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    Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom


    McCarthy, Charley G.P. and Fitzpatrick, David A. (2017) Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom. Advances in genetics, 100. pp. 211-266. ISSN 0065-2660

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    Abstract

    Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.

    Item Type: Article
    Keywords: Fungi; Fungal genomics; Fungal phylogeny; Phylogenomics; Supertrees; Bayesian supertrees; Supermatrix; Composition vector; Gene content; 1000 Fungal Genomes Project;
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 11534
    Identification Number: https://doi.org/10.1016/bs.adgen.2017.09.006
    Depositing User: David Fitzpatrick
    Date Deposited: 30 Oct 2019 15:27
    Journal or Publication Title: Advances in genetics
    Publisher: Elsevier
    Refereed: Yes
    URI:

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