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Items: 43

1.

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.

PMID:
31548643
2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

PMID:
28860010
8.

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.

9.

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.

10.

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.

PMID:
28003260
11.

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.

12.

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.

PMID:
27106850
13.

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.

PMID:
26903035
14.

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.

PMID:
26420599
15.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

Divakar PK, Crespo A, Wedin M, Leavitt SD, Hawksworth DL, Myllys L, McCune B, Randlane T, Bjerke JW, Ohmura Y, Schmitt I, Boluda CG, Alors D, Roca-Valiente B, Del-Prado R, Ruibal C, Buaruang K, Núñez-Zapata J, Amo de Paz G, Rico VJ, Molina MC, Elix JA, Esslinger TL, Tronstad IK, Lindgren H, Ertz D, Gueidan C, Saag L, Mark K, Singh G, Dal Grande F, Parnmen S, Beck A, Benatti MN, Blanchon D, Candan M, Clerc P, Goward T, Grube M, Hodkinson BP, Hur JS, Kantvilas G, Kirika PM, Lendemer J, Mattsson JE, Messuti MI, Miadlikowska J, Nelsen M, Ohlson JI, Pérez-Ortega S, Saag A, Sipman HJ, Sohrabi M, Thell A, Thor G, Truong C, Yahr R, Upreti DK, Cubas P, Lumbsch HT.

New Phytol. 2015 Dec;208(4):1217-26. doi: 10.1111/nph.13553. Epub 2015 Aug 24.

16.

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.

PMID:
26151649
17.

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.

PMID:
25701073
18.

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.

19.

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.

20.

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.

21.

Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi.

U'Ren JM, Riddle JM, Monacell JT, Carbone I, Miadlikowska J, Arnold AE.

Mol Ecol Resour. 2014 Sep;14(5):1032-48. doi: 10.1111/1755-0998.12252. Epub 2014 Apr 10.

PMID:
24628864
22.

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.

23.

Molecular phylogeny of the Entomophthoromycota.

Gryganskyi AP, Humber RA, Smith ME, Miadlikowska J, Wu S, Voigt K, Walther G, Anishchenko IM, Vilgalys R.

Mol Phylogenet Evol. 2012 Nov;65(2):682-94. doi: 10.1016/j.ympev.2012.07.026. Epub 2012 Aug 2. Erratum in: Mol Phylogenet Evol. 2013 Mar;66(3):1099. Miadlikovska, Jolanta [corrected to Miadlikowska, Jolanta].

PMID:
22877646
24.

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.

PMID:
22772026
25.

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.

26.

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.

PMID:
21642348
27.

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.

PMID:
20943548
28.

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.

PMID:
20625714
29.

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.

PMID:
20525584
30.

Lichens.

Lutzoni F, Miadlikowska J.

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

31.

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.

PMID:
19453383
32.

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.

Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou M, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW.

Syst Biol. 2009 Apr;58(2):224-39. doi: 10.1093/sysbio/syp020. Epub 2009 Jun 4.

PMID:
20525580
33.

Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha.

Ertz D, Miadlikowska J, Lutzoni F, Dessein S, Raspé O, Vigneron N, Hofstetter V, Diederich P.

Mycol Res. 2009 Jan;113(Pt 1):141-52. doi: 10.1016/j.mycres.2008.09.002. Epub 2008 Sep 27.

PMID:
18929650
34.

A higher-level phylogenetic classification of the Fungi.

Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüssler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N.

Mycol Res. 2007 May;111(Pt 5):509-47. Epub 2007 Mar 13. Review.

PMID:
17572334
35.

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.

Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lücking R, Hestmark G, Otalora MG, Rauhut A, Büdel B, Scheidegger C, Timdal E, Stenroos S, Brodo I, Perlmutter GB, Ertz D, Diederich P, Lendemer JC, May P, Schoch CL, Arnold AE, Gueidan C, Tripp E, Yahr R, Robertson C, Lutzoni F.

Mycologia. 2006 Nov-Dec;98(6):1088-103.

PMID:
17486983
36.

Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.

Geiser DM, Gueidan C, Miadlikowska J, Lutzoni F, Kauff F, Hofstetter V, Fraker E, Schoch CL, Tibell L, Untereiner WA, Aptroot A.

Mycologia. 2006 Nov-Dec;98(6):1053-64.

PMID:
17486980
37.

A five-gene phylogeny of Pezizomycotina.

Spatafora JW, Sung GH, Johnson D, Hesse C, O'Rourke B, Serdani M, Spotts R, Lutzoni F, Hofstetter V, Miadlikowska J, Reeb V, Gueidan C, Fraker E, Lumbsch T, Lücking R, Schmitt I, Hosaka K, Aptroot A, Roux C, Miller AN, Geiser DM, Hafellner J, Hestmark G, Arnold AE, Büdel B, Rauhut A, Hewitt D, Untereiner WA, Cole MS, Scheidegger C, Schultz M, Sipman H, Schoch CL.

Mycologia. 2006 Nov-Dec;98(6):1018-28.

PMID:
17486977
38.

Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).

Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F.

Mol Phylogenet Evol. 2007 Jul;44(1):412-26. Epub 2006 Oct 25.

PMID:
17207641
39.

Reconstructing the early evolution of Fungi using a six-gene phylogeny.

James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schüssler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lücking R, Büdel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R.

Nature. 2006 Oct 19;443(7113):818-22.

PMID:
17051209
40.

Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages.

Higgins KL, Arnold AE, Miadlikowska J, Sarvate SD, Lutzoni F.

Mol Phylogenet Evol. 2007 Feb;42(2):543-55. Epub 2006 Jul 26.

PMID:
17005421
41.

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lücking R, Lumbsch T, O'Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim YW, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R.

Am J Bot. 2004 Oct;91(10):1446-80. doi: 10.3732/ajb.91.10.1446.

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