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Duke Herbarium : Publications since January 2017

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

Lutzoni, Francois M.

  1. Magain, N; Miadlikowska, J; Mueller, O; Gajdeczka, M; Truong, C; Salamov, AA; Dubchak, I; Grigoriev, IV; Goffinet, B; Sérusiaux, E; Lutzoni, F, 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., Molecular Phylogenetics and Evolution, vol. 117 (December, 2017), pp. 10-29 [doi]  [abs]
  2. Heiđmarsson, S; Gueidan, C; Miadlikowska, J; Lutzoni, F, Multi-locus phylogeny supports the placement of endocarpon pulvinatum within staurothele s. Str. (lichenised ascomycetes, eurotiomycetes, verrucariaceae), Phytotaxa, vol. 306 no. 1 (May, 2017), pp. 37-48 [doi]  [abs]
  3. Carbone, I; White, JB; Miadlikowska, J; Arnold, AE; Miller, MA; Kauff, F; U'Ren, JM; May, G; Lutzoni, F, 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, vol. 33 no. 8 (April, 2017), pp. 1160-1168 [doi]  [abs]
  4. Darnajoux, R; Zhang, X; McRose, DL; Miadlikowska, J; Lutzoni, F; Kraepiel, AML; Bellenger, J-P, Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates., New Phytologist, vol. 213 no. 2 (January, 2017), pp. 680-689 [doi]  [abs]
  5. Magain, N; Miadlikowska, J; Goffinet, B; Sérusiaux, E; Lutzoni, F, Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota)., Systematic Biology (OUP), vol. 66 no. 1 (January, 2017), pp. 74-99 [doi]  [abs]

Manos, Paul S.

  1. Meireles, JE; Manos, PS, Pervasive migration across rainforest and sandy coastal plain Aechmea nudicaulis (Bromeliaceae) populations despite contrasting environmental conditions., Molecular Ecology, vol. 27 no. 5 (March, 2018), pp. 1261-1272 [doi]  [abs]
  2. Harnik, PG; Maherali, H; Miller, JH; Manos, PS, Geographic range velocity and its association with phylogeny and life history traits in North American woody plants, Ecology and Evolution, vol. 8 no. 5 (March, 2018), pp. 2632-2644 [doi]  [abs]
  3. Deng, M; Jiang, X-L; Hipp, AL; Manos, PS; Hahn, M, Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia., Molecular Phylogenetics and Evolution, vol. 119 (February, 2018), pp. 170-181 [doi]  [abs]
  4. Hipp, AL; Manos, PS; González-Rodríguez, A; Hahn, M; Kaproth, M; McVay, JD; Avalos, SV; Cavender-Bares, J, Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity., New Phytologist, vol. 217 no. 1 (January, 2018), pp. 439-452 [doi]  [abs]
  5. Hauser, DA; Keuter, A; McVay, JD; Hipp, AL; Manos, PS, The evolution and diversification of the red oaks of the California Floristic Province ( Quercus section Lobatae , series Agrifoliae ), American journal of botany, vol. 104 no. 10 (October, 2017), pp. 1581-1595 [doi]
  6. Fitz-Gibbon, S; Hipp, AL; Pham, KK; Manos, PS; Sork, VL, Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)., Genome / National Research Council Canada = Genome / Conseil national de recherches Canada, vol. 60 no. 9 (September, 2017), pp. 743-755 [doi]  [abs]
  7. Pham, KK; Hipp, AL; Manos, PS; Cronn, RC, A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny., Genome / National Research Council Canada = Genome / Conseil national de recherches Canada, vol. 60 no. 9 (September, 2017), pp. 720-732 [doi]  [abs]
  8. McVay, JD; Hauser, D; Hipp, AL; Manos, PS, Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America., Genome / National Research Council Canada = Genome / Conseil national de recherches Canada, vol. 60 no. 9 (September, 2017), pp. 733-742 [doi]  [abs]
  9. McVay, JD; Hipp, AL; Manos, PS, A genetic legacy of introgression confounds phylogeny and biogeography in oaks., Proceedings of the Royal Society of London: Biological Sciences, vol. 284 no. 1854 (May, 2017) [doi]  [abs]
  10. Yu, Y; Xiang, Q; Manos, PS; Soltis, DE; Soltis, PS; Song, B-H; Cheng, S; Liu, X; Wong, G, Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences., PloS one, vol. 12 no. 2 (January, 2017), pp. e0171361 [doi]  [abs]

Miadlikowska, Jolanta M.

  1. Magain, N; Miadlikowska, J; Mueller, O; Gajdeczka, M; Truong, C; Salamov, AA; Dubchak, I; Grigoriev, IV; Goffinet, B; Sérusiaux, E; Lutzoni, F, 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., Molecular Phylogenetics and Evolution, vol. 117 (December, 2017), pp. 10-29 [doi]  [abs]
  2. Heiđmarsson, S; Gueidan, C; Miadlikowska, J; Lutzoni, F, Multi-locus phylogeny supports the placement of endocarpon pulvinatum within staurothele s. Str. (lichenised ascomycetes, eurotiomycetes, verrucariaceae), Phytotaxa, vol. 306 no. 1 (May, 2017), pp. 37-48 [available here], [doi]  [abs]
  3. Carbone, I; White, JB; Miadlikowska, J; Arnold, AE; Miller, MA; Kauff, F; U'Ren, JM; May, G; Lutzoni, F, 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, vol. 33 no. 8 (April, 2017), pp. 1160-1168 [available here], [doi]  [abs]
  4. Magain, N; Miadlikowska, J; Goffinet, B; Sérusiaux, E; Lutzoni, F, Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota)., Systematic Biology (OUP), vol. 66 no. 1 (January, 2017), pp. 74-99 [available here], [doi]  [abs]
  5. Darnajoux, R; Zhang, X; McRose, DL; Miadlikowska, J; Lutzoni, F; Kraepiel, AML; Bellenger, J-P, Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates., New Phytologist, vol. 213 no. 2 (January, 2017), pp. 680-689 [available here], [doi]  [abs]
  6. Gryganskyi, A. P., Humber, R. A., Miadlikowska, J., Smith, M., Wu, S., Rubinstein, N., Voigt, K., Walter, G., Anihchenko, I. M., Vilgalys, R., Molecular Phylogeny of Entomophthoralean Fungi., Molecular Phylogenetics and Evolution, vol. 65 (2017), pp. 682-694 [available here]
  7. Miadlikowska, J. and Lutzoni, F., Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits., American Journal of Botany, vol. 91 (2017), pp. 449–464 [available here]

Pryer, Kathleen M.

  1. Dijkhuizen, LW; Brouwer, P; Bolhuis, H; Reichart, G-J; Koppers, N; Huettel, B; Bolger, AM; Li, F-W; Cheng, S; Liu, X; Wong, GK-S; Pryer, K; Weber, A; Bräutigam, A; Schluepmann, H, Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify., New Phytologist, vol. 217 no. 1 (January, 2018), pp. 453-466 [doi]  [abs]
  2. Song, M; Kuo, L-Y; Huiet, L; Pryer, KM; Rothfels, CJ; Li, F-W, A novel chloroplast gene reported for flagellate plants., American journal of botany, vol. 105 no. 1 (January, 2018), pp. 117-121 [doi]  [abs]
  3. Rothfels, CJ; Pryer, KM; Li, F-W, Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing., New Phytologist, vol. 213 no. 1 (January, 2017), pp. 413-429 [doi]  [abs]

Shaw, A. Jonathan

  1. Yousefi, N; Hassel, K; Flatberg, KI; Kemppainen, P; Trucchi, E; Shaw, AJ; Kyrkjeeide, MO; Szövényi, P; Stenøien, HK, Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum., American journal of botany (July, 2017) [doi]  [abs]
  2. Carter, BE; Larraín, J; Manukjanová, A; Shaw, B; Shaw, AJ; Heinrichs, J; de Lange, P; Suleiman, M; Thouvenot, L; von Konrat, M, Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta)., Molecular Phylogenetics and Evolution, vol. 107 (February, 2017), pp. 16-26 [doi]  [abs]
  3. Patiño, J; Wang, J; Renner, MAM; Gradstein, SR; Laenen, B; Devos, N; Shaw, AJ; Vanderpoorten, A, Range size heritability and diversification patterns in the liverwort genus Radula., Molecular Phylogenetics and Evolution, vol. 106 (January, 2017), pp. 73-85 [doi]  [abs]

Vilgalys, Rytas J.

  1. Cregger, MA; Veach, AM; Yang, ZK; Crouch, MJ; Vilgalys, R; Tuskan, GA; Schadt, CW, The Populus holobiont: Dissecting the effects of plant niches and genotype on the microbiome, Microbiome, vol. 6 no. 1 (January, 2018) [doi]  [abs]
  2. Vélez, JM; Tschaplinski, TJ; Vilgalys, R; Schadt, CW; Bonito, G; Hameed, K; Engle, N; Hamilton, CE, Erratum to "Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees" [Fungal Ecol. 27 (Part A) (June 2017) 78-86], Fungal Ecology (January, 2018) [doi]
  3. Johansen, RB; Johnston, P; Mieczkowski, P; Perry, GL; Robeson, MS; Vilgalys, R; Burns, BR, Scattered far and wide: A broadly distributed temperate dune grass finds familiar fungal root associates in its invasive range, Soil Biology & Biochemistry, vol. 112 (September, 2017), pp. 177-190 [doi]
  4. Uehling, J; Gryganskyi, A; Hameed, K; Tschaplinski, T; Misztal, PK; Wu, S; Desirò, A; Vande Pol, N; Du, Z; Zienkiewicz, A; Zienkiewicz, K; Morin, E; Tisserant, E; Splivallo, R; Hainaut, M; Henrissat, B; Ohm, R; Kuo, A; Yan, J; Lipzen, A; Nolan, M; LaButti, K; Barry, K; Goldstein, AH; Labbé, J; Schadt, C; Tuskan, G; Grigoriev, I; Martin, F; Vilgalys, R; Bonito, G, Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens., Environmental Microbiology, vol. 19 no. 8 (August, 2017), pp. 2964-2983 [doi]  [abs]
  5. Smith, ME; Henkel, TW; Williams, GC; Aime, MC; Fremier, AK; Vilgalys, R, Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa , New Phytologist, vol. 215 no. 1 (July, 2017), pp. 443-453 [doi]
  6. Vélez, JM; Tschaplinski, TJ; Vilgalys, R; Schadt, CW; Bonito, G; Hameed, K; Engle, N; Hamilton, CE, Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees, Fungal Ecology, vol. 27 (June, 2017), pp. 78-86 [doi]  [abs]
  7. Gryganskyi, AP; Mullens, BA; Gajdeczka, MT; Rehner, SA; Vilgalys, R; Hajek, AE, Hijacked: Co-option of host behavior by entomophthoralean fungi., edited by Sheppard, DC, PLoS pathogens, vol. 13 no. 5 (May, 2017), pp. e1006274 [doi]
  8. Branco, S; Bi, K; Liao, H-L; Gladieux, P; Badouin, H; Ellison, CE; Nguyen, NH; Vilgalys, R; Peay, KG; Taylor, JW; Bruns, TD, Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes., edited by Giraud, T; Koskella, B; Laine, A-L, Molecular Ecology, vol. 26 no. 7 (April, 2017), pp. 2063-2076 [doi]  [abs]
  9. Li, Z; Yao, Q; Dearth, SP; Entler, MR; Castro Gonzalez, HF; Uehling, JK; Vilgalys, RJ; Hurst, GB; Campagna, SR; Labbé, JL; Pan, C, Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system., Environmental Microbiology, vol. 19 no. 3 (March, 2017), pp. 1041-1053 [doi]  [abs]
  10. Rosenthal, LM; Larsson, K-H; Branco, S; Chung, JA; Glassman, SI; Liao, H-L; Peay, KG; Smith, DP; Talbot, JM; Taylor, JW; Vellinga, EC; Vilgalys, R; Bruns, TD, Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal, Mycologia, vol. 109 no. 1 (January, 2017), pp. 115-127 [doi]
  11. Bonito, G; Hameed, K; Toome-Heller, M; Healy, R; Reid, C; Liao, H-L; Aime, MC; Schadt, C; Vilgalys, R, Atractiella rhizophila , sp. nov., an endorrhizal fungus isolated from the Populus root microbiome, Mycologia, vol. 109 no. 1 (January, 2017), pp. 18-26 [doi]
  12. 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]
  13. 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]
  14. 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]
  15. 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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