T-BAS Citations

Assembling the Microbial Tree of Life


If you use T-BAS please cite:

T-BAS v2.3

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

T-BAS core features

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

D3.js

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/

If you use the MSAViewer to create a Figure for publication then also cite:

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

If you use a T-BAS reference tree and metadata please cite:

Pezizomycotina tree

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

Bacterial tree

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

Fungal tree

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

Lecanoromycetes tree

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.

Ramularia tree

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

Aspergillus section Flavi tree

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

Fusarium solani species complex tree

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

Xylariaceae tree

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

Sebacinales tree

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

Peltigera tree

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

Laboulbeniomycetes tree

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

section Peltidea tree

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

section Peltigera+Retifoveatae tree

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

section Chloropeltigera tree

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

section Polydactylon tree

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 tree

Archaea (unpublished)

Bacteria genomic tree

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 original Hug et al tree

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

covid2 tree

covid2 (unpublished)
Fungi 267 tree

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

Fungi tree

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 tree

Fungi v5 (unpublished)

Fungi v5 taxid tree

Fungi v5 taxid (unpublished)
Fusarium species complex tree

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

Graphideae tree

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

Helotiales sclerotinioid clade v1 tree

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

Lecanoraceae tree

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

Lecanoromycetes v1 tree

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.

Leotiomycetes v1 tree

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

Life 16 tree

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

life3 tree

Bacteria v3 (unpublished)

Passalidae tree

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 tree

Pezizomycotina v2.1 (unpublished)

Phytophthora CoxI tree

Phytophthora CoxI (unpublished)
Phytophthora Nuclear tree

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

Ramularia v1 tree

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

Rhizoctonia v1 tree

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

Rhizoctonia v2 1 tree

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

Rhizoctonia v2 tree

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

Trebouxia clade A tree

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

Trebouxia clade C tree

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

Trebouxia clade I tree

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

Trebouxia clade S tree

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

Trebouxia tree

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