resources and disturbances (response traits), and traits that determine effects of plants on ecosystem functions (effect traits), such as biogeochemical cycling or propensity to disturbance, remains rudimentary. We present a framework using concepts and results from community ecology, ecosystem ecology and evolutionary biology to provide this linkage. Ecosystem functioning is the end result of the operation of multiple environmental filters in a hierarchy of scales which, by selecting individuals with appropriate responses, result in assemblages with varying trait composition. Functional linkages and trade‐offs among traits, each of which relates to one or several processes, determine whether or not filtering by different factors gives a match, and whether ecosystem effects can be easily deduced from the knowledge of the filters. To illustrate this framework we analyse a set of key environmental factors and ecosystem processes. While traits associated with response to nutrient gradients strongly overlapped with those determining net primary production, little direct overlap was found between response to fire and flammability. We hypothesize that these patterns reflect general trends. Responses to resource availability would be determined by traits that are also involved in biogeochemical cycling, because both these responses and effects are driven by the trade‐off between acquisition and conservation. On the other hand, regeneration and demographic traits associated with response to disturbance, which are known to have little connection with adult traits involved in plant ecophysiology, would be of little relevance to ecosystem processes. This framework is likely to be broadly applicable, although caution must be exercised to use trait linkages and trade‐offs appropriate to the scale, environmental conditions and evolutionary context. It may direct the selection of plant functional types for vegetation models at a range of scales, and help with the design of experimental studies of relationships between plant diversity and ecosystem properties.",
    url = "https://doi.org/10.1046/j.1365-2435.2002.00664.x",
    doi = "10.1046/j.1365-2435.2002.00664.x",
    openalex = "W2168173042",
    references = "doi1010079783642809132, doi101007bf00002772, doi101023a1004327224729, openalexw2097450069, openalexw2169917233"
}

Four vascular plant lineages, the ferns, sphenopsids, progymnosperms, and seed plants, evolved laminated leaves in the Paleozoic. A principal coordinate analysis of 641 leaf species from North American and European floras ranging in age from Middle Devonian through the end of the Permian shows that the clades followed parallel trajectories of evolution: each clade exhibits rapid radiation of leaf morphologies from simple (and similar) forms in the Late Devonian/Early Carboniferous to diverse, differentiated leaf forms, with strong constraint on further diversification beginning in the mid Carboniferous. Similar morphospace trajectories have been documented in studies of morphological evolution in animals; however, plant fossils present unique opportunities for understanding the developmental processes that underlie such patterns. Detailed comparison of venation in Paleozoic leaves with that of modern leaves for which developmental mechanisms are known suggests developmental interpretations for the origination and early evolution of leaves. The parallel evolution of a marginal meristem by the modification of developmental mechanisms available in the common ancestor of all groups resulted in the pattern of leaf evolution repeated by each clade. Early steps of leaf evolution were followed by constraint on further diversification as the possible elaborations of marginal growth were exhausted. Hypotheses of development in Paleozoic leaves can be tested by the study of living plants with analogous leaf morphologies.

@article{doi1016660094837320020280070eodpat20co2,
    author = "Boyce, C. Kevin and Knoll, Andrew H.",
    title = "Evolution of developmental potential and the multiple independent origins of leaves in Paleozoic vascular plants",
    year = "2002",
    journal = "Paleobiology",
    abstract = "Four vascular plant lineages, the ferns, sphenopsids, progymnosperms, and seed plants, evolved laminated leaves in the Paleozoic. A principal coordinate analysis of 641 leaf species from North American and European floras ranging in age from Middle Devonian through the end of the Permian shows that the clades followed parallel trajectories of evolution: each clade exhibits rapid radiation of leaf morphologies from simple (and similar) forms in the Late Devonian/Early Carboniferous to diverse, differentiated leaf forms, with strong constraint on further diversification beginning in the mid Carboniferous. Similar morphospace trajectories have been documented in studies of morphological evolution in animals; however, plant fossils present unique opportunities for understanding the developmental processes that underlie such patterns. Detailed comparison of venation in Paleozoic leaves with that of modern leaves for which developmental mechanisms are known suggests developmental interpretations for the origination and early evolution of leaves. The parallel evolution of a marginal meristem by the modification of developmental mechanisms available in the common ancestor of all groups resulted in the pattern of leaf evolution repeated by each clade. Early steps of leaf evolution were followed by constraint on further diversification as the possible elaborations of marginal growth were exhausted. Hypotheses of development in Paleozoic leaves can be tested by the study of living plants with analogous leaf morphologies.",
    url = "https://doi.org/10.1666/0094-8373(2002)028<0070:eodpat>2.0.co;2",
    doi = "10.1666/0094-8373(2002)028<0070:eodpat>2.0.co;2",
    openalex = "W2138585600",
    references = "doi101002j153721971959tb07030x, doi101002j153721971989tb11359x"
}

@article{doi101046j109583392003t01100158x,
    author = "GROUP*, THE ANGIOSPERM PHYLOGENY",
    title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II",
    year = "2003",
    journal = "Botanical Journal of the Linnean Society",
    url = "https://doi.org/10.1046/j.1095-8339.2003.t01-1-00158.x",
    doi = "10.1046/j.1095-8339.2003.t01-1-00158.x",
    openalex = "W2980373194",
    references = "doi1023072399846"
}

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.

@article{doi101071sb03015,
    author = "Small, Randall L. and Cronn, Richard and Wendel, Jonathan F.",
    title = "Use of nuclear genes for phylogeny reconstruction in plants",
    year = "2004",
    journal = "Australian Systematic Botany",
    abstract = "Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.",
    url = "https://doi.org/10.1071/sb03015",
    doi = "10.1071/sb03015",
    openalex = "W1929440565"
}

Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastructural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classification at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly flagellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least five monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. The reorganization of taxa stimulated by molecular analyses is expected to continue as more data accumulate and new taxa and habitats are sampled.

@article{doi103732ajb91101535,
    author = "Lewis, Louise A. and McCourt, Richard M.",
    title = "Green algae and the origin of land plants",
    year = "2004",
    journal = "American Journal of Botany",
    abstract = "Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastructural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classification at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly flagellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least five monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. The reorganization of taxa stimulated by molecular analyses is expected to continue as more data accumulate and new taxa and habitats are sampled.",
    url = "https://doi.org/10.3732/ajb.91.10.1535",
    doi = "10.3732/ajb.91.10.1535",
    openalex = "W2121480880",
    references = "doi101007bf01403990"
}

@article{doi101016jcell200602008,
    author = "Chisholm, Stephen T. and Coaker, Gitta and Day, Brad and Staskawicz, Brian J.",
    title = "Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response",
    year = "2006",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2006.02.008",
    doi = "10.1016/j.cell.2006.02.008",
    openalex = "W2040210770"
}

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

@article{doi101126science1150646,
    author = "Rensing, Stefan A. and Lang, Daniel and Zimmer, Andreas and Terry, Astrid and Salamov, Asaf and Shapiro, Harris and Nishiyama, Tomoaki and Perroud, Pierre‐François and Lindquist, Erika and Kamisugi, Yasuko and Tanahashi, Takako and Sakakibara, Keiko and Fujita, Tomomichi and Oishi, Kazuko and Shin‐I, Tadasu and Kuroki, Yoko and Toyoda, Atsushi and Suzuki, Yutaka and Hashimoto, Shinichi and Yamaguchi, Kazuo and Sugano, Sumio and Kohara, Yuji and Fujiyama, Asao and Anterola, Aldwin M. and Aoki, Setsuyuki and Ashton, Neil W. and Barbazuk, W. Brad and Barker, Elizabeth I. and Bennetzen, Jeffrey L. and Blankenship, Robert E. and Cho, Sung Hyun and Dutcher, Susan K. and Estelle, Mark and Fawcett, Jeffrey A. and Gundlach, Heidrun and Hanada, Kousuke and Heyl, Alexander and Hicks, Karen A. and Hughes, Jon and Lohr, Martin and Mayer, Klaus and Melkozernov, Alexander N. and Murata, Takashi and Nelson, David R. and Pils, Birgit and Prigge, Michael J. and Reiss, Bernd and Renner, Tanya and Rombauts, Stéphane and Rushton, Paul J. and Sanderfoot, Anton A. and Schween, Gabriele and Shiu, Shin‐Han and Stueber, Kurt and Theodoulou, Frederica L. and Tu, Hank and de Peer, Yves Van and Verrier, Paul and Waters, Elizabeth R. and Wood, Andrew J. and Yang, Lixing and Cove, David J. and Cuming, Andrew C. and Hasebe, Mitsuyasu and Lucas, Susan and Mishler, Brent D. and Reski, Ralf and Grigoriev, Igor V. and Quatrano, Ralph S. and Boore, Jeffrey L.",
    title = "The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants",
    year = "2007",
    journal = "Science",
    abstract = "We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.",
    url = "https://doi.org/10.1126/science.1150646",
    doi = "10.1126/science.1150646",
    openalex = "W2153488363",
    references = "doi10103837918, doi101126science1128691, doi101126science29054941151"
}

A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophyllales. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geissolomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linderniaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopularity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. Separate papers in this same volume deal with a new linear order for APG, subfamilial names that can be used for more accurate communication in Amaryllidaceae s.l., Asparagaceace s.l. and Xanthorrheaceae s.l. (all Asparagales) and a formal supraordinal classification for the flowering plants.

@article{doi101111j10958339200900996x,
    author = "GROUP, THE ANGIOSPERM PHYLOGENY",
    title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III",
    year = "2009",
    journal = "Botanical Journal of the Linnean Society",
    abstract = "A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophyllales. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geissolomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linderniaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopularity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. Separate papers in this same volume deal with a new linear order for APG, subfamilial names that can be used for more accurate communication in Amaryllidaceae s.l., Asparagaceace s.l. and Xanthorrheaceae s.l. (all Asparagales) and a formal supraordinal classification for the flowering plants.",
    url = "https://doi.org/10.1111/j.1095-8339.2009.00996.x",
    doi = "10.1111/j.1095-8339.2009.00996.x",
    openalex = "W4245471709",
    references = "doi101046j109583392003t01100158x, doi101073pnas0708072104, doi101073pnas0709121104, doi101073pnas0813376106, doi101111j175348871981tb06752x, doi1023072484473, doi1023072992015, doi103732ajb0800047, doi103732ajb891132, doi105860choice453190, openalexw2961549061"
}

@article{openalexw3148514506,
    author = "Apg",
    title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III",
    year = "2009",
    journal = "Botanical Journal of the Linnean Society",
    openalex = "W3148514506"
}

@article{doi101038nature09916,
    author = "Jiao, Yuannian and Wickett, Norman J. and Ayyampalayam, Saravanaraj and Chanderbali, André S. and Landherr, Lena and Ralph, Paula E. and Tomsho, Lynn P. and Hu, Yi and Liang, Haiying and Soltis, Pamela S. and Soltis, Pamela S. and Clifton, Sandra W. and Schlarbaum, Scott E. and Schuster, Stephan C. and Mā, Hong and Leebens‐Mack, Jim and dePamphilis, Claude W.",
    title = "Ancestral polyploidy in seed plants and angiosperms",
    year = "2011",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature09916",
    doi = "10.1038/nature09916",
    openalex = "W2001374342",
    references = "doi1010020471250953bi0203s00, doi1010079783642866593, doi10103837918, doi10103875556, doi101038nature06148, doi101073pnas0900906106, doi101093bioinformatics179847, doi101093bioinformaticsbtl446, doi101093bioinformaticsbtp348, doi101093nargkh340, doi101093nargkl315, doi101093sysbio274401, doi101126science1128691, doi101196annals1438005, doi1023072412923"
}

Abstract Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy‐in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log‐normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait‐based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

@article{doi101111j13652486201102451x,
    author = "Kattge, Jens and Dı́az, Soledad and Lavorel, Sandra and Prentice, I. Colin and Leadley, Paul and Bönisch, Gerhard and Garnier, Éric and Westoby, Mark and Reich, Peter B. and Wright, Ian J. and Cornelissen, J. H. C. and Violle, Cyrille and Harrison, Sandy P. and van Bodegom, Peter M. and Reichstein, Markus and Enquist, Brian J. and Soudzilovskaia, Nadejda A. and Ackerly, David D. and Anand, M. and Atkin, Owen K. and Bahn, Michael and Baker, Timothy R. and Baldocchi, Dennis and Bekker, R.M. and Blanco, C. and Blonder, Benjamin and Bond, William J. and Bradstock, Ross A. and Bunker, Dan and Casanoves, Fernando and Cavender‐Bares, Jeannine and Chambers, Jeffrey Q. and Chapin, F. Stuart and Chave, Jérôme and Coomes, David A. and Cornwell, William K. and Craine, Joseph M. and Dobrin, Barbara and Duarte, Leandro and Durka, Walter and Elser, James J. and Esser, G. and Estiarte, Marc and Fagan, William F. and Fang, Jinwei and Fernández‐Méndez, Fernando and Fidélis, Alessandra and Finegan, Bryan and Flores, Olivier and FORD, HENRY and Frank, Dorothea and Freschet, Grégoire T. and Fyllas, Nikolaos M. and Gallagher, Rachael V. and GREEN, W. A. and Gutiérrez, Álvaro G. and Hickler, Thomas and Higgins, Steven I. and Hodgson, J. G. and Jalili, Amir and Jansen, Steven and Joly, Carlos Alfredo and Kerkhoff, Andrew J. and Kirkup, Donald W. and Kitajima, Kaoru and Kleyer, Michael and Klotz, Stefan and Knops, Johannes M. H. and Krämer, K. and Kühn, Ingolf and Kurokawa, H. and Laughlin, Daniel C. and Lee, Tali D. and Leishman, Michelle R. and Lens, Frederic and Lenz, Tanja I. and Lewis, Simon L. and Lloyd, Jon and Llusià, Joan and Louault, Frédérique and Ma, Sai and Mahecha, Miguel D. and Manning, Peter and Massad, Tara Joy and Medlyn, Belinda E. and Messier, J. and Moles, Angela T. and Müller, Sandra Cristina and Nadrowski, Karin and NAEEM, S. and Niinemets, Ülo and Nöllert, Stephanie and Nuske, Alison and Ogaya, Romà and Oleksyn, Jacek and Onipchenko, V. G. and Onoda, Yusuke and Ordóñez, Jenny and Overbeck, Gerhard E. and Ozinga, W.A.",
    title = "TRY – a global database of plant traits",
    year = "2011",
    journal = "Global Change Biology",
    abstract = "Abstract Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy‐in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log‐normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40\% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75\% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait‐based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.",
    url = "https://doi.org/10.1111/j.1365-2486.2011.02451.x",
    doi = "10.1111/j.1365-2486.2011.02451.x",
    openalex = "W2162584119",
    references = "doi101007bf00386231, doi1010160165176580900245, doi101016jtree200602002, doi101023a1004327224729, doi101038nature02403, doi101046j13652435200200664x, doi101046j13652486200300569x, doi101071bt02124, doi101086283244, doi101111j00301299200715559x, doi101111j14610248200600924x, doi101111j14610248200801219x, doi101146annurevecolsys33010802150452, doi1011552009421425"
}

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

@article{doi101073pnas1323926111,
    author = "Wickett, Norman J. and Mirarab, Siavash and Nguyen, Nam and Warnow, Tandy and Carpenter, Eric and Matasci, Naim and Ayyampalayam, Saravanaraj and Barker, Michael S. and Burleigh, J. Gordon and Gitzendanner, Matthew A. and Ruhfel, Brad R. and Wafula, Eric and Der, Joshua P. and Graham, Sean W. and Mathews, Sarah and Melkonian, Michael and Soltis, Pamela S. and Soltis, Pamela S. and Miles, Nicholas W. and Rothfels, Carl J. and Pokorny, Lisa and Shaw, A. Jonathan and DeGironimo, Lisa and Stevenson, Dennis and Surek, Barbara and Villarreal, Juan Carlos and Roure, Béatrice and Philippe, Hervé and dePamphilis, Claude W. and Chen, Tao and Deyholos, Michael K. and Baucom, Regina S. and Kutchan, Toni M. and Augustin, Megan M. and Wang, Jun and Zhang, Yong and Tian, Zhijian and Yan, Zhixiang and Wu, Xiaolei and Sun, Xiao and Wong, Gane Ka‐Shu and Leebens-Mack, James",
    title = "Phylotranscriptomic analysis of the origin and early diversification of land plants",
    year = "2014",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.",
    url = "https://doi.org/10.1073/pnas.1323926111",
    doi = "10.1073/pnas.1323926111",
    openalex = "W2013277649",
    references = "doi101016jtree200901009, doi101016s0022283605803602, doi10103837918, doi101046j109583392003t01100158x, doi101093bioinformatics83275, doi101093bioinformaticsbtl446, doi101093sysbio463523, doi101093sysbiosyt022, doi101111boj12385, doi101111j10958339200900996x, doi101111j10960031200800217x, doi1011861471214811104, doi101371journalpcbi1002195, doi1023072346830, openalexw3148514506"
}

Summary The leaf economics spectrum (LES) provides a useful framework for examining species strategies as shaped by their evolutionary history. However, that spectrum, as originally described, involved only two key resources (carbon and nutrients) and one of three economically important plant organs. Herein, I evaluate whether the economics spectrum idea can be broadly extended to water – the third key resource –stems, roots and entire plants and to individual, community and ecosystem scales. My overarching hypothesis is that strong selection along trait trade‐off axes, in tandem with biophysical constraints, results in convergence for any taxon on a uniformly fast, medium or slow strategy (i.e. rates of resource acquisition and processing) for all organs and all resources. Evidence for economic trait spectra exists for stems and roots as well as leaves, and for traits related to water as well as carbon and nutrients. These apply generally within and across scales (within and across communities, climate zones, biomes and lineages). There are linkages across organs and coupling among resources, resulting in an integrated whole‐plant economics spectrum. Species capable of moving water rapidly have low tissue density, short tissue life span and high rates of resource acquisition and flux at organ and individual scales. The reverse is true for species with the slow strategy. Different traits may be important in different conditions, but as being fast in one respect generally requires being fast in others, being fast or slow is a general feature of species. Economic traits influence performance and fitness consistent with trait‐based theory about underlying adaptive mechanisms. Traits help explain differences in growth and survival across resource gradients and thus help explain the distribution of species and the assembly of communities across light, water and nutrient gradients. Traits scale up – fast traits are associated with faster rates of ecosystem processes such as decomposition or primary productivity, and slow traits with slow process rates. Synthesis. Traits matter. A single ‘fast–slow’ plant economics spectrum that integrates across leaves, stems and roots is a key feature of the plant universe and helps to explain individual ecological strategies, community assembly processes and the functioning of ecosystems.

@article{doi1011111365274512211,
    author = "Reich, Peter B.",
    title = "The world‐wide ‘fast–slow’ plant economics spectrum: a traits manifesto",
    year = "2014",
    journal = "Journal of Ecology",
    abstract = "Summary The leaf economics spectrum (LES) provides a useful framework for examining species strategies as shaped by their evolutionary history. However, that spectrum, as originally described, involved only two key resources (carbon and nutrients) and one of three economically important plant organs. Herein, I evaluate whether the economics spectrum idea can be broadly extended to water – the third key resource –stems, roots and entire plants and to individual, community and ecosystem scales. My overarching hypothesis is that strong selection along trait trade‐off axes, in tandem with biophysical constraints, results in convergence for any taxon on a uniformly fast, medium or slow strategy (i.e. rates of resource acquisition and processing) for all organs and all resources. Evidence for economic trait spectra exists for stems and roots as well as leaves, and for traits related to water as well as carbon and nutrients. These apply generally within and across scales (within and across communities, climate zones, biomes and lineages). There are linkages across organs and coupling among resources, resulting in an integrated whole‐plant economics spectrum. Species capable of moving water rapidly have low tissue density, short tissue life span and high rates of resource acquisition and flux at organ and individual scales. The reverse is true for species with the slow strategy. Different traits may be important in different conditions, but as being fast in one respect generally requires being fast in others, being fast or slow is a general feature of species. Economic traits influence performance and fitness consistent with trait‐based theory about underlying adaptive mechanisms. Traits help explain differences in growth and survival across resource gradients and thus help explain the distribution of species and the assembly of communities across light, water and nutrient gradients. Traits scale up – fast traits are associated with faster rates of ecosystem processes such as decomposition or primary productivity, and slow traits with slow process rates. Synthesis. Traits matter. A single ‘fast–slow’ plant economics spectrum that integrates across leaves, stems and roots is a key feature of the plant universe and helps to explain individual ecological strategies, community assembly processes and the functioning of ecosystems.",
    url = "https://doi.org/10.1111/1365-2745.12211",
    doi = "10.1111/1365-2745.12211",
    openalex = "W2127928904",
    references = "doi101023a1004327224729, doi101038nature02403, doi101046j13652435200200664x, doi101046j13652745199800306x, doi101086283244, doi101098rspb20081919, doi101104pp107101352, doi101111j00301299200715559x, doi101111j109583121989tb00492x, doi101111j13652486201102451x, doi101111j14610248200801219x, doi101111j14610248200901285x, doi101111j14610248200901314x, doi101111j14610248200901410x, doi101146annureves11110180001313, doi1018900012965819970781958cafasa20co2, doi1023072259756, doi1023074549, doi1034172009143, openalexw1564371012, openalexw2097450069, openalexw2169917233"
}

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

@article{doi101073pnas1423041112,
    author = "Hinchliff, Cody E. and Smith, Stephen A. and Allman, James F. and Burleigh, J. Gordon and Chaudhary, Ruchi and Coghill, Lyndon M. and Crandall, Keith A. and Deng, Jiabin and Drew, Bryan T. and Gazis, Romina and Gude, Karl and Hibbett, David S. and Katz, Laura A. and Laughinghouse, Haywood Dail and McTavish, Emily Jane and Midford, Peter and Owen, Christopher L. and Ree, Richard H. and Rees, Jonathan and Soltis, Pamela S. and Williams, Tiffani L. and Cranston, Karen",
    title = "Synthesis of phylogeny and taxonomy into a comprehensive tree of life",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.",
    url = "https://doi.org/10.1073/pnas.1423041112",
    doi = "10.1073/pnas.1423041112",
    openalex = "W2951002538",
    references = "doi101073pnas1110633108, doi105962bhltitle46292, doi105962bhltitle68064"
}

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

@article{doi101128mmbr0005014,
    author = "Hardoim, Pablo R. and van Overbeek, Leonard S. and Berg, Gabriele and Pirttilä, Anna Maria and Compant, Stéphane and Campisano, Andrea and Döring, Matthias and Sessitsch, Angela",
    title = "The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes",
    year = "2015",
    journal = "Microbiology and Molecular Biology Reviews",
    abstract = "All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.",
    url = "https://doi.org/10.1128/mmbr.00050-14",
    doi = "10.1128/mmbr.00050-14",
    openalex = "W2172598864",
    references = "doi101016b9780123705266x50016, doi101016jtplants201204001, doi101038nrmicro3109, doi101146annurevarplant050312120106, doi101146annurevcellbio21012704131001, openalexw1486903121"
}

© 2016 The Linnean Society of London. An update of the Angiosperm Phylogeny Group (APG) classification of the orders and families of angiosperms is presented. Several new orders are recognized: Boraginales, Dilleniales, Icacinales, Metteniusiales and Vahliales. This brings the total number of orders and families recognized in the APG system to 64 and 416, respectively. We propose two additional informal major clades, superrosids and superasterids, that each comprise the additional orders that are included in the larger clades dominated by the rosids and asterids. Families that made up potentially monofamilial orders, Dasypogonaceae and Sabiaceae, are instead referred to Arecales and Proteales, respectively. Two parasitic families formerly of uncertain positions are now placed: Cynomoriaceae in Saxifragales and Apodanthaceae in Cucurbitales. Although there is evidence that some families recognized in APG III are not monophyletic, we make no changes in Dioscoreales and Santalales relative to APG III and leave some genera in Lamiales unplaced (e.g. Peltanthera). These changes in familial circumscription and recognition have all resulted from new results published since APG III, except for some changes simply due to nomenclatural issues, which include substituting Asphodelaceae for Xanthorrhoeaceae (Asparagales) and Francoaceae for Melianthaceae (Geraniales); however, in Francoaceae we also include Bersamaceae, Ledocarpaceae, Rhynchothecaceae and Vivianiaceae. Other changes to family limits are not drastic or numerous and are mostly focused on some members of the lamiids, especially the former Icacinaceae that have long been problematic with several genera moved to the formerly monogeneric Metteniusaceae, but minor changes in circumscription include Aristolochiaceae (now including Lactoridaceae and Hydnoraceae; Aristolochiales), Maundiaceae (removed from Juncaginaceae; Alismatales), Restionaceae (now re-including Anarthriaceae and Centrolepidaceae; Poales), Buxaceae (now including Haptanthaceae; Buxales), Peraceae (split from Euphorbiaceae; Malpighiales), recognition of Petenaeaceae (Huerteales), Kewaceae, Limeaceae, Macarthuriaceae and Microteaceae (all Caryophyllales), Petiveriaceae split from Phytolaccaceae (Caryophyllales), changes to the generic composition of Ixonanthaceae and Irvingiaceae (with transfer of Allantospermum from the former to the latter; Malpighiales), transfer of Pakaraimaea (formerly Dipterocarpaceae) to Cistaceae (Malvales), transfer of Borthwickia, Forchhammeria, Stixis and Tirania (formerly all Capparaceae) to Resedaceae (Brassicales), Nyssaceae split from Cornaceae (Cornales), Pteleocarpa moved to Gelsemiaceae (Gentianales), changes to the generic composition of Gesneriaceae (Sanango moved from Loganiaceae) and Orobanchaceae (now including Lindenbergiaceae and Rehmanniaceae) and recognition of Mazaceae distinct from Phrymaceae (all Lamiales).

@article{doi101111boj12385,
    author = "Group, The Angiosperm Phylogeny",
    title = "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV",
    year = "2016",
    journal = "Botanical Journal of the Linnean Society",
    abstract = "© 2016 The Linnean Society of London. An update of the Angiosperm Phylogeny Group (APG) classification of the orders and families of angiosperms is presented. Several new orders are recognized: Boraginales, Dilleniales, Icacinales, Metteniusiales and Vahliales. This brings the total number of orders and families recognized in the APG system to 64 and 416, respectively. We propose two additional informal major clades, superrosids and superasterids, that each comprise the additional orders that are included in the larger clades dominated by the rosids and asterids. Families that made up potentially monofamilial orders, Dasypogonaceae and Sabiaceae, are instead referred to Arecales and Proteales, respectively. Two parasitic families formerly of uncertain positions are now placed: Cynomoriaceae in Saxifragales and Apodanthaceae in Cucurbitales. Although there is evidence that some families recognized in APG III are not monophyletic, we make no changes in Dioscoreales and Santalales relative to APG III and leave some genera in Lamiales unplaced (e.g. Peltanthera). These changes in familial circumscription and recognition have all resulted from new results published since APG III, except for some changes simply due to nomenclatural issues, which include substituting Asphodelaceae for Xanthorrhoeaceae (Asparagales) and Francoaceae for Melianthaceae (Geraniales); however, in Francoaceae we also include Bersamaceae, Ledocarpaceae, Rhynchothecaceae and Vivianiaceae. Other changes to family limits are not drastic or numerous and are mostly focused on some members of the lamiids, especially the former Icacinaceae that have long been problematic with several genera moved to the formerly monogeneric Metteniusaceae, but minor changes in circumscription include Aristolochiaceae (now including Lactoridaceae and Hydnoraceae; Aristolochiales), Maundiaceae (removed from Juncaginaceae; Alismatales), Restionaceae (now re-including Anarthriaceae and Centrolepidaceae; Poales), Buxaceae (now including Haptanthaceae; Buxales), Peraceae (split from Euphorbiaceae; Malpighiales), recognition of Petenaeaceae (Huerteales), Kewaceae, Limeaceae, Macarthuriaceae and Microteaceae (all Caryophyllales), Petiveriaceae split from Phytolaccaceae (Caryophyllales), changes to the generic composition of Ixonanthaceae and Irvingiaceae (with transfer of Allantospermum from the former to the latter; Malpighiales), transfer of Pakaraimaea (formerly Dipterocarpaceae) to Cistaceae (Malvales), transfer of Borthwickia, Forchhammeria, Stixis and Tirania (formerly all Capparaceae) to Resedaceae (Brassicales), Nyssaceae split from Cornaceae (Cornales), Pteleocarpa moved to Gelsemiaceae (Gentianales), changes to the generic composition of Gesneriaceae (Sanango moved from Loganiaceae) and Orobanchaceae (now including Lindenbergiaceae and Rehmanniaceae) and recognition of Mazaceae distinct from Phrymaceae (all Lamiales).",
    url = "https://doi.org/10.1111/boj.12385",
    doi = "10.1111/boj.12385",
    openalex = "W2166152751",
    references = "doi1010079783642143977, doi101046j109583392003t01100158x, doi101073pnas1323926111, doi101111j10958339200900996x, doi101111j109600311996tb00196x, doi101111j155856461985tb00420x, doi1023071222465, doi1023072399846, doi10230725065646, doi103732ajb0800047, openalexw3148514506, openalexw70084438"
}

Abstract Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

@article{doi101111jse12229,
    author = "I, PPG",
    title = "A community‐derived classification for extant lycophytes and ferns",
    year = "2016",
    journal = "Journal of Systematics and Evolution",
    abstract = "Abstract Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.",
    url = "https://doi.org/10.1111/jse.12229",
    doi = "10.1111/jse.12229",
    openalex = "W2552168024",
    references = "doi101073pnas1323926111, doi101111boj12385, doi101111j10958339200900996x"
}

@article{doi101016jcell201709030,
    author = "Bowman, John L. and Kohchi, Takayuki and Yamato, Katsuyuki T. and Jenkins, Jerry and Shu, Shengqiang and Ishizaki, Kimitsune and Yamaoka, Shohei and Nishihama, Ryuichi and Nakamura, Yasukazu and Berger, Frédéric and Adam, Catherine and Aki, Shiori S. and Althoff, Felix and Araki, Takashi and Arteaga‐Vázquez, Mario A. and Balasubrmanian, Sureshkumar and Barry, Kerrie and Bauer, Diane and Boehm, Christian R. and Briginshaw, Liam N. and Caballero-Pérez, Juan and Catarino, Bruno and Chen, Feng and Chiyoda, Shota and Chovatia, Mansi and Davies, Kevin M. and Delmans, Mihails and Demura, Taku and Dierschke, Tom and Dolan, Liam and Dorantes-Acosta, Ana E. and Eklund, D. Magnus and Florent, Stevie N. and Flores‐Sandoval, Eduardo and Fujiyama, Asao and Fukuzawa, Hideya and Galik, Bence and Grimanelli, Daniel and Grimwood, Jane and Grossniklaus, Ueli and Hamada, Takahiro and Haseloff, Jim and Hetherington, Alexander J. and Higo, Asuka and Hirakawa, Yuki and Hundley, Hope N. and Ikeda, Yoko and Inoue, Keisuke and Inoue, Shin‐ichiro and Ishida, Sakiko and Jia, Qidong and Kakita, Mitsuru and Kanazawa, Takehiko and Kawai, Yosuke and Kawashima, Tomokazu and Kennedy, Megan and Kinose, Keita and Kinoshita, Toshinori and Kohara, Yuji and Koide, Eri and Komatsu, Kenji and Kopischke, Sarah and Kubo, Minoru and Kyozuka, Junko and Lagercrantz, Ulf and Lin, Shih‐Shun and Lindquist, Erika and Lipzen, Anna and Lu, Chia-Wei and Luna, Efraín De and Martienssen, Robert A. and Minamino, Naoki and Mizutani, Masaharu and Mizutani, Miya and Mochizuki, Nobuyoshi and Monte, Isabel and Mosher, Rebecca A. and Nagasaki, Hideki and Nakagami, Hirofumi and Naramoto, Satoshi and Nishitani, Kazuhiko and Ohtani, Misato and Okamoto, Takashi and Okumura, Masaki and Phillips, Jeremy and Pollak, Bernardo and Reinders, Anke and Rövekamp, Moritz and Sano, Ryosuke and Sawa, Shinichiro and Schmid, Marc W. and Shirakawa, Makoto and Solano, Roberto and Spunde, Alex and Suetsugu, Noriyuki and Sugano, Sumio and Sugiyama, Akifumi and Sun, Rui and Suzuki, Yutaka and Takenaka, Mizuki",
    title = "Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome",
    year = "2017",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2017.09.030",
    doi = "10.1016/j.cell.2017.09.030",
    openalex = "W2763628303",
    references = "doi101038nrg201726, doi101073pnas1323926111, doi101111nph12643"
}

This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.

@article{doi101002ajb21019,
    author = "Smith, Stephen A. and Brown, Joseph W.",
    title = "Constructing a broadly inclusive seed plant phylogeny",
    year = "2018",
    journal = "American Journal of Botany",
    abstract = "This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.",
    url = "https://doi.org/10.1002/ajb2.1019",
    doi = "10.1002/ajb2.1019",
    openalex = "W2792688220",
    references = "doi101038nature11631, doi101038nature12872, doi101038ncomms16047, doi101038ncomms2958, doi101073pnas1323926111, doi101093oxfordjournalsmolbeva003974, doi101111nph13264, doi101111syen12037"
}

-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

@article{doi101038s4147701801888,
    author = "Li, Fay‐Wei and Brouwer, Paul and Carretero‐Paulet, Lorenzo and Cheng, Shifeng and de Vries, Jan and Delaux, Pierre‐Marc and Eily, Ariana Noel and Koppers, Nils and Kuo, Li‐Yaung and Li, Zheng and Simenc, Mathew and Small, Ian and Wafula, Eric and Angarita, Stephany and Barker, Michael S. and Bräutigam, Andrea and dePamphilis, Claude W. and Gould, Sven B. and Hosmani, Prashant S. and Huang, Yao-Moan and Hüettel, Bruno and Kato, Yoichiro and Liu, Xin and Maere, Steven and McDowell, Rose and Mueller, Lukas A. and Nierop, Klaas G.J. and Rensing, Stefan A. and Robison, Tanner A. and Rothfels, Carl J. and Sigel, Erin M. and Song, Yue and Timilsena, Prakash Raj and de Peer, Yves Van and Wang, Hongli and Wilhelmsson, Per K.I. and Wolf, Paul G. and Xu, Xun and Der, Joshua P. and Schluepmann, Henriette and Wong, Gane Ka‐Shu and Pryer, Kathleen M.",
    title = "Fern genomes elucidate land plant evolution and cyanobacterial symbioses",
    year = "2018",
    journal = "Nature Plants",
    abstract = "-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.",
    url = "https://doi.org/10.1038/s41477-018-0188-8",
    doi = "10.1038/s41477-018-0188-8",
    openalex = "W2809850047",
    references = "doi101093nargkt371, doi101186s128590182129y, doi103732apps1600016"
}

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.

@article{doi101073pnas1719588115,
    author = "Morris, Jennifer L. and Puttick, Mark N. and Clark, James and Edwards, Dianne and Kenrick, Paul and Pressel, Silvia and Wellman, Charles H. and Yang, Ziheng and Schneider, Harald and Donoghue, Philip C. J.",
    title = "The timescale of early land plant evolution",
    year = "2018",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.",
    url = "https://doi.org/10.1073/pnas.1719588115",
    doi = "10.1073/pnas.1719588115",
    openalex = "W2789151108",
    references = "doi101016jgca200511032, doi101073pnas1001225107, doi101073pnas1323926111, doi101093molbevmsm193, doi101093sysbiosyr107, doi101098rstb19980195, doi101098rstb20110271, doi101111j14698137201103794x, doi102475ajs3012182"
}

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.

@article{doi101186s4016801804450,
    author = "Hassani, M. Amine and Durán, Paloma and Hacquard, Stéphane",
    title = "Microbial interactions within the plant holobiont",
    year = "2018",
    journal = "Microbiome",
    abstract = {Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.},
    url = "https://doi.org/10.1186/s40168-018-0445-0",
    doi = "10.1186/s40168-018-0445-0",
    openalex = "W2795321853",
    references = "doi101126science1256688, doi101371journalpbio1002226, doi101371journalpbio1002352"
}

Green plants (Viridiplantae) include around 450,000-500,000 species 1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

@article{doi101038s4158601916932,
    author = "Initiative, One Thousand Plant Transcriptomes",
    title = "One thousand plant transcriptomes and the phylogenomics of green plants",
    year = "2019",
    journal = "Nature",
    abstract = "Green plants (Viridiplantae) include around 450,000-500,000 species 1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.",
    url = "https://doi.org/10.1038/s41586-019-1693-2",
    doi = "10.1038/s41586-019-1693-2",
    openalex = "W2981543307",
    references = "doi101016jtree200901009, doi101038nature09916, doi101073pnas1323926111, doi10108014786440109462720, doi101093aobmcp044, doi101093bioinformaticsbtu033, doi101093bioinformaticsbtv351, doi101093genetics15141531, doi101093molbevmsm088, doi101093molbevmsx116, doi101093nargkf436, doi101093nargkh340, doi101093nargkr944, doi101371journalpcbi1002195, doi101371journalpone0009490, doi1023072346830"
}

@incollection{birks2020expedition,
    author = "Birks, John",
    title = "Expedition Botany/Hobby Botany",
    year = "2020",
    booktitle = "Curious about Nature",
    url = "https://doi.org/10.1017/9781108552172.014",
    doi = "10.1017/9781108552172.014",
    pages = "151-155"
}

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

@article{doi101038s4147702006182,
    author = "Li, Fay‐Wei and Nishiyama, Tomoaki and Waller, Manuel and Frangedakis, Eftychios and Keller, Jean and Li, Zheng and Fernández‐Pozo, Noé and Barker, Michael S. and Bennett, Tom and Blázquez, Miguel Á. and Cheng, Shifeng and Cuming, Andrew C. and de Vries, Jan and de Vries, Sophie and Delaux, Pierre‐Marc and Diop, Issa and Harrison, C. J. O. and Hauser, Duncan and Hernández‐García, Jorge and Kirbis, Alexander and Meeks, John C. and Monte, Isabel and Mutte, Sumanth and Neubauer, Anna and Quandt, Dietmar and Robison, Tanner A. and Shimamura, Masaki and Rensing, Stefan A. and Villarreal, Juan Carlos and Weijers, Dolf and Wicke, Susann and Wong, Gane Ka‐Shu and Sakakibara, Keiko and Szövényi, Péter",
    title = "Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts",
    year = "2020",
    journal = "Nature Plants",
    abstract = "Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.",
    url = "https://doi.org/10.1038/s41477-020-0618-2",
    doi = "10.1038/s41477-020-0618-2",
    openalex = "W3011850984",
    references = "doi101038s4158601916932"
}

The unveiling of the angiosperm (flowering plant) tree of life over the past three decades has been one of the great success stories of modern plant biology. Flowering plants underpin most terrestrial biomes: they fix vast amounts of terrestrial carbon, in turn producing a substantial fraction of planetary oxygen, and drive major biogeochemical cycles. The bulk of human calories are derived either directly (crops) or indirectly (fodder) from angiosperms, as are many medicines, fuel, dyes, beverages, timber, fibers, and other materials. Countless indispensable and mundane items that impact human existence find their origins in flowering plants, and without them, life would be decidedly drearier—imagine a world without herbs, spices, or garden flowers, for example. In this context, the importance of a comprehensive understanding of the angiosperm tree of life cannot be overstated. The tree of life is the fundamental, biological roadmap to the evolution and properties of plants (e.g., Wong et al., 2020). For evolutionary biologists, phylogenies allow us to better understand the spectacular rise of the flowering plants to dominance over the past 140 million or so years (e.g., Lutzoni et al., 2018; Ramírez-Barahona et al., 2020). Information about angiosperm phylogenetic relationships also underpins modern angiosperm classification (e.g., APG IV, 2016), and helps us to better understand species origins and boundaries (e.g., Fazekas et al., 2009). Today, tree of life research is undergoing a renaissance due to the development of powerful, new phylogenomic methods (Dodsworth et al., 2019). In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set (Johnson et al., 2019), and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.

@article{doi101002ajb21703,
    author = "Baker, William J. and Dodsworth, Steven and Forest, Félix and Graham, Sean W. and Johnson, Matthew G. and McDonnell, Angela and Pokorny, Lisa and Tate, Jennifer A. and Wicke, Susann and Wickett, Norman J.",
    title = "Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants",
    year = "2021",
    journal = "American Journal of Botany",
    abstract = "The unveiling of the angiosperm (flowering plant) tree of life over the past three decades has been one of the great success stories of modern plant biology. Flowering plants underpin most terrestrial biomes: they fix vast amounts of terrestrial carbon, in turn producing a substantial fraction of planetary oxygen, and drive major biogeochemical cycles. The bulk of human calories are derived either directly (crops) or indirectly (fodder) from angiosperms, as are many medicines, fuel, dyes, beverages, timber, fibers, and other materials. Countless indispensable and mundane items that impact human existence find their origins in flowering plants, and without them, life would be decidedly drearier—imagine a world without herbs, spices, or garden flowers, for example. In this context, the importance of a comprehensive understanding of the angiosperm tree of life cannot be overstated. The tree of life is the fundamental, biological roadmap to the evolution and properties of plants (e.g., Wong et al., 2020). For evolutionary biologists, phylogenies allow us to better understand the spectacular rise of the flowering plants to dominance over the past 140 million or so years (e.g., Lutzoni et al., 2018; Ramírez-Barahona et al., 2020). Information about angiosperm phylogenetic relationships also underpins modern angiosperm classification (e.g., APG IV, 2016), and helps us to better understand species origins and boundaries (e.g., Fazekas et al., 2009). Today, tree of life research is undergoing a renaissance due to the development of powerful, new phylogenomic methods (Dodsworth et al., 2019). In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set (Johnson et al., 2019), and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.",
    url = "https://doi.org/10.1002/ajb2.1703",
    doi = "10.1002/ajb2.1703",
    openalex = "W3184323062",
    references = "doi101038s4158601916932, doi101073pnas0905845106, doi101073pnas1323926111, doi101073pnas1720115115, doi101073pnas84249054, doi101093sysbio463523, doi101111boj12385, doi101186s128590182129y, doi1023072399846, doi103732apps1600016"
}

Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale et al., 2020). The ability to sequence a customizable predefined genomic subset for several dozens or even hundreds of taxa allows in-depth analyses and the testing of phylogenetic hypotheses in ways that were not previously possible (reviewed in McKain et al., 2018). The most popular methods for targeted sequencing of genomic loci in phylogenomics include (long-)amplicon sequencing (Rothfels et al., 2017) and hybridization capture (Mandel et al., 2014; Weitemier et al., 2014). Targeted amplicon sequencing is based on single-fragment PCR amplification or by using multiplexing methods such as a microfluidic PCR-based amplification of multiple pre-selected genomic regions (e.g., Zhang and Ozdemir, 2009; Ho et al., 2014), which can then be pooled and sequenced. Massively parallel amplicon sequencing was first used in medical diagnostics (Turner et al., 2009) and was later applied to metazoan phylogenetics (Bybee et al., 2011; O’Neill et al., 2013). Microfluidic PCR and long-amplicon sequencing were subsequently applied in plant systematics (Uribe-Convers et al., 2014, 2016; Gostel et al., 2015). Amplicon-based methods can be time consuming as they require careful optimization and validation of primers. These methods are also susceptible to many of the common problems in PCR (such as nonspecific products, inability to amplify large loci in their entirety, or simply no products). Recently, amplicon approaches have been largely supplanted by hybridization-based targeted enrichment, which allows for relatively rapid probe design with reference to a few related transcriptomes or genomes, and allows simultaneous and efficient recovery of many hundreds of genes. Target enrichment via hybridization-based sequence capture can use customized or universal probes (short nucleotide fragments between 80 and 120 bp in length, also called baits). This versatile and powerful approach relies on probes to capture complementary sets of genomic targets from whole genome DNA or cDNA samples using solid-phase or in-solution hybridization (Gnirke et al., 2009; Mamanova et al., 2010; Cronn et al., 2012). To account for frequent (ancient) whole genome duplication events, plant systematists can identify sets of consistently low-to-single-copy markers that balance two common issues: ensuring recovery across a broad range of taxa, while containing sufficient phylogenetic informativeness. Target regions can be customized to address specific research questions, including targeting genes common to a metabolic pathway (Gardner et al., 2016; Folk et al., 2021) or genes of agronomic interest (Witek et al., 2016; Soto Gomez et al., 2019). The targets are often complete genes or exonic sequences, but non-coding DNA such as introns or untranslated regions can also be enriched. In-solution capture of the probe targets depends on the thermodynamics of hybridization. This process is governed, in part, by the DNA complexity of the bait and the probe length. Longer probes tolerate more mismatches, making them more suitable for capture across different species. Higher tiling density (the degree to which probes overlap, e.g., 75%) can compensate for failures of specific probes to hybridize or for low-quality input material, such as those stemming from historical herbarium specimens, so-called herbariomic approaches (Brewer et al., 2019). While overlapping probes increase the chance of capturing the target of interest via neighboring probes, there is a trade-off, as a higher tiling density tends to reduce the number of loci that can be examined per capture kit. Targeted enrichment of nuclear genes also overcomes several potential drawbacks of estimating phylogenies from organelle data alone. The single-locus behavior of organellar DNAs means that only a single history is provided: the entire plastid genome is expected to function as a single linkage group (Birky, 2001; but see Zhang et al., 2020). Organellar data are also prone to high rates of genetic drift in small population sizes, which could lead to a less accurate estimate of lineage differentiation, compared with large sets of nuclear genes (reviewed in Wicke and Schneeweiss, 2015). Although target capture data provide many more gene histories, analysis of these data requires specific bioinformatic approaches, including assembly of gene sequences without genomic references and detection of local gene duplication events that violate assumptions of orthology. In this regard, the plant systematics community has been innovative in addressing the related computational challenges, resulting in the wide adoption of targeted sequencing for plant systematics in recent years. Angiosperms353 is a tool for enabling phylogenomic-level analysis of any angiosperm group at any scale; the targeted genes and associated probes (Johnson et al., 2019) were developed from a set of low-copy nuclear genes used to infer the phylogeny of all green plants (One Thousand Plant Transcriptomes Initiative et al., 2019) to facilitate the collection of phylogenomic data in a relatively cost-effective and repeatable way. When considering Angiosperms353, it is important to distinguish between the low-copy orthologous genes found in all angiosperms and the 120-bp probe sequences used to enrich genomic libraries. The genes were selected based on copy number (ideally, genes that are single copy across more than 1400 available plant transcriptomes) and contain useful phylogenetic signal at deep and recent time scales. The probe sequences were designed from ~600 angiosperm transcriptomes and genomes, and were selected to maximize sequence similarity to other angiosperms, while minimizing the number of sequences used for probe design. Distinguishing the genes from the probes is important when considering the advantages, limitations, and future directions for Angiosperms353 in phylogenetic systematics, as discussed below. Although initial reports of the utility of Angiosperms353 genes and probes have been promising (Dodsworth et al., 2019), a few key questions remain: (1) Can Angiosperms353 probes truly be used to reliably recover orthologous genes across all groups of flowering plants?; (2) Is an angiosperm-wide probe design the most efficient for all targeted sequencing projects?; (3) What new bioinformatics tools are needed to apply Angiosperms353 genes to previously intractable research questions?; and (4) Are Angiosperms353 genes variable enough within species to extend the utility of the probes to population genetic studies? In this special issue and its companion issue in the American Journal of Botany (Baker et al., 2021b), the papers collected address these questions and demonstrate a number of ways in which research employing Angiosperms353 will benefit future angiosperm phylogenomic studies. This issue of Applications in Plant Sciences is focused on a variety of methodological issues, including comparisons between the Angiosperms353 probe set and taxon-specific probe sets, the development of new tools for specific lineages, a new lab technique to enrich libraries using Angiosperms353 and taxon-specific probe sets simultaneously, and bioinformatic approaches to facilitate careful assembly and analysis of data obtained using the Angiosperms353 kit. Low-to-single-copy nuclear markers have been an important tool in evolutionary studies of angiosperms (e.g., Small et al., 2004; Wu et al., 2006; Duarte et al., 2010). The identification of a set of hundreds of nuclear markers shared across angiosperms has facilitated the design of probes for targeted enrichment and subsequent high-throughput sequencing (Johnson et al., 2019). In this issue, three papers address the application and expansion of the Angiosperms353 loci. These papers build on existing resources to design new lineage-specific probes that contain the Angiosperms353 loci (Eserman et al., 2021; Ufimov et al., 2021), generate careful comparisons of the performance of an existing lineage-specific probe set with the Angiosperms353 probe set (Siniscalchi et al., 2021), and investigate the efficacy of simultaneous enrichment of libraries using universal and lineage-specific probes in a single hybridization reaction (Hendriks et al., 2021). Eserman et al. (2021) describe the development of Orchidaceae963, a new bait set that incorporates 254 of the Angiosperms353 loci, which they tested on members of three subfamilies of Orchidaceae. This resource will facilitate systematic work in the family and is also expected to be useful in population and conservation genomic studies. The incorporation of the Angiosperms353 loci along with custom marker genes is becoming more common (Yardeni et al., 2019; Jantzen et al., 2020; Christe et al., 2021; Ogutcen et al., 2021), and will allow collaboration between research teams and foster data sharing across studies. Comparative analyses of the custom sets and the Angiosperms353 set will naturally follow (e.g., see Larridon et al., 2020; Shah et al., 2021). For example, Ufimov et al. (2021) found a similar amount of parsimony informative sites using the Angiosperms353 probe set and a custom probe set in their study of Rosaceae subtribe Malinae. They also showed that the custom probes allowed for improved locus recovery rates across samples and lower levels of gene tree discordance (but see Yardeni et al., 2019). Siniscalchi et al. (2021) compared their lineage-specific Compositae1061 probes with the Angiosperms353 probes in eight members of the sunflower family. Although they were able to recover more loci on average with the lineage-specific probes, they found lower levels of paralogy in the gene trees based on the Angiosperms353 loci, which may simplify downstream analyses of the latter versus the former. Hendriks et al. (2021) performed a test case for combining both lineage-specific (i.e., Brassicaceae) and universal probes in a single hybridization reaction to simultaneously enrich libraries for both sets of loci. They found high levels of enrichment and locus recovery for both sets of targets across 26 Brassicaceae samples that included 16 samples from a single tribe and 10 samples reflecting broader sampling across the family. Their study shows that it is possible to generate data for multiple probe sets with little extra cost or work per sample. Taken together, these papers highlight that researchers have several options when choosing loci for target capture in flowering plants. The Angiosperms353 genes provide a ready set of loci that are low copy and reliably recovered using the universal Angiosperms353 probes, or by using custom probes designed with orthologs of the Angiosperms353 genes from the target taxa. The feasibility of combining probe sets during hybridization suggests additional flexibility. There is a trade-off, as custom probe designs will have higher per-sample costs and require existing sequence data in the focal group. However, far fewer probes will be needed for the Angiosperms353 genes in a custom design, allowing for additional loci for a given number of probes. Whichever choice is made, by including Angiosperms353 in a target capture project, researchers will benefit the entire phylogenetics community by enabling meta-analysis that parallels the broad adoption of single-gene markers in past decades. The development of Angiosperms353 into a common tool for molecular phylogenetics and population genetics has been paralleled by the need for new analytical workflows. One of the most active areas of tool development is in using extensions to existing tools to facilitate analysis of Angiosperms353 data. In this issue, three tools specifically tie in with HybPiper (Johnson et al., 2016), a popular tool for assembly and recovery of genes and flanking regions from target-capture sequencing reads. A common issue identified with Angiosperms353 data assembled using HybPiper is relatively low sequence recovery (e.g., Gaynor et al., 2020), but it is often unclear whether the issue lies with the molecular tools (i.e., poor hybridization between probes and target DNA) or bioinformatic tools (i.e., poor recovery in HybPiper or other tools). To test this, McLay et al. (2021) developed new target files to improve the mapping frequency of reads to Angiosperms353 target genes, a result independently confirmed by Slimp et al. (2021) and Lee et al. (2021). McLay et al. (2021) also provide a workflow that uses a hidden Markov model to choose clade-specific target sequences from a database of potential Angiosperms353 sequences. Their results indicate that the sequence divergence between the Angiosperms353 probe sequences and the target DNA of angiosperms during nucleic acid hybridization and subsequent sequencing is more forgiving than the effect of the same divergence on gene recovery during bioinformatic analysis. For researchers struggling with poor target enrichment efficiency using Angiosperms353, McLay et al. provide a potential bioinformatic solution that may reduce the need to re-enrich libraries. Their approach is to improve the target file used to recover genes in HybPiper by selecting more appropriate orthologs of the Angiosperms353 genes. Nauheimer et al. (2021) describe HybPhaser, a method for detecting hybrid taxa using HybPiper assemblies. Using an Angiosperms353 data set collected for Nepenthes, they employ an innovative two-step strategy in which an initial phylogeny is first used to identify representatives of different clades that have low heterozygosity (and are thus presumably not hybrids). In the second step, reads from putative hybrids are mapped to these chosen clade representatives. Differential mapping information is then used to phase hybrid sequences, which can then be placed on a multiply-labeled tree to identify hybrid origins. The HybPhaser method also has promise for addressing a common issue in target-capture phylogenetics: the identification of paralogous genes. This builds upon previous work using clade references to identify paralogs (Gardner et al., 2021), but the development of a more generalizable workflow in HybPhaser will be of use to many researchers unsure about whether target-captured genes are single copy in their data. Slimp et al. (2021) also describe new methods for downstream analysis of HybPiper output, for use in population genomic studies and the calculation of within-species demographic parameters. Their method adapts previously described workflows (Kates et al., 2018) to use HybPiper “supercontigs” (targeted coding regions and flanking non-coding regions) as reference sequences within species. Within-species variants can then be assessed jointly and used with standard population genomics programs (also see Beck et al., 2021 and Wenzell et al., 2021). Slimp et al. further demonstrate that the Angiosperms353 loci are variable within populations of several species, which suggests that genome-scale estimation of population parameters is now feasible without the need to develop taxon-specific methods. Since its initial publication, there has been a rapid and substantial uptake of Angiosperms353 to address systematics questions. The papers in this issue and its companion American Journal of Botany issue further illustrate that the utility of data generated through target enrichment extends beyond phylogenomics, with promising applications into population and conservation genomics. Of course, with the adaptability of data comes a requirement for flexible and innovative methods to process and analyze these data. While new methods and novel applications are already emerging, we recognize that there are some challenges and improvements that lie ahead. The need to evaluate the efficiency of recovering the targeted loci, both in vitro and in silico, is reflected in several papers in this issue, highlighting the distinction between targeted Angiosperms353 genes and the probes used to recover them. The papers presented here and in the companion issue build further evidence that the Angiosperms353 genes can be reliably recovered across the diversity of flowering plant species, with strong phylogenetic signal at scales ranging from deep time to the population level. Several papers in this issue describe innovations in how these target genes are recovered. Custom probe sets can still provide additional phylogenetic resolution within focal taxa by capturing more genes with the same number of probes, but the inclusion of Angiosperms353 loci along with custom probe sets will enable meta-analyses to compare species across flowering plants. In silico, the use of enhanced target files offers potential improvements for the assembly of enriched sequence libraries and illustrates that newly available genomic data can be used to complement the original Angiosperms353 target file and probe set. In this regard, the availability of an ever-increasing number of complete flowering plant genome and transcriptome sequences (e.g., One Thousand Plant Transcriptomes Initiative et al., 2019), and the massive increase in available sequence data facilitated by Angiosperms353, should allow for future refinement of the probes and choice of target sequences to better represent the diversity of angiosperms and maximize the length of sequences recovered across a broader set of taxa, including those with extremely altered lifestyles that affect the rate of sequence evolution, such as in heterotrophic taxa (e.g., Lam et al., 2018). Of course, the utility of Angiosperms353 data, or any other set of target enrichment data, relies on the accessibility of these genomic resources. Currently, there is no central data repository specifically tailored to access target enrichment data in a way that is not taxon specific. The Kew Tree of Life Explorer (https://treeoflife.kew.org/) was recently launched (Baker et al., 2021a) to make freely available pre- and post-publication Angiosperms353 data for thousands of taxa. The continued development of accessible tools to store and distribute these data will accelerate the progress that has been made thus far. For example, the ability to download a specific set of genes for a specific set of taxa from a central repository, rather than having to download and then filter multiple data sets from publication-specific repositories, would significantly improve the ability to incorporate existing data for addressing new research questions. Similarly, a centralized repository for uploading assembled and annotated target enrichment data generated for any taxon across the entire tree of life facilitates standardization and accessibility. A streamlined set of tools for identifying Angiosperms353 homologs for building custom probe sets would also increase the efficiency of data collection, much like how MarkerMiner (Chamala et al., 2015) provides a way to identify orthologs from a starting data set. The adoption of Angiosperms353 and target enrichment more generally in angiosperm systematics should cultivate further growth in data and in methods, as we have seen in this special issue. As more people use these data and methods, the opportunities for positive developments will only increase further, and improvements to existing probe sets, the development of new probe sets, opportunities to create solutions to challenges such as the resolution of paralogs, and the establishment of companion databases are all likely to be addressed head-on and embraced by the angiosperm systematics community. We thank all authors and reviewers for their valuable contributions to this special issue of Applications in Plant Sciences. We also acknowledge the tireless work of the APPS publications team, especially Managing Editor Beth Parada and Editor-in-Chief Theresa Culley.

@article{doi101002aps311443,
    author = "McDonnell, Angela and Baker, William J. and Dodsworth, Steven and Forest, Félix and Graham, Sean W. and Johnson, Matthew G. and Pokorny, Lisa and Tate, Jennifer A. and Wicke, Susann and Wickett, Norman J.",
    title = "Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics",
    year = "2021",
    journal = "Applications in Plant Sciences",
    abstract = "Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale et al., 2020). The ability to sequence a customizable predefined genomic subset for several dozens or even hundreds of taxa allows in-depth analyses and the testing of phylogenetic hypotheses in ways that were not previously possible (reviewed in McKain et al., 2018). The most popular methods for targeted sequencing of genomic loci in phylogenomics include (long-)amplicon sequencing (Rothfels et al., 2017) and hybridization capture (Mandel et al., 2014; Weitemier et al., 2014). Targeted amplicon sequencing is based on single-fragment PCR amplification or by using multiplexing methods such as a microfluidic PCR-based amplification of multiple pre-selected genomic regions (e.g., Zhang and Ozdemir, 2009; Ho et al., 2014), which can then be pooled and sequenced. Massively parallel amplicon sequencing was first used in medical diagnostics (Turner et al., 2009) and was later applied to metazoan phylogenetics (Bybee et al., 2011; O’Neill et al., 2013). Microfluidic PCR and long-amplicon sequencing were subsequently applied in plant systematics (Uribe-Convers et al., 2014, 2016; Gostel et al., 2015). Amplicon-based methods can be time consuming as they require careful optimization and validation of primers. These methods are also susceptible to many of the common problems in PCR (such as nonspecific products, inability to amplify large loci in their entirety, or simply no products). Recently, amplicon approaches have been largely supplanted by hybridization-based targeted enrichment, which allows for relatively rapid probe design with reference to a few related transcriptomes or genomes, and allows simultaneous and efficient recovery of many hundreds of genes. Target enrichment via hybridization-based sequence capture can use customized or universal probes (short nucleotide fragments between 80 and 120 bp in length, also called baits). This versatile and powerful approach relies on probes to capture complementary sets of genomic targets from whole genome DNA or cDNA samples using solid-phase or in-solution hybridization (Gnirke et al., 2009; Mamanova et al., 2010; Cronn et al., 2012). To account for frequent (ancient) whole genome duplication events, plant systematists can identify sets of consistently low-to-single-copy markers that balance two common issues: ensuring recovery across a broad range of taxa, while containing sufficient phylogenetic informativeness. Target regions can be customized to address specific research questions, including targeting genes common to a metabolic pathway (Gardner et al., 2016; Folk et al., 2021) or genes of agronomic interest (Witek et al., 2016; Soto Gomez et al., 2019). The targets are often complete genes or exonic sequences, but non-coding DNA such as introns or untranslated regions can also be enriched. In-solution capture of the probe targets depends on the thermodynamics of hybridization. This process is governed, in part, by the DNA complexity of the bait and the probe length. Longer probes tolerate more mismatches, making them more suitable for capture across different species. Higher tiling density (the degree to which probes overlap, e.g., 75\%) can compensate for failures of specific probes to hybridize or for low-quality input material, such as those stemming from historical herbarium specimens, so-called herbariomic approaches (Brewer et al., 2019). While overlapping probes increase the chance of capturing the target of interest via neighboring probes, there is a trade-off, as a higher tiling density tends to reduce the number of loci that can be examined per capture kit. Targeted enrichment of nuclear genes also overcomes several potential drawbacks of estimating phylogenies from organelle data alone. The single-locus behavior of organellar DNAs means that only a single history is provided: the entire plastid genome is expected to function as a single linkage group (Birky, 2001; but see Zhang et al., 2020). Organellar data are also prone to high rates of genetic drift in small population sizes, which could lead to a less accurate estimate of lineage differentiation, compared with large sets of nuclear genes (reviewed in Wicke and Schneeweiss, 2015). Although target capture data provide many more gene histories, analysis of these data requires specific bioinformatic approaches, including assembly of gene sequences without genomic references and detection of local gene duplication events that violate assumptions of orthology. In this regard, the plant systematics community has been innovative in addressing the related computational challenges, resulting in the wide adoption of targeted sequencing for plant systematics in recent years. Angiosperms353 is a tool for enabling phylogenomic-level analysis of any angiosperm group at any scale; the targeted genes and associated probes (Johnson et al., 2019) were developed from a set of low-copy nuclear genes used to infer the phylogeny of all green plants (One Thousand Plant Transcriptomes Initiative et al., 2019) to facilitate the collection of phylogenomic data in a relatively cost-effective and repeatable way. When considering Angiosperms353, it is important to distinguish between the low-copy orthologous genes found in all angiosperms and the 120-bp probe sequences used to enrich genomic libraries. The genes were selected based on copy number (ideally, genes that are single copy across more than 1400 available plant transcriptomes) and contain useful phylogenetic signal at deep and recent time scales. The probe sequences were designed from \textasciitilde 600 angiosperm transcriptomes and genomes, and were selected to maximize sequence similarity to other angiosperms, while minimizing the number of sequences used for probe design. Distinguishing the genes from the probes is important when considering the advantages, limitations, and future directions for Angiosperms353 in phylogenetic systematics, as discussed below. Although initial reports of the utility of Angiosperms353 genes and probes have been promising (Dodsworth et al., 2019), a few key questions remain: (1) Can Angiosperms353 probes truly be used to reliably recover orthologous genes across all groups of flowering plants?; (2) Is an angiosperm-wide probe design the most efficient for all targeted sequencing projects?; (3) What new bioinformatics tools are needed to apply Angiosperms353 genes to previously intractable research questions?; and (4) Are Angiosperms353 genes variable enough within species to extend the utility of the probes to population genetic studies? In this special issue and its companion issue in the American Journal of Botany (Baker et al., 2021b), the papers collected address these questions and demonstrate a number of ways in which research employing Angiosperms353 will benefit future angiosperm phylogenomic studies. This issue of Applications in Plant Sciences is focused on a variety of methodological issues, including comparisons between the Angiosperms353 probe set and taxon-specific probe sets, the development of new tools for specific lineages, a new lab technique to enrich libraries using Angiosperms353 and taxon-specific probe sets simultaneously, and bioinformatic approaches to facilitate careful assembly and analysis of data obtained using the Angiosperms353 kit. Low-to-single-copy nuclear markers have been an important tool in evolutionary studies of angiosperms (e.g., Small et al., 2004; Wu et al., 2006; Duarte et al., 2010). The identification of a set of hundreds of nuclear markers shared across angiosperms has facilitated the design of probes for targeted enrichment and subsequent high-throughput sequencing (Johnson et al., 2019). In this issue, three papers address the application and expansion of the Angiosperms353 loci. These papers build on existing resources to design new lineage-specific probes that contain the Angiosperms353 loci (Eserman et al., 2021; Ufimov et al., 2021), generate careful comparisons of the performance of an existing lineage-specific probe set with the Angiosperms353 probe set (Siniscalchi et al., 2021), and investigate the efficacy of simultaneous enrichment of libraries using universal and lineage-specific probes in a single hybridization reaction (Hendriks et al., 2021). Eserman et al. (2021) describe the development of Orchidaceae963, a new bait set that incorporates 254 of the Angiosperms353 loci, which they tested on members of three subfamilies of Orchidaceae. This resource will facilitate systematic work in the family and is also expected to be useful in population and conservation genomic studies. The incorporation of the Angiosperms353 loci along with custom marker genes is becoming more common (Yardeni et al., 2019; Jantzen et al., 2020; Christe et al., 2021; Ogutcen et al., 2021), and will allow collaboration between research teams and foster data sharing across studies. Comparative analyses of the custom sets and the Angiosperms353 set will naturally follow (e.g., see Larridon et al., 2020; Shah et al., 2021). For example, Ufimov et al. (2021) found a similar amount of parsimony informative sites using the Angiosperms353 probe set and a custom probe set in their study of Rosaceae subtribe Malinae. They also showed that the custom probes allowed for improved locus recovery rates across samples and lower levels of gene tree discordance (but see Yardeni et al., 2019). Siniscalchi et al. (2021) compared their lineage-specific Compositae1061 probes with the Angiosperms353 probes in eight members of the sunflower family. Although they were able to recover more loci on average with the lineage-specific probes, they found lower levels of paralogy in the gene trees based on the Angiosperms353 loci, which may simplify downstream analyses of the latter versus the former. Hendriks et al. (2021) performed a test case for combining both lineage-specific (i.e., Brassicaceae) and universal probes in a single hybridization reaction to simultaneously enrich libraries for both sets of loci. They found high levels of enrichment and locus recovery for both sets of targets across 26 Brassicaceae samples that included 16 samples from a single tribe and 10 samples reflecting broader sampling across the family. Their study shows that it is possible to generate data for multiple probe sets with little extra cost or work per sample. Taken together, these papers highlight that researchers have several options when choosing loci for target capture in flowering plants. The Angiosperms353 genes provide a ready set of loci that are low copy and reliably recovered using the universal Angiosperms353 probes, or by using custom probes designed with orthologs of the Angiosperms353 genes from the target taxa. The feasibility of combining probe sets during hybridization suggests additional flexibility. There is a trade-off, as custom probe designs will have higher per-sample costs and require existing sequence data in the focal group. However, far fewer probes will be needed for the Angiosperms353 genes in a custom design, allowing for additional loci for a given number of probes. Whichever choice is made, by including Angiosperms353 in a target capture project, researchers will benefit the entire phylogenetics community by enabling meta-analysis that parallels the broad adoption of single-gene markers in past decades. The development of Angiosperms353 into a common tool for molecular phylogenetics and population genetics has been paralleled by the need for new analytical workflows. One of the most active areas of tool development is in using extensions to existing tools to facilitate analysis of Angiosperms353 data. In this issue, three tools specifically tie in with HybPiper (Johnson et al., 2016), a popular tool for assembly and recovery of genes and flanking regions from target-capture sequencing reads. A common issue identified with Angiosperms353 data assembled using HybPiper is relatively low sequence recovery (e.g., Gaynor et al., 2020), but it is often unclear whether the issue lies with the molecular tools (i.e., poor hybridization between probes and target DNA) or bioinformatic tools (i.e., poor recovery in HybPiper or other tools). To test this, McLay et al. (2021) developed new target files to improve the mapping frequency of reads to Angiosperms353 target genes, a result independently confirmed by Slimp et al. (2021) and Lee et al. (2021). McLay et al. (2021) also provide a workflow that uses a hidden Markov model to choose clade-specific target sequences from a database of potential Angiosperms353 sequences. Their results indicate that the sequence divergence between the Angiosperms353 probe sequences and the target DNA of angiosperms during nucleic acid hybridization and subsequent sequencing is more forgiving than the effect of the same divergence on gene recovery during bioinformatic analysis. For researchers struggling with poor target enrichment efficiency using Angiosperms353, McLay et al. provide a potential bioinformatic solution that may reduce the need to re-enrich libraries. Their approach is to improve the target file used to recover genes in HybPiper by selecting more appropriate orthologs of the Angiosperms353 genes. Nauheimer et al. (2021) describe HybPhaser, a method for detecting hybrid taxa using HybPiper assemblies. Using an Angiosperms353 data set collected for Nepenthes, they employ an innovative two-step strategy in which an initial phylogeny is first used to identify representatives of different clades that have low heterozygosity (and are thus presumably not hybrids). In the second step, reads from putative hybrids are mapped to these chosen clade representatives. Differential mapping information is then used to phase hybrid sequences, which can then be placed on a multiply-labeled tree to identify hybrid origins. The HybPhaser method also has promise for addressing a common issue in target-capture phylogenetics: the identification of paralogous genes. This builds upon previous work using clade references to identify paralogs (Gardner et al., 2021), but the development of a more generalizable workflow in HybPhaser will be of use to many researchers unsure about whether target-captured genes are single copy in their data. Slimp et al. (2021) also describe new methods for downstream analysis of HybPiper output, for use in population genomic studies and the calculation of within-species demographic parameters. Their method adapts previously described workflows (Kates et al., 2018) to use HybPiper “supercontigs” (targeted coding regions and flanking non-coding regions) as reference sequences within species. Within-species variants can then be assessed jointly and used with standard population genomics programs (also see Beck et al., 2021 and Wenzell et al., 2021). Slimp et al. further demonstrate that the Angiosperms353 loci are variable within populations of several species, which suggests that genome-scale estimation of population parameters is now feasible without the need to develop taxon-specific methods. Since its initial publication, there has been a rapid and substantial uptake of Angiosperms353 to address systematics questions. The papers in this issue and its companion American Journal of Botany issue further illustrate that the utility of data generated through target enrichment extends beyond phylogenomics, with promising applications into population and conservation genomics. Of course, with the adaptability of data comes a requirement for flexible and innovative methods to process and analyze these data. While new methods and novel applications are already emerging, we recognize that there are some challenges and improvements that lie ahead. The need to evaluate the efficiency of recovering the targeted loci, both in vitro and in silico, is reflected in several papers in this issue, highlighting the distinction between targeted Angiosperms353 genes and the probes used to recover them. The papers presented here and in the companion issue build further evidence that the Angiosperms353 genes can be reliably recovered across the diversity of flowering plant species, with strong phylogenetic signal at scales ranging from deep time to the population level. Several papers in this issue describe innovations in how these target genes are recovered. Custom probe sets can still provide additional phylogenetic resolution within focal taxa by capturing more genes with the same number of probes, but the inclusion of Angiosperms353 loci along with custom probe sets will enable meta-analyses to compare species across flowering plants. In silico, the use of enhanced target files offers potential improvements for the assembly of enriched sequence libraries and illustrates that newly available genomic data can be used to complement the original Angiosperms353 target file and probe set. In this regard, the availability of an ever-increasing number of complete flowering plant genome and transcriptome sequences (e.g., One Thousand Plant Transcriptomes Initiative et al., 2019), and the massive increase in available sequence data facilitated by Angiosperms353, should allow for future refinement of the probes and choice of target sequences to better represent the diversity of angiosperms and maximize the length of sequences recovered across a broader set of taxa, including those with extremely altered lifestyles that affect the rate of sequence evolution, such as in heterotrophic taxa (e.g., Lam et al., 2018). Of course, the utility of Angiosperms353 data, or any other set of target enrichment data, relies on the accessibility of these genomic resources. Currently, there is no central data repository specifically tailored to access target enrichment data in a way that is not taxon specific. The Kew Tree of Life Explorer (https://treeoflife.kew.org/) was recently launched (Baker et al., 2021a) to make freely available pre- and post-publication Angiosperms353 data for thousands of taxa. The continued development of accessible tools to store and distribute these data will accelerate the progress that has been made thus far. For example, the ability to download a specific set of genes for a specific set of taxa from a central repository, rather than having to download and then filter multiple data sets from publication-specific repositories, would significantly improve the ability to incorporate existing data for addressing new research questions. Similarly, a centralized repository for uploading assembled and annotated target enrichment data generated for any taxon across the entire tree of life facilitates standardization and accessibility. A streamlined set of tools for identifying Angiosperms353 homologs for building custom probe sets would also increase the efficiency of data collection, much like how MarkerMiner (Chamala et al., 2015) provides a way to identify orthologs from a starting data set. The adoption of Angiosperms353 and target enrichment more generally in angiosperm systematics should cultivate further growth in data and in methods, as we have seen in this special issue. As more people use these data and methods, the opportunities for positive developments will only increase further, and improvements to existing probe sets, the development of new probe sets, opportunities to create solutions to challenges such as the resolution of paralogs, and the establishment of companion databases are all likely to be addressed head-on and embraced by the angiosperm systematics community. We thank all authors and reviewers for their valuable contributions to this special issue of Applications in Plant Sciences. We also acknowledge the tireless work of the APPS publications team, especially Managing Editor Beth Parada and Editor-in-Chief Theresa Culley.",
    url = "https://doi.org/10.1002/aps3.11443",
    doi = "10.1002/aps3.11443",
    openalex = "W3185917419",
    references = "doi101002ajb21703, doi101002aps311443, doi101038nbt1523, doi101038nbt3540, doi101038nmeth1419, doi101038s4158601916932, doi101071sb03015, doi101093sysbiosyy086, doi101146annurevgenet35102401090231, doi101186147121481061, doi103732apps1400042, doi103732apps1600016"
}

@article{doi101016jmolp202106028,
    author = "Hansen, Cecilie Cetti and Nelson, David R. and Møller, Birger Lindberg and Werck‐Reichhart, Danièle",
    title = "Plant cytochrome P450 plasticity and evolution",
    year = "2021",
    journal = "Molecular Plant",
    url = "https://doi.org/10.1016/j.molp.2021.06.028",
    doi = "10.1016/j.molp.2021.06.028",
    openalex = "W3174736387",
    references = "doi101038s4158601916932, doi101146annurevarplant050213040027"
}

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

@article{doi101111tpj15135,
    author = "Eichmann, Ruth and Richards, Luke and Schäfer, Patrick",
    title = "Hormones as go-betweens in plant microbiome assembly.",
    year = "2021",
    journal = "The Plant journal: for cell and molecular biology",
    abstract = "The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC8629125/",
    doi = "10.1111/tpj.15135",
    openalex = "W3110836224",
    pmcid = "PMC8629125",
    pmid = "33332645",
    references = "doi101016jtplants201204001, doi101038nature05286, doi101038nprot2007199, doi101038nrmicro3109, doi101146annurevarplant042809112122, doi101146annurevarplant050312120106, doi101146annurevcellbio092910154055, doi101146annurevphyto082712102340, doi101146annurevphyto43040204135923, doi1060642012963401"
}

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.

@article{doi101111jipb13415,
    author = "Guo, Cen and Luo, Yang and Gao, Lian‐Ming and Yi, Ting‐Shuang and Li, Hongtao and Yang, Junbo and D, Li",
    title = "Phylogenomics and the flowering plant tree of life",
    year = "2022",
    journal = "Journal of Integrative Plant Biology",
    abstract = "The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.",
    url = "https://doi.org/10.1111/jipb.13415",
    doi = "10.1111/jipb.13415",
    openalex = "W4309766482",
    references = "doi101002ajb21703, doi101016jympev201812023, doi101038nbt1883, doi101038nmeth2109, doi101038nrg2484, doi101038s415980160028x, doi101073pnas1903871116, doi101093bioinformaticsbtp348, doi101093bioinformaticsbtu170, doi101093molbevmsu300, doi101093nargkf436, doi101093oxfordjournalsmolbeva026334, doi101093sysbiosyaa013, doi101093sysbiosyab035, doi101111boj12385, doi101111jipb13246, doi101186s1291502000931z, doi101186s13059020021545"
}

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.

@article{doi101111tpj16142,
    author = "Stull, Gregory W. and Pham, Kasey and Soltis, Pamela S. and Soltis, Pamela S.",
    title = "Deep reticulation: the long legacy of hybridization in vascular plant evolution",
    year = "2023",
    journal = "The Plant Journal",
    abstract = "Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.",
    url = "https://doi.org/10.1111/tpj.16142",
    doi = "10.1111/tpj.16142",
    openalex = "W4320494454",
    references = "doi101016jppees201002002, doi101093sysbiosyab035"
}

The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota. Another variant of the disease triangle emerged from the recently formulated pathobiome paradigm, which deviates from the classical "one pathogen" etiology of infectious disease in favor of a scenario in which disease represents a conditional outcome of complex interactions between and among a host, its microbiota (including microbes with pathogenic potential), and the environment. The result is a version of the original disease triangle where "pathogen" is substituted with "microbiota." Here, as part of a careful and concise review of the origin, history, and usage of the disease triangle, I propose a next step in its evolution, which is to replace the word "disease" in the center of the host-microbiota-environment triad with the word "health." This triangle highlights health as a desirable outcome (rather than disease as an unwanted state) and as an emergent property of host-microbiota-environment interactions. Applied to the discipline of plant pathology, the health triangle offers an expanded range of targets and approaches for the diagnosis, prediction, restoration, and maintenance of plant health outcomes. Its applications are not restricted to infectious diseases only, and its underlying framework is more inclusive of all microbial contributions to plant well-being, including those by mycorrhizal fungi and nitrogen-fixing bacteria, for which there never was a proper place in the plant disease triangle. The plant health triangle also may have an edge as an education and communication tool to convey and stress the importance of healthy plants and their associated microbiota to a broader public and stakeholdership.

@article{doi101146annurevphyto121423042021,
    author = "Leveau, Johan H. J.",
    title = "Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes",
    year = "2024",
    journal = "Annual Review of Phytopathology",
    abstract = {The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota. Another variant of the disease triangle emerged from the recently formulated pathobiome paradigm, which deviates from the classical "one pathogen" etiology of infectious disease in favor of a scenario in which disease represents a conditional outcome of complex interactions between and among a host, its microbiota (including microbes with pathogenic potential), and the environment. The result is a version of the original disease triangle where "pathogen" is substituted with "microbiota." Here, as part of a careful and concise review of the origin, history, and usage of the disease triangle, I propose a next step in its evolution, which is to replace the word "disease" in the center of the host-microbiota-environment triad with the word "health." This triangle highlights health as a desirable outcome (rather than disease as an unwanted state) and as an emergent property of host-microbiota-environment interactions. Applied to the discipline of plant pathology, the health triangle offers an expanded range of targets and approaches for the diagnosis, prediction, restoration, and maintenance of plant health outcomes. Its applications are not restricted to infectious diseases only, and its underlying framework is more inclusive of all microbial contributions to plant well-being, including those by mycorrhizal fungi and nitrogen-fixing bacteria, for which there never was a proper place in the plant disease triangle. The plant health triangle also may have an edge as an education and communication tool to convey and stress the importance of healthy plants and their associated microbiota to a broader public and stakeholdership.},
    url = "https://doi.org/10.1146/annurev-phyto-121423-042021",
    doi = "10.1146/annurev-phyto-121423-042021",
    openalex = "W4396212608",
    references = "doi101146annurevarplant102820032704"
}

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking a step-change in the generation of data for phylogenetic inference. While this advancement has facilitated the resolution of many phylogenetic relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common in plant evolution. The proliferation of methods designed to analyse target capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we guide researchers through the target capture bioinformatic workflow, with a particular focus on robust phylogenetic inference in the presence of conflict. Through the workflow, we highlight key considerations for reducing artefactual conflict, synthesise strategies for managing paralogs, explain the causes and measurement of conflict, and summarise current methods for investigating biological processes underlying conflict. While we draw from examples in the Australian flora, this review is broadly relevant for any researcher working with target capture data. We conclude that conflict is often inherent and inevitable in plant phylogenetic research, but when properly managed, target capture data can provide unprecedented insight into the extraordinary and complex evolutionary histories of plants.

@misc{doi1032942x2wp6v,
    author = "Joyce, Elizabeth and Schmidt‐Lebuhn, Alexander N. and Orel, Harvey K. and Nge, Francis J. and Anderson, Benjamin and Hammer, Timothy and McLay, Todd G. B.",
    title = "Navigating phylogenetic conflict and evolutionary inference in plants with target capture data",
    year = "2024",
    abstract = "Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking a step-change in the generation of data for phylogenetic inference. While this advancement has facilitated the resolution of many phylogenetic relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common in plant evolution. The proliferation of methods designed to analyse target capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we guide researchers through the target capture bioinformatic workflow, with a particular focus on robust phylogenetic inference in the presence of conflict. Through the workflow, we highlight key considerations for reducing artefactual conflict, synthesise strategies for managing paralogs, explain the causes and measurement of conflict, and summarise current methods for investigating biological processes underlying conflict. While we draw from examples in the Australian flora, this review is broadly relevant for any researcher working with target capture data. We conclude that conflict is often inherent and inevitable in plant phylogenetic research, but when properly managed, target capture data can provide unprecedented insight into the extraordinary and complex evolutionary histories of plants.",
    url = "https://doi.org/10.32942/x2wp6v",
    doi = "10.32942/x2wp6v",
    openalex = "W4399038239",
    references = "doi103389fpls20231063174"
}

Target capture has rapidly become a preferred approach for plant systematic and evolutionary research, marking a step change in the generation of data for phylogenetic inference. Although this advancement has facilitated the resolution of many relationships, phylogenetic conflict continues to be reported and is often attributed to genome duplication, reticulation, incomplete lineage sorting or rapid speciation – common processes in plant evolution. The proliferation of methods for analysing target-capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we break down the causes of conflict and guide researchers through a target-capture bioinformatic workflow, with a particular focus on robust phylogenetic inference in the presence of conflict. Through the workflow, we highlight key considerations for reducing artefactual conflict, managing paralogs and assessing conflict, and discuss current methods for investigating causes of conflict. Although we draw from examples in the Australian flora, this review is broadly relevant for any researcher working with target-capture data. We conclude that conflict is often inherent in plant phylogenomic datasets, and, although further methodological development is needed, when conflict is carefully investigated, target-capture data can provide unprecedented insight into the extraordinary evolutionary histories of plants.

@article{doi101071sb24011,
    author = "Joyce, Elizabeth and Schmidt‐Lebuhn, Alexander N. and Orel, Harvey K. and Nge, Francis J. and Anderson, Brendan M. and Hammer, Timothy and McLay, Todd G. B.",
    title = "Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data",
    year = "2025",
    journal = "Australian Systematic Botany",
    abstract = "Target capture has rapidly become a preferred approach for plant systematic and evolutionary research, marking a step change in the generation of data for phylogenetic inference. Although this advancement has facilitated the resolution of many relationships, phylogenetic conflict continues to be reported and is often attributed to genome duplication, reticulation, incomplete lineage sorting or rapid speciation – common processes in plant evolution. The proliferation of methods for analysing target-capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we break down the causes of conflict and guide researchers through a target-capture bioinformatic workflow, with a particular focus on robust phylogenetic inference in the presence of conflict. Through the workflow, we highlight key considerations for reducing artefactual conflict, managing paralogs and assessing conflict, and discuss current methods for investigating causes of conflict. Although we draw from examples in the Australian flora, this review is broadly relevant for any researcher working with target-capture data. We conclude that conflict is often inherent in plant phylogenomic datasets, and, although further methodological development is needed, when conflict is carefully investigated, target-capture data can provide unprecedented insight into the extraordinary evolutionary histories of plants.",
    url = "https://doi.org/10.1071/sb24011",
    doi = "10.1071/sb24011",
    openalex = "W4410110220",
    references = "doi103389fpls20231063174"
}

The generation and analysis of genome-scale data – genomics – is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for the widescale use of genomics in evolutionary and conservation biology. We introduce and describe a national-scale collaboration conceived to build genomic resources and capability for understanding the Australian flora: the Genomics for Australian Plants (GAP) Framework Initiative. We outline (a) the history of the project including the collaborative framework, partners and funding; (b) GAP principles such as rigour in design, sample verification and documentation, data management and data accessibility; and (c) the structure of the consortium and the four associated activity streams (reference genomes, phylogenomics, conservation genomics and training), with the rationale and aims for each of these. We show, through discussion of successes and challenges, the value of this multi-institutional consortium approach and the enablers, such as well-curated collections and national collaborative research infrastructure, all of which have led to a substantial increase in capacity and delivery of biodiversity knowledge outcomes.

@article{doi101071sb24022,
    author = "Simpson, Lalita and Cantrill, David J. and Byrne, Margaret and Allnutt, Theodore R. and King, Graham J.W. and Lum, Mabel and Bkhetan, Ziad Al and Andrew, Rose L. and Baker, William J. and Barrett, Matthew D. and Batley, Jacqueline and Berry, Oliver and Binks, Rachel M. and Bragg, Jason G. and Broadhurst, Linda and Brown, Gillian K. and Bruhl, Jeremy J. and Edwards, Richard J. and Ferguson, Scott and Forest, Félix and Gustafsson, Johan and Hammer, Timothy and Holmes, Gareth D. and Jackson, Chris and James, Elizabeth A. and Jones, Ashley and Kersey, Paul and Leitch, Ilia J. and Maurin, Olivier and McLay, Todd G. B. and Murphy, Daniel J. and Nargar, Katharina and Nauheimer, Lars and Sauquet, Hervé and Schmidt‐Lebuhn, Alexander N. and Shepherd, Kelly Anne and Syme, Anna and Waycott, Michelle and Wilson, Trevor and Crayn, Darren M.",
    title = "The Genomics for Australian Plants (GAP) framework initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora",
    year = "2025",
    journal = "Australian Systematic Botany",
    abstract = "The generation and analysis of genome-scale data – genomics – is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for the widescale use of genomics in evolutionary and conservation biology. We introduce and describe a national-scale collaboration conceived to build genomic resources and capability for understanding the Australian flora: the Genomics for Australian Plants (GAP) Framework Initiative. We outline (a) the history of the project including the collaborative framework, partners and funding; (b) GAP principles such as rigour in design, sample verification and documentation, data management and data accessibility; and (c) the structure of the consortium and the four associated activity streams (reference genomes, phylogenomics, conservation genomics and training), with the rationale and aims for each of these. We show, through discussion of successes and challenges, the value of this multi-institutional consortium approach and the enablers, such as well-curated collections and national collaborative research infrastructure, all of which have led to a substantial increase in capacity and delivery of biodiversity knowledge outcomes.",
    url = "https://doi.org/10.1071/sb24022",
    doi = "10.1071/sb24022",
    openalex = "W4410109179",
    references = "doi101111nph20263, doi103389fpls20231063174"
}