Assembling the Microbial Tree of Life
Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Magain, N., U'Ren, J. M. and F. Lutzoni. 2019. T-BAS version 2.1: Tree-Based Alignment Selector toolkit for evolutionary placement of DNA sequences and viewing alignments and specimen metadata on curated and custom trees. ( https://mra.asm.org/content/8/29/e00328-19 ) DOI: 10.1128/mra.00328-19
Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U'Ren, J. M., May, G. and F. Lutzoni. 2017. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization; an example with the Pezizomycotina tree of life. Bioinformatics 33: 1160-1168. DOI: 10.1093/bioinformatics/btw808
Bostock M, Ogievetsky V, Heer J. D(3): Data-Driven Documents. IEEE Trans Vis Comput Graph. 2011;17(12):2301-9. Epub 2011/10/29. doi: 10.1109/TVCG.2011.185. PubMed PMID: 22034350. https://d3js.org/
Yachdav, Guy, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna E. Lewis, Burkhard Rost, and Tatyana Goldberg. "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." Bioinformatics (2016): btw474. DOI: 10.1093/bioinformatics/btw474
Carbone, I. White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U'Ren, J. M., May, G. and F. Lutzoni. 2016. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 2016, DOI: 10.1093/bioinformatics/btw808 (https://academic.oup.com/bioinformatics/article/2730230/T-BAS-Tree-Based-Alignment-Selector-toolkit-for) DOI: 10.1093/bioinformatics/btw808
Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F. 2016. A new view of the tree of life. Nat Microbiol 1:16048. DOI: 10.1038/nmicrobiol.2016.48
James, T.Y., Kauff, F., Schoch, C.L., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H.T., Rauhut, A., Reeb, V., Arnold, A.E., Amtoft, A., Stajich, J.E., Hosaka, K., Sung, G.H., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J.M., Slot, J.C., Wang, Z., Wilson, A.W., Schussler, A., Longcore, J.E., O'Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P.M., Powell, M.J., Taylor, J.W., White, M.M., Griffith, G.W., Davies, D.R., Humber, R.A., Morton, J.B., Sugiyama, J., Rossman, A.Y., Rogers, J.D., Pfister, D.H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R.A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R.A., Serdani, M., Crous, P.W., Hughes, K.W., Matsuura, K., Langer, E., Langer, G., Untereiner, W.A., Lucking, R., Budel, B., Geiser, D.M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D.S., Lutzoni, F., McLaughlin, D.J., Spatafora, J.W., and Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822. DOI: 10.1038/nature05110
Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lucking R et al. . 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98(6):1088-103.
Videira SI, Groenewald JZ, Kolecka A, van Haren L, Boekhout T, Crous PW. 2015. Elucidating the Ramularia eucalypti species complex. Persoonia 34:50-64. DOI: 10.3767/003158515x685670
Moore, G.G., Olarte, R.A., Horn, B.W., Elliott, J.L., Singh, R., O'Neal, C.J., and Carbone, I. 2017. Global population structure and adaptive evolution of aflatoxin-producing fungi. Ecol Evol 7:9179-9191. DOI: 10.1002/ece3.3464
O'Donnell, K., Sutton, D.A., Wiederhold, N., Robert, V.A., Crous, P.W., and Geiser, D.M. 2016. Veterinary Fusarioses within the United States. J Clin Microbiol 54:2813-2819 DOI: 10.1128/jcm.01607-16
U'Ren, J.M., Miadlikowska, J., Zimmerman, N.B., Lutzoni, F., Stajich, J.E., and Arnold, A.E. 2016. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Mol Phylogenet Evol 98:210-232. DOI: 10.1016/j.ympev.2016.02.010
Garnica, S., Riess, K., Schon, M.E., Oberwinkler, F., and Setaro, S.D. 2016. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage. PloS one 11:e0149531. DOI: 10.1371/journal.pone.0149531
Chagnon P-L, Magain N, Miadlikowska J, Lutzoni F. 2019. Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera. Journal of Ecology doi:10.1111/1365-2745.13207. DOI: 10.1111/1365-2745.13207
Haelewaters D, Pfliegler WP, Gorczak M, Pfister DH. 2019. Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales. Mol Phylogenet Evol 133:286-301. DOI: 10.1016/j.ympev.2019.01.007
Miadlikowska, J., Magain, N., Pardo-De la Hoz, C. J., Niu, D., Goward, T., Sérusiaux, E. and Lutzoni, F. 2018. Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision. Plant and Fungal Systematics 63:45–64. DOI: 10.2478/pfs-2018-0007
Magain, N., Truong, C., Goward, T., Niu, D., Goffinet, B., Sérusiaux, E., Vitikainen, O., Lutzoni, F., and Miadlikowska, J. 2018. Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in Peltigera section Peltigera (lichenized Ascomycota: Lecanoromycetes). Taxon 67:836–870. DOI: 10.12705/675.3
Pardo De la Hoz, C. J., Magain, N., Lutzoni, F., Goward, T., Restrepo, S., and Miadlikowska, J. 2018 Contrasting symbiotic patterns in two closely related lineages of trimembered lichens of the genus Peltigera. Frontiers in Microbiology 9:2770. DOI: 10.3389/fmicb.2018.02770. DOI: 10.3389/fmicb.2018.02770
Magain, N., Miadlikowska, J., Mueller, O., Gajdeczka, M., Truong, C., Salamov, A., Dubchak, I., Grigoriev, I. V., Goffinet, B., Sérusiaux, E., and Lutzoni, F. 2017. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. 25th anniversary issue of Molecular Phylogenetics and Evolution 117:10–29. DOI: 10.1016/j.ympev.2017.08.013
Archaea (unpublished)
Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F. 2016. A new view of the tree of life. Nat Microbiol 1:16048. DOI: 10.1038/nmicrobiol.2016.48
Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F. 2016. A new view of the tree of life. Nat Microbiol 1:16048. DOI: 10.1038/nmicrobiol.2016.48
Li, Y., J. L. Steenwyk, Y. Chang, Y. Wang, T. Y. James, J. E. Stajich, J. W. Spatafora, M. Groenewald, C. W. Dunn, C. T. Hittinger, X.-X. Shen and A. Rokas (2021). A genome-scale phylogeny of the kingdom Fungi. Current Biology 31(8): 1653-1665.e1655. https://doi.org/10.1016/j.cub.2021.01.074
James, T.Y., Kauff, F., Schoch, C.L., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H.T., Rauhut, A., Reeb, V., Arnold, A.E., Amtoft, A., Stajich, J.E., Hosaka, K., Sung, G.H., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J.M., Slot, J.C., Wang, Z., Wilson, A.W., Schussler, A., Longcore, J.E., O'Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P.M., Powell, M.J., Taylor, J.W., White, M.M., Griffith, G.W., Davies, D.R., Humber, R.A., Morton, J.B., Sugiyama, J., Rossman, A.Y., Rogers, J.D., Pfister, D.H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R.A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R.A., Serdani, M., Crous, P.W., Hughes, K.W., Matsuura, K., Langer, E., Langer, G., Untereiner, W.A., Lucking, R., Budel, B., Geiser, D.M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D.S., Lutzoni, F., McLaughlin, D.J., Spatafora, J.W., and Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822. DOI: 10.1038/nature05110
Fungi v5 (unpublished)
O’Donnell, K., Cigelnik, E., & Nirenberg, H. I. (1998). Molecular Systematics and Phylogeography of the Gibberella fujikuroi Species Complex. Mycologia, 90(3), 465–493. https://doi.org/10.2307/3761407
Medeiros, I., & Lutzoni, F. (2022). Contribution to a modern treatment of Graphidaceae biodiversity in South Africa: Genera of tribe Graphideae with hyaline ascospores. The Lichenologist, 54(5), 253-270. doi:10.1017/S0024282922000263
Gómez -Zapata PA, Haelewaters D, Quijada L, Pfister DH, Aime MC. 2021. Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations. MycoKeys 78: 21-47. DOI: 10.3897/mycokeys.78.62046
Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12: 774839. DOI: 10.3389/fmicb.2021.774839
Zhao, X., Leavitt, S.D., Zhao, Z.T., Zhang, L.L., Arup, U., Grube, M., Pérez-Ortega, S., Printzen, C., Śliwa, L., Kraichak, E., Divakar, P.K., Crespo A., and & Lumbsch, H.T. (2016) Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence. Fungal Diversity 78: 293–304. DOI: 10.1007/s13225-015-0354-5
Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lucking R et al. . 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98(6):1088-103.
Haelewaters D, Park D, Johnston PR. 2021. Multilocus phylogenetic analysis reveals that Cyttariales is a synonym of Helotiales. Mycological Progress 20: 1323-1330. DOI: 10.1007/s11557-021-01736-2
Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F. 2016. A new view of the tree of life. Nat Microbiol 1:16048. DOI: 10.1038/nmicrobiol.2016.48
Bacteria v3 (unpublished)
Beza-Beza, C. F.; Jiménez-Ferbans, L.; McKenna, D. D. 2020. Phylogeny and systematics of wood-degrading neotropical bess beetles (Coleoptera: Passalidae: Passalinae). Arthropod Systematics & Phylogeny 78(2), 287 – 308. DOI: 10.26049/ASP78-2-2020-05
Pezizomycotina v2.1 (unpublished)
Coomber, A., Saville, A., Carbone, I. and J. B. Ristaino. 2023. An open-access T-BAS phylogeny for emerging Phytophthora species. PLoS One In Press
Videira SI, Groenewald JZ, Kolecka A, van Haren L, Boekhout T, Crous PW. 2015. Elucidating the Ramularia eucalypti species complex. Persoonia 34:50-64. http://dx.doi.org/10.3767/003158515X685670
Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619. DOI: 10.1016/j.funbio.2016.01.012
Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619. DOI: 10.1016/j.funbio.2016.01.012
Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619. DOI: 10.1016/j.funbio.2016.01.012
Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839
Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821
Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839
Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821
Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839
Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821
Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L. and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839
Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821
Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839
Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821