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Duke Herbarium : Publications since January 2021

List all publications in the database.    :chronological  alphabetical  combined  bibtex listing:

Lutzoni, Francois M.

  1. Chen, K-H; Liao, H-L; Arnold, AE; Korotkin, HB; Wu, SH; Matheny, PB; Lutzoni, F, Comparative transcriptomics of fungal endophytes in co-culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates., The New Phytologist, vol. 234 no. 5 (June, 2022), pp. 1832-1847 [doi]  [abs]
  2. Geml, J; Arnold, AE; Semenova-Nelsen, TA; Nouhra, ER; Drechsler-Santos, ER; Góes-Neto, A; Morgado, LN; Ódor, P; Hegyi, B; Oriol, G; Ibáñez, A; Tedersoo, L; Lutzoni, F, Community dynamics of soil-borne fungal communities along elevation gradients in neotropical and palaeotropical forests., Molecular Ecology, vol. 31 no. 7 (April, 2022), pp. 2044-2060 [doi]  [abs]
  3. Franco, MEE; Wisecaver, JH; Arnold, AE; Ju, Y-M; Slot, JC; Ahrendt, S; Moore, LP; Eastman, KE; Scott, K; Konkel, Z; Mondo, SJ; Kuo, A; Hayes, RD; Haridas, S; Andreopoulos, B; Riley, R; LaButti, K; Pangilinan, J; Lipzen, A; Amirebrahimi, M; Yan, J; Adam, C; Keymanesh, K; Ng, V; Louie, K; Northen, T; Drula, E; Henrissat, B; Hsieh, H-M; Youens-Clark, K; Lutzoni, F; Miadlikowska, J; Eastwood, DC; Hamelin, RC; Grigoriev, IV; U'Ren, JM, Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes., The New Phytologist, vol. 233 no. 3 (February, 2022), pp. 1317-1330 [doi]  [abs]
  4. Pardo-De la Hoz, CJ; Medeiros, ID; Gibert, JP; Chagnon, P-L; Magain, N; Miadlikowska, J; Lutzoni, F, Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks., Ecology and Evolution, vol. 12 no. 3 (February, 2022), pp. e8649 [doi]  [abs]
  5. Medeiros, ID; Mazur, E; Miadlikowska, J; Flakus, A; Rodriguez-Flakus, P; Pardo-De la Hoz, CJ; Cieślak, E; Śliwa, L; Lutzoni, F, 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, vol. 12 (December, 2021) [doi]  [abs]
  6. Cornet, L; Magain, N; Baurain, D; Lutzoni, F, Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens., Molecular Phylogenetics and Evolution, vol. 162 (September, 2021), pp. 107100 [doi]  [abs]
  7. Crous, PW; Hernández-Restrepo, M; Schumacher, RK; Cowan, DA; Maggs-Kölling, G; Marais, E; Wingfield, MJ; Yilmaz, N; Adan, OCG; Akulov, A; Duarte, EÁ; Berraf-Tebbal, A; Bulgakov, TS; Carnegie, AJ; de Beer, ZW; Decock, C; Dijksterhuis, J; Duong, TA; Eichmeier, A; Hien, LT; Houbraken, JAMP; Khanh, TN; Liem, NV; Lombard, L; Lutzoni, FM; Miadlikowska, JM; Nel, WJ; Pascoe, IG; Roets, F; Roux, J; Samson, RA; Shen, M; Spetik, M; Thangavel, R; Thanh, HM; Thao, LD; van Nieuwenhuijzen, EJ; Zhang, JQ; Zhang, Y; Zhao, LL; Groenewald, JZ, New and Interesting Fungi. 4., Fungal Systematics and Evolution, vol. 7 (June, 2021), pp. 255-343 [doi]  [abs]
  8. Oita, S; Ibáñez, A; Lutzoni, F; Miadlikowska, J; Geml, J; Lewis, LA; Hom, EFY; Carbone, I; U'Ren, JM; Arnold, AE, Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale., Communications Biology, vol. 4 no. 1 (March, 2021), pp. 313 [doi]  [abs]

Manos, Paul S.

  1. Crowl, AA; Fritsch, PW; Tiley, GP; Lynch, NP; Ranney, TG; Ashrafi, H; Manos, PS, A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)., Am J Bot, vol. 109 no. 10 (October, 2022), pp. 1596-1606 [doi]  [abs]
  2. Zhou, B-F; Yuan, S; Crowl, AA; Liang, Y-Y; Shi, Y; Chen, X-Y; An, Q-Q; Kang, M; Manos, PS; Wang, B, Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere., Nature Communications, vol. 13 no. 1 (March, 2022), pp. 1320 [doi]  [abs]
  3. Manos, PS; Hipp, AL, An updated infrageneric classification of the north american oaks (Quercus subgenus quercus): Review of the contribution of phylogenomic data to biogeography and species diversity, Forests, vol. 12 no. 6 (June, 2021) [doi]  [abs]

Miadlikowska, Jolanta M.

  1. McMullin, RT; Miadlikowska, J, Two rare Peltigera species new to the Canadian Arctic, P. islandica and P. lyngei, Plant and Fungal Systematics, vol. 67 no. 1 (July, 2022), pp. 17-23 [doi]  [abs]
  2. Franco, MEE; Wisecaver, JH; Arnold, AE; Ju, Y-M; Slot, JC; Ahrendt, S; Moore, LP; Eastman, KE; Scott, K; Konkel, Z; Mondo, SJ; Kuo, A; Hayes, RD; Haridas, S; Andreopoulos, B; Riley, R; LaButti, K; Pangilinan, J; Lipzen, A; Amirebrahimi, M; Yan, J; Adam, C; Keymanesh, K; Ng, V; Louie, K; Northen, T; Drula, E; Henrissat, B; Hsieh, H-M; Youens-Clark, K; Lutzoni, F; Miadlikowska, J; Eastwood, DC; Hamelin, RC; Grigoriev, IV; U'Ren, JM, Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes., The New Phytologist, vol. 233 no. 3 (February, 2022), pp. 1317-1330 [doi]  [abs]
  3. Pardo-De la Hoz, CJ; Medeiros, ID; Gibert, JP; Chagnon, P-L; Magain, N; Miadlikowska, J; Lutzoni, F, Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks., Ecology and Evolution, vol. 12 no. 3 (February, 2022), pp. e8649 [doi]  [abs]
  4. Medeiros, ID; Mazur, E; Miadlikowska, J; Flakus, A; Rodriguez-Flakus, P; Pardo-De la Hoz, CJ; Cieślak, E; Śliwa, L; Lutzoni, F, 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, vol. 12 (December, 2021) [doi]  [abs]
  5. Crous, PW; Hernández-Restrepo, M; Schumacher, RK; Cowan, DA; Maggs-Kölling, G; Marais, E; Wingfield, MJ; Yilmaz, N; Adan, OCG; Akulov, A; Duarte, EÁ; Berraf-Tebbal, A; Bulgakov, TS; Carnegie, AJ; de Beer, ZW; Decock, C; Dijksterhuis, J; Duong, TA; Eichmeier, A; Hien, LT; Houbraken, JAMP; Khanh, TN; Liem, NV; Lombard, L; Lutzoni, FM; Miadlikowska, JM; Nel, WJ; Pascoe, IG; Roets, F; Roux, J; Samson, RA; Shen, M; Spetik, M; Thangavel, R; Thanh, HM; Thao, LD; van Nieuwenhuijzen, EJ; Zhang, JQ; Zhang, Y; Zhao, LL; Groenewald, JZ, New and Interesting Fungi. 4., Fungal Systematics and Evolution, vol. 7 (June, 2021), pp. 255-343 [doi]  [abs]
  6. Oita, S; Ibáñez, A; Lutzoni, F; Miadlikowska, J; Geml, J; Lewis, LA; Hom, EFY; Carbone, I; U'Ren, JM; Arnold, AE, Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale., Communications Biology, vol. 4 no. 1 (March, 2021), pp. 313 [doi]  [abs]
  7. Stone, DF; Mccune, B; Pardo-De La Hoz, CJ; Magain, N; Miadlikowska, J, Sinuicella denisonii, a new genus and species in the Peltigeraceae from western North America, Lichenologist, vol. 53 no. 2 (March, 2021), pp. 185-192 [doi]  [abs]

Pryer, Kathleen M.

  1. Windham, MD; Huiet, L; Metzgar, JS; Ranker, TA; Yatskievych, G; Haufler, CH; Pryer, KM, Once more unto the breach, dear friends: Resolving the origins and relationships of the Pellaea wrightiana hybrid complex., American Journal of Botany, vol. 109 no. 5 (May, 2022), pp. 821-850 [doi]  [abs]
  2. Windham, MD; Pryer, KM, FIRST REPORT OF UTAH FRAGILE FERN (CYSTOPTERIS: CYSTOPTERIDACEAE) FROM NEW MEXICO, AND NEW NOMENCLATURAL COMBINATIONS IN CYSTOPTERIS TENNESEENSIS, Journal of the Botanical Research Institute of Texas, vol. 16 no. 1 (January, 2022) [doi]  [abs]
  3. Windham, MD; Pryer, KM; Allphin, L, AN OVERVIEW OF NEW MEXICAN BOECHERA (BRASSICACEAE) INCLUDING THREE NEW SPECIES AND THIRTEEN NEW NOMENCLATURAL COMBINATIONS, Journal of the Botanical Research Institute of Texas, vol. 16 no. 1 (January, 2022), pp. 9-24 [doi]  [abs]
  4. Heron, K; Windham, MD; Farrar, DR; Pryer, KM, Looking Back on 130 Years of Fern and Lycophyte Research in Glacier National Park, Montana: A Modern Taxonomic Account, American Fern Journal, vol. 111 no. 4 (October, 2021), pp. 223-250, American Fern Society [doi]  [abs]
  5. Fauskee, BD; Sigel, EM; Pryer, KM; Grusz, AL, Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes., Am J Bot, vol. 108 no. 5 (May, 2021), pp. 820-827 [doi]  [abs]
  6. Sosa, K; Pryer, KM; Huiet, L; Yatskievych, G; Windham, MD, Cheilanthes ecuadorensis: A New Species of Cheilanthes s. s. (Pteridaceae) from Northern South America, Systematic Botany, vol. 46 no. 2 (April, 2021), pp. 249-259 [doi]  [abs]
  7. Grusz, AL; Windham, MD; Picard, KT; Pryer, KM; Schuettpelz, E; Haufler, CH, A drought-driven model for the evolution of obligate apomixis in ferns: evidence from pellaeids (Pteridaceae)., American Journal of Botany, vol. 108 no. 2 (February, 2021), pp. 263-283 [doi]  [abs]

Shaw, A. Jonathan

  1. Carrell, AA; Lawrence, TJ; Cabugao, KGM; Carper, DL; Pelletier, DA; Lee, JH; Jawdy, SS; Grimwood, J; Schmutz, J; Hanson, PJ; Shaw, AJ; Weston, DJ, Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming., The New Phytologist, vol. 234 no. 6 (June, 2022), pp. 2111-2125 [doi]  [abs]
  2. Duffy, AM; Ricca, M; Robinson, S; Aguero, B; Johnson, MG; Stenøien, HK; Flatberg, KI; Hassel, K; Shaw, AJ, Heterogeneous genetic structure in eastern North American peat mosses (Sphagnum), Biological Journal of the Linnean Society, vol. 135 no. 4 (April, 2022), pp. 692-707 [doi]  [abs]
  3. Carrell, AA; Veličković, D; Lawrence, TJ; Bowen, BP; Louie, KB; Carper, DL; Chu, RK; Mitchell, HD; Orr, G; Markillie, LM; Jawdy, SS; Grimwood, J; Shaw, AJ; Schmutz, J; Northen, TR; Anderton, CR; Pelletier, DA; Weston, DJ, Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism., The Isme Journal, vol. 16 no. 4 (April, 2022), pp. 1074-1085 [doi]  [abs]
  4. Piatkowski, BT; Yavitt, JB; Turetsky, MR; Shaw, AJ, Natural selection on a carbon cycling trait drives ecosystem engineering by Sphagnum (peat moss)., Proceedings of the Royal Society B: Biological Sciences, vol. 288 no. 1957 (August, 2021), pp. 20210609 [doi]  [abs]
  5. Meleshko, O; Martin, MD; Korneliussen, TS; Schröck, C; Lamkowski, P; Schmutz, J; Healey, A; Piatkowski, BT; Shaw, AJ; Weston, DJ; Flatberg, KI; Szövényi, P; Hassel, K; Stenøien, HK, Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus., Molecular Biology and Evolution, vol. 38 no. 7 (June, 2021), pp. 2750-2766 [doi]  [abs]

Vilgalys, Rytas J.

  1. Milani, T; Hoeksema, JD; Jobbágy, EG; Rojas, JA; Vilgalys, R; Teste, FP, Co-invading ectomycorrhizal fungal succession in pine-invaded mountain grasslands, Fungal Ecology, vol. 60 (December, 2022) [doi]  [abs]
  2. Policelli, N; Hoeksema, JD; Moyano, J; Vilgalys, R; Vivelo, S; Bhatnagar, JM, Global pine tree invasions are linked to invasive root symbionts., The New Phytologist (October, 2022) [doi]
  3. Hackman, JJ; Rose, BD; Frank, HER; Vilgalys, R; Cook, RL; Garcia, K, NPK fertilizer use in loblolly pine plantations: Who are we really feeding?, Forest Ecology and Management, vol. 520 (September, 2022) [doi]  [abs]
  4. Gryganskyi, AP; Nie, Y; Hajek, AE; Hodge, KT; Liu, X-Y; Aadland, K; Voigt, K; Anishchenko, IM; Kutovenko, VB; Kava, L; Vuek, A; Vilgalys, R; Huang, B; Stajich, JE, The Early Terrestrial Fungal Lineage of Conidiobolus-Transition from Saprotroph to Parasitic Lifestyle., Journal of Fungi (Basel, Switzerland), vol. 8 no. 8 (July, 2022), pp. 789 [doi]  [abs]
  5. Erlandson, SR; Margis, R; Ramirez, A; Nguyen, N; Lofgren, LA; Liao, H-L; Vilgalys, R; Kennedy, PG; Peay, KG, Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens., The New Phytologist, vol. 234 no. 6 (June, 2022), pp. 1910-1913 [doi]  [abs]
  6. Fremin, BJ; Bhatt, AS; Kyrpides, NC; Global Phage Small Open Reading Frame (GP-SmORF) Consortium,, Thousands of small, novel genes predicted in global phage genomes., Cell Reports, vol. 39 no. 12 (June, 2022), pp. 110984 [doi]  [abs]
  7. Barge, EG; Leopold, DR; Rojas, A; Vilgalys, R; Busby, PE, Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism., Molecular Ecology, vol. 31 no. 10 (May, 2022), pp. 3018-3030 [doi]  [abs]
  8. Wang, H; Tian, J; Chen, H; Ho, M; Vilgalys, R; Bu, ZJ; Liu, X; Richardson, CJ, Vegetation and microbes interact to preserve carbon in many wooded peatlands, Communications Earth & Environment, vol. 2 no. 1 (December, 2021) [doi]  [abs]
  9. Liao, HL; Bonito, G; Hameed, K; Wu, SH; Chen, KH; Labbé, J; Schadt, CW; Tuskan, GA; Martin, F; Kuo, A; Barry, K; Grigoriev, IV; Vilgalys, R, Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi, Frontiers in Microbiology, vol. 12 (November, 2021) [doi]  [abs]
  10. Tian, J; Wang, H; Vilgalys, R; Ho, M; Flanagan, N; Richardson, CJ, Response of fungal communities to fire in a subtropical peatland, Plant and Soil, vol. 466 no. 1-2 (September, 2021), pp. 525-543 [doi]  [abs]
  11. Peng, L; Shan, X; Wang, Y; Martin, F; Vilgalys, R; Yuan, Z, Hybrid Genome Assembly and Gene Repertoire of the Root Endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes)., Molecular Plant Microbe Interactions : Mpmi, vol. 34 no. 6 (June, 2021), pp. 711-714 [doi]  [abs]
  12. Lofgren, LA; Nguyen, NH; Vilgalys, R; Ruytinx, J; Liao, H-L; Branco, S; Kuo, A; LaButti, K; Lipzen, A; Andreopoulos, W; Pangilinan, J; Riley, R; Hundley, H; Na, H; Barry, K; Grigoriev, IV; Stajich, JE; Kennedy, PG, Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi., The New Phytologist, vol. 230 no. 2 (April, 2021), pp. 774-792 [doi]  [abs]
  13. Vélez, JM; Morris, RM; Vilgalys, R; Labbé, J; Schadt, CW, Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives., Plos One, vol. 16 no. 1 (January, 2021), pp. e0231367 [doi]  [abs]
  14. PB Matheny, JM Curtis, V Hofstetter, MC Aime, JM Moncalvo, ZW Ge, JC Slot, JF Ammirati, TJ Baroni, NL Bougher, KW Hughes, DJ Lodge, RW Kerrigan, MT Seidl, DK Aanen, M DeNitis, GM Daniele, DE Desjardin, BR Kropp, LL Norvell, A Parker, EC Vellinga, R Vilgalys, DS Hibbett, Major clades of Agaricales: a multilocus phylogenetic overview., Mycologia, United States, vol. 98 no. 6 (October, 2007), pp. 982-95, ISSN 0027-5514  [abs]
  15. JM Moncalvo, RH Nilsson, B Koster, SM Dunham, T Bernauer, PB Matheny, TM Porter, S Margaritescu, M Weiss, S Garnica, E Danell, G Langer, E Langer, E Larsson, KH Larsson, R Vilgalys, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods., Mycologia, United States, vol. 98 no. 6 (October, 2007), pp. 937-48, ISSN 0027-5514  [abs]
  16. TY James, PM Letcher, JE Longcore, SE Mozley-Standridge, D Porter, MJ Powell, GW Griffith, R Vilgalys, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)., Mycologia, United States, vol. 98 no. 6 (October, 2007), pp. 860-71, ISSN 0027-5514  [abs]
  17. AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR., Mycologia, United States, vol. 99 no. 2 (September, 2007), pp. 185-206, ISSN 0027-5514  [abs]

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