@book{hottinger1963les1,
    author = "Hottinger, L",
    title = "Les alvolines palognes, exemple d'un genre polyphyltique, in von Koenigswald, G. H. R., ed., Evolutionary Trends in Foraminifera",
    year = "1963",
    publisher = "Amsterdam, Elsevier, p. 298-314",
    note = "talkorigins\_source = {true}; raw\_reference = {Hottinger, L., 1963, Les alvolines palognes, exemple d'un genre polyphyltique, in von Koenigswald, G. H. R., ed., Evolutionary Trends in Foraminifera: Amsterdam, Elsevier, p. 298-314.}"
}

@article{vanvalen1965evolutionary,
    author = "van Valen, Leigh",
    title = "Evolutionary Trends in Foraminifera. G. H. R. von Koenigswald, J. D. Emeis, W. L. Buning, C. W. Wagner",
    year = "1965",
    journal = "The Quarterly Review of Biology",
    url = "https://doi.org/10.1086/404560",
    doi = "10.1086/404560",
    number = "2",
    pages = "188-189",
    volume = "40"
}

@article{norris1994evolutionary,
    author = "Norris, R.D. and Corfield, R.M. and Cartlidge, J.E.",
    title = "Evolutionary ecology ofGloborotalia (Globoconella) (planktic foraminifera)",
    year = "1994",
    journal = "Marine Micropaleontology",
    url = "https://doi.org/10.1016/0377-8398(94)90004-3",
    doi = "10.1016/0377-8398(94)90004-3",
    number = "2",
    pages = "121-145",
    volume = "23"
}

@misc{hancock2004polyphyletic,
    author = "Hancock, John M.",
    title = "Polyphyletic",
    year = "2004",
    booktitle = "Dictionary of Bioinformatics and Computational Biology",
    url = "https://doi.org/10.1002/0471650129.dob0550",
    doi = "10.1002/0471650129.dob0550"
}

@misc{crossref2007polyphyletic,
    title = "Polyphyletic",
    year = "2007",
    booktitle = "Hawley's Condensed Chemical Dictionary",
    url = "https://doi.org/10.1002/9780470114735.hawley13186",
    doi = "10.1002/9780470114735.hawley13186",
    pages = "1017-1018"
}

@incollection{ernoult2007la,
    author = "Ernoult, Nathalie",
    title = "La guerre et le genre: le contre-exemple platonicien",
    year = "2007",
    booktitle = "Problèmes du genre en Grèce ancienne",
    url = "https://doi.org/10.4000/books.psorbonne.33280",
    doi = "10.4000/books.psorbonne.33280",
    pages = "171-184"
}

@article{gonzalezdonoso2007the,
    author = "Gonzalez-Donoso, J. M. and Linares, D. and Robaszynski, F.",
    title = "THE ROTALIPORIDS, A POLYPHYLETIC GROUP OF ALBIAN-CENOMANIAN PLANKTONIC FORAMINIFERA: EMENDATION OF GENERA",
    year = "2007",
    journal = "The Journal of Foraminiferal Research",
    url = "https://doi.org/10.2113/gsjfr.37.2.175",
    doi = "10.2113/gsjfr.37.2.175",
    number = "2",
    pages = "175-186",
    volume = "37"
}

@incollection{crossref2008polyphyletic,
    title = "Polyphyletic",
    year = "2008",
    booktitle = "Encyclopedia of Genetics, Genomics, Proteomics and Informatics",
    url = "https://doi.org/10.1007/978-1-4020-6754-9\_13231",
    doi = "10.1007/978-1-4020-6754-9\_13231",
    pages = "1533-1533"
}

@article{egan2016parsing,
    author = "Egan, Ashley N. and Vatanparast, Mohammad and Cagle, William",
    title = "Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny",
    year = "2016",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2016.08.001",
    doi = "10.1016/j.ympev.2016.08.001",
    pages = "44-59",
    volume = "104"
}

@incollection{crossref2018koenigswald,
    title = "Koenigswald",
    year = "2018",
    booktitle = "Koch, Jurij - Kokontis",
    url = "https://doi.org/10.1515/9783110579024-087",
    doi = "10.1515/9783110579024-087",
    pages = "164-165"
}

@misc{zeng2020the,
    author = "Zeng, Liping and Dehesh, Katayoon",
    title = "The MEP-pathway genes are polyphyletic origin and evolutionary conserved",
    year = "2020",
    abstract = "Background Isoprenoids are amongst the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol dicyclophosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes. Results Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. Conclusion Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.",
    url = "https://doi.org/10.21203/rs.3.rs-112826/v1",
    doi = "10.21203/rs.3.rs-112826/v1"
}