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Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests.

Darnajoux R, Magain N, Renaudin M, Lutzoni F, Bellenger JP, Zhang X.

Proc Natl Acad Sci U S A. 2019 Dec 3;116(49):24682-24688. doi: 10.1073/pnas.1913314116. Epub 2019 Nov 14.


Host availability drives distributions of fungal endophytes in the imperilled boreal realm.

U'Ren JM, Lutzoni F, Miadlikowska J, Zimmerman NB, Carbone I, May G, Arnold AE.

Nat Ecol Evol. 2019 Oct;3(10):1430-1437. doi: 10.1038/s41559-019-0975-2. Epub 2019 Sep 23.


The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.

Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM Jr, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB.

BMC Genomics. 2019 Jul 23;20(1):605. doi: 10.1186/s12864-019-5629-x.


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.

Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Magain N, U'Ren JM, Lutzoni F.

Microbiol Resour Announc. 2019 Jul 18;8(29). pii: e00328-19. doi: 10.1128/MRA.00328-19.


Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium.

Chen KH, Liao HL, Bellenger JP, Lutzoni F.

Environ Microbiol. 2019 Jul;21(7):2273-2289. doi: 10.1111/1462-2920.14605. Epub 2019 Apr 9.


Contemporaneous radiations of fungi and plants linked to symbiosis.

Lutzoni F, Nowak MD, Alfaro ME, Reeb V, Miadlikowska J, Krug M, Arnold AE, Lewis LA, Swofford DL, Hibbett D, Hilu K, James TY, Quandt D, Magallón S.

Nat Commun. 2018 Dec 21;9(1):5451. doi: 10.1038/s41467-018-07849-9.


Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera.

Pardo-De la Hoz CJ, Magain N, Lutzoni F, Goward T, Restrepo S, Miadlikowska J.

Front Microbiol. 2018 Nov 16;9:2770. doi: 10.3389/fmicb.2018.02770. eCollection 2018.


Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales.

Korotkin HB, Swenie RA, Miettinen O, Budke JM, Chen KH, Lutzoni F, Smith ME, Matheny PB.

Am J Bot. 2018 Nov;105(11):1869-1887. doi: 10.1002/ajb2.1183. Epub 2018 Oct 26.


Bioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen-forming genus Peltigera.

Lu J, Magain N, Miadlikowska J, Coyle JR, Truong C, Lutzoni F.

Am J Bot. 2018 Jul;105(7):1198-1211. doi: 10.1002/ajb2.1119. Epub 2018 Jul 12.


Strong specificity and network modularity at a very fine phylogenetic scale in the lichen genus Peltigera.

Chagnon PL, Magain N, Miadlikowska J, Lutzoni F.

Oecologia. 2018 Jul;187(3):767-782. doi: 10.1007/s00442-018-4159-6. Epub 2018 May 14.


RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi.

Chen KH, Liao HL, Arnold AE, Bonito G, Lutzoni F.

New Phytol. 2018 Jun;218(4):1597-1611. doi: 10.1111/nph.15092. Epub 2018 Mar 31.


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.

Magain N, Miadlikowska J, Mueller O, Gajdeczka M, Truong C, Salamov AA, Dubchak I, Grigoriev IV, Goffinet B, Sérusiaux E, Lutzoni F.

Mol Phylogenet Evol. 2017 Dec;117:10-29. doi: 10.1016/j.ympev.2017.08.013. Epub 2017 Aug 30.


Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota).

Magain N, Miadlikowska J, Goffinet B, Sérusiaux E, Lutzoni F.

Syst Biol. 2017 Jan 1;66(1):74-99. doi: 10.1093/sysbio/syw065.


Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni.

van Nieuwenhuijzen EJ, Miadlikowska JM, Houbraken JA, Adan OC, Lutzoni FM, Samson RA.

Stud Mycol. 2016 Sep;85:107-124. doi: 10.1016/j.simyco.2016.11.008. Epub 2016 Nov 27.


T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Kauff F, U'Ren JM, May G, Lutzoni F.

Bioinformatics. 2017 Apr 15;33(8):1160-1168. doi: 10.1093/bioinformatics/btw808.


Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates.

Darnajoux R, Zhang X, McRose DL, Miadlikowska J, Lutzoni F, Kraepiel AM, Bellenger JP.

New Phytol. 2017 Jan;213(2):680-689. doi: 10.1111/nph.14166. Epub 2016 Sep 2.


Erratum to: Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.

Chagnon PL, U'Ren JM, Miadlikowska J, Lutzoni F, Arnold AE.

Oecologia. 2016 Jun;181(2):633. No abstract available.


Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).

U'Ren JM, Miadlikowska J, Zimmerman NB, Lutzoni F, Stajich JE, Arnold AE.

Mol Phylogenet Evol. 2016 May;98:210-32. doi: 10.1016/j.ympev.2016.02.010. Epub 2016 Feb 20.


Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.

Chagnon PL, U'Ren JM, Miadlikowska J, Lutzoni F, Arnold AE.

Oecologia. 2016 Jan;180(1):181-91. doi: 10.1007/s00442-015-3457-5. Epub 2015 Sep 29. Erratum in: Oecologia. 2016 Jun;181(2):633.


A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda).

Oono R, Lefèvre E, Simha A, Lutzoni F.

Fungal Biol. 2015 Oct;119(10):917-928. doi: 10.1016/j.funbio.2015.07.003. Epub 2015 Jul 17.


The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift.

Gaya E, Fernández-Brime S, Vargas R, Lachlan RF, Gueidan C, Ramírez-Mejía M, Lutzoni F.

Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11600-5. doi: 10.1073/pnas.1507072112. Epub 2015 Aug 31.


Determination of elemental baseline using peltigeralean lichens from Northeastern Canada (Québec): Initial data collection for long term monitoring of the impact of global climate change on boreal and subarctic area in Canada.

Darnajoux R, Lutzoni F, Miadlikowska J, Bellenger JP.

Sci Total Environ. 2015 Nov 15;533:1-7. doi: 10.1016/j.scitotenv.2015.06.030. Epub 2015 Jul 4.


Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.

Chen KH, Miadlikowska J, Molnár K, Arnold AE, U'Ren JM, Gaya E, Gueidan C, Lutzoni F.

Mol Phylogenet Evol. 2015 Apr;85:117-30. doi: 10.1016/j.ympev.2015.01.008. Epub 2015 Feb 17.


Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.

Oono R, Lutzoni F, Arnold AE, Kaye L, U'Ren JM, May G, Carbone I.

Am J Bot. 2014 Aug;101(8):1362-74. doi: 10.3732/ajb.1400141. Epub 2014 Aug 15.


Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).

Miadlikowska J, Richardson D, Magain N, Ball B, Anderson F, Cameron R, Lendemer J, Truong C, Lutzoni F.

Am J Bot. 2014 Jul;101(7):1141-1156. Epub 2014 Jul 11.


A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

Miadlikowska J, Kauff F, Högnabba F, Oliver JC, Molnár K, Fraker E, Gaya E, Hafellner J, Hofstetter V, Gueidan C, Otálora MA, Hodkinson B, Kukwa M, Lücking R, Björk C, Sipman HJ, Burgaz AR, Thell A, Passo A, Myllys L, Goward T, Fernández-Brime S, Hestmark G, Lendemer J, Lumbsch HT, Schmull M, Schoch CL, Sérusiaux E, Maddison DR, Arnold AE, Lutzoni F, Stenroos S.

Mol Phylogenet Evol. 2014 Oct;79:132-68. doi: 10.1016/j.ympev.2014.04.003. Epub 2014 Apr 18.


Is vanadium a biometal for boreal cyanolichens?

Darnajoux R, Constantin J, Miadlikowska J, Lutzoni F, Bellenger JP.

New Phytol. 2014 May;202(3):765-71. doi: 10.1111/nph.12777. Epub 2014 Mar 18.


High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.

McDonald TR, Mueller O, Dietrich FS, Lutzoni F.

BMC Genomics. 2013 Apr 4;14:225. doi: 10.1186/1471-2164-14-225.


Assessing population structure and host specialization in lichenized cyanobacteria.

O'Brien HE, Miadlikowska J, Lutzoni F.

New Phytol. 2013 Apr;198(2):557-66. doi: 10.1111/nph.12165. Epub 2013 Feb 13.


Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes.

Gazis R, Miadlikowska J, Lutzoni F, Arnold AE, Chaverri P.

Mol Phylogenet Evol. 2012 Oct;65(1):294-304. doi: 10.1016/j.ympev.2012.06.019. Epub 2012 Jul 4.


Host and geographic structure of endophytic and endolichenic fungi at a continental scale.

U'Ren JM, Lutzoni F, Miadlikowska J, Laetsch AD, Arnold AE.

Am J Bot. 2012 May;99(5):898-914. doi: 10.3732/ajb.1100459. Epub 2012 Apr 26.


Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota).

Geml J, Kauff F, Brochmann C, Lutzoni F, Laursen GA, Redhead SA, Taylor DL.

Fungal Biol. 2012 Mar;116(3):388-400. doi: 10.1016/j.funbio.2011.12.009. Epub 2011 Dec 30.


Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).

Gaya E, Högnabba F, Holguin A, Molnar K, Fernández-Brime S, Stenroos S, Arup U, Søchting U, Van den Boom P, Lücking R, Sipman HJ, Lutzoni F.

Mol Phylogenet Evol. 2012 May;63(2):374-87. doi: 10.1016/j.ympev.2012.01.012. Epub 2012 Jan 28.


Molecular phylogeny of Heteroplacidium, Placidium, and related catapyrenioid genera (Verrucariaceae, lichen-forming Ascomycota).

Prieto M, Martínez I, Aragón G, Gueidan C, Lutzoni F.

Am J Bot. 2012 Jan;99(1):23-35. doi: 10.3732/ajb.1100239. Epub 2011 Dec 30.


Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.

Hodkinson BP, Gottel NR, Schadt CW, Lutzoni F.

Environ Microbiol. 2012 Jan;14(1):147-61. doi: 10.1111/j.1462-2920.2011.02560.x. Epub 2011 Sep 12.


Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.

McDonald TR, Dietrich FS, Lutzoni F.

Mol Biol Evol. 2012 Jan;29(1):51-60. doi: 10.1093/molbev/msr123. Epub 2011 Jun 16.


Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota).

Schmull M, Miadlikowska J, Pelzer M, Stocker-Wörgötter E, Hofstetter V, Fraker E, Hodkinson BP, Reeb V, Kukwa M, Lumbsch HT, Kauff F, Lutzoni F.

Mycologia. 2011 Sep-Oct;103(5):983-1003. doi: 10.3852/10-234. Epub 2011 Jun 3.


Expansion of the Stictidaceae by the addition of the saxicolous lichen-forming genus Ingvariella.

Fernández-Brime S, Llimona X, Molnar K, Stenroos S, Högnabba F, Björk C, Lutzoni F, Gaya E.

Mycologia. 2011 Jul-Aug;103(4):755-63. doi: 10.3852/10-287. Epub 2011 Apr 6.


Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.

Gaya E, Redelings BD, Navarro-Rosinés P, Llimona X, De Cáceres M, Lutzoni F.

Mycologia. 2011 Mar-Apr;103(2):361-78. doi: 10.3852/10-120. Epub 2010 Dec 7.


Single origin and subsequent diversification of central Andean endemic Umbilicaria species.

Hestmark G, Miadlikowska J, Kauff F, Fraker E, Molnar K, Lutzoni F.

Mycologia. 2011 Jan-Feb;103(1):45-56. doi: 10.3852/10-012. Epub 2010 Sep 19.


Fungal and algal gene expression in early developmental stages of lichen-symbiosis.

Joneson S, Armaleo D, Lutzoni F.

Mycologia. 2011 Mar-Apr;103(2):291-306. doi: 10.3852/10-064. Epub 2010 Sep 19.


Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens.

U'ren JM, Lutzoni F, Miadlikowska J, Arnold AE.

Microb Ecol. 2010 Aug;60(2):340-53. doi: 10.1007/s00248-010-9698-2. Epub 2010 Jul 13.


A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?

Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F.

Syst Biol. 2009 Jun;58(3):283-97. doi: 10.1093/sysbio/syp001. Epub 2009 Jul 11.


Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes).

Otálora MA, Martínez I, O'Brien H, Molina MC, Aragón G, Lutzoni F.

Mol Phylogenet Evol. 2010 Sep;56(3):1089-95. doi: 10.1016/j.ympev.2010.05.013. Epub 2010 May 20.


Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis.

Prieto M, Martínez I, Aragón G, Otálora MA, Lutzoni F.

Mycologia. 2010 Mar-Apr;102(2):291-304.


Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota).

Otálora MA, Aragón G, Molina MC, Martínez I, Lutzoni F.

Mycologia. 2010 Mar-Apr;102(2):279-90.


Phylogeny of rock-inhabiting fungi related to Dothideomycetes.

Ruibal C, Gueidan C, Selbmann L, Gorbushina AA, Crous PW, Groenewald JZ, Muggia L, Grube M, Isola D, Schoch CL, Staley JT, Lutzoni F, de Hoog GS.

Stud Mycol. 2009;64:123-133S7. doi: 10.3114/sim.2009.64.06.


The search for the fungal tree of life.

McLaughlin DJ, Hibbett DS, Lutzoni F, Spatafora JW, Vilgalys R.

Trends Microbiol. 2009 Nov;17(11):488-97. doi: 10.1016/j.tim.2009.08.001. Epub 2009 Sep 24. Review.



Lutzoni F, Miadlikowska J.

Curr Biol. 2009 Jul 14;19(13):R502-3. doi: 10.1016/j.cub.2009.04.034. No abstract available.


Assessing reproductive isolation in highly diverse communities of the lichen-forming fungal genus peltigera.

O'Brien HE, Miadlikowska J, Lutzoni F.

Evolution. 2009 Aug;63(8):2076-86. doi: 10.1111/j.1558-5646.2009.00685.x. Epub 2009 Mar 17.


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