Publications
Peer-Reviewed Articles and Book Chapters
2026
Grewe, F, & Lumbsch, HT (2026) The myth of asexual fungi. Trends in Genetics. pdf
Dehnert, G, Lazarcik, J, Haney, S, Strom, SM, Maddox, JD, Grewe, F, & Cornelius Ruhs, E (2026) Bald Eagles as bio-sentinels: Monitoring and fingerprinting PFAS contamination. Environmental Research: 124413. pdf
de Abreu, J, Barcenas-Peña, A, Poengsungnoen, V, Wang, X, Huang, J-P, Lumbsch, HT, & Grewe, F (2026) High-Throughput Sequencing Supports Strong Geographical Patterns in the Cladia aggregata Complex (Ascomycota, Lecanorales) and Identifies the Asian Clade as an Independent Species. Journal of Fungi 12. pdf
2025
Sun, Y, Doellman, MM, Barcenas-Pena, A, Poengsungnoen, V, Huhndorf, S, Lumbsch, HT, & Grewe, F (2025) High-quality draft genome sequence of the tropical lichen-forming fungus Lecanora helva (Lecanoraceae, Ascomycota). Microbiology Resource Announcements 14: e0061025. pdf
Søchting, U, Friedl, T, Moestrup, Ø, Grewe, F, Sun, Y, Çakır, YT, Ganzera, M, Glaser, K, Heesch, S, Hammerle, F, Nimptsch, D, Olberg, B, & Karsten, U (2025) Mass development of a filamentous and likely nitrophilous aerophytic green alga on tree bark: Apatococcus ammoniophilus sp. nov. (Chlorophyta, Trebouxiophyceae). Frontiers in Microbiology 16. pdf
Patterson, BD, Chaves, HER, Soares, AER, Vilela, JF, & Grewe, F (2025) Complete mitochondrial genomes support the composition and rank of the American weasel genus Neogale (Carnivora: Mustelidae). Journal of Animal Diversity 7(1): 41–48. pdf
Otero, A, Lumbsch, HT, Degtjarenko, P, & Grewe, F (2025) Speciation continuum in non-model organisms: Revisiting the species-pair concept in lichens. Molecular Phylogenetics and Evolution, 108407. pdf
Maddox, JD, Zahnle, E, McDonnell, K, Grewe, F, Gnoske, TP, Bates, JM, & Hackett, SJ (2025) The complete mitogenomes of all four Cryptospiza species (Aves: Estrildidae). Mitochondrial DNA B Resources 10(1): 77–82. web
Herbst, R, Stille, D, Gwilliam, GF, Konrat, M v., Campbell, T, Gaswick, W, Grewe, F, Hansen, K, Iacobelli, F, Jellema, K, Kawasaki, ML, Kreider, D, Ree, RH, Rodriguez, Y, & Wolpert, A (2025) Unlocking the Past: The Potential of Large Language Models to Revolutionize Transcription of Natural History Collections. Data Intelligence 7(2): 237–264. web
Ametrano, CG, Jensen, J, Lumbsch, HT, & Grewe, F (2025) UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina). Systematic Biology. web
2024
Mercado-Díaz, JA, Grewe, F, Lücking, R, Moncada, B, Rivera-Queralta, Y, Motito-Marín, Á, & Lumbsch, HT (2024) Genome-wide assessment of putative endemism and phylogeography of Cladonia sandstedei (Ascomycota: Cladoniaceae) in the Caribbean. The Lichenologist 56(5): 219–235. pdf
Doellman, MM, Sun, Y, Barcenas-Pena, A, Lumbsch, HT, & Grewe, F (2024) Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae). BMC Genomics 25(1): 1003. web
2023
Barcenas-Pena, A, Divakar, PK, Crespo, A, Nunez-Zapata, J, Lumbsch, HT, & Grewe, F (2023) Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota). Journal of Fungi 9(12): 1180. web
Ter Steege, H, Fortes, EA, Rozendaal, DMA, Erkens, RHJ, Sabatier, D, Aymard, G, Duijm, E, Eurlings, M, Grewe, F, Pombo, MM, Gomes, VF, de Mansano, VF, & de Oliveira, SM (2023) Molecular phylogeny and evolution of inflorescence types in Eperua. American Journal of Botany, e16229. web
Barcenas-Peña, A, Sipman, HJM, Wirth, V, Grewe, F, & Lumbsch, HT (2023) Using morphological, chemical, and molecular data to study the diversity of Xanthoparmelia species from South Africa (Ascomycota, Parmeliaceae). The Lichenologist 55(5): 265–273. pdf
Widhelm, TJ, Rao, A, Grewe, F, & Lumbsch, HT (2023) High-throughput sequencing confirms the boundary between traditionally considered species pairs in a group of lichenized fungi (Peltigeraceae, Pseudocyphellaria). Botanical Journal of the Linnean Society: boac048. web
Otero, A, Barcenas-Pena, A, Lumbsch, HT, & Grewe, F (2023) Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota). Journal of Fungi 9(1): 99. web
2022
Keuler, RJ, Jensen, A, Barcena-Pena, A, Grewe, F, Lumbsch, HT, Huang, JP, & Leavitt, SD (2022) Interpreting Phylogenetic Conflict: Hybridization in the Most Speciose Genus of Lichen-Forming Fungi. Molecular Phylogenetics and Evolution 174: 107543. pdf
Cowles, SA, Witt, CC, Bonaccorso, E, Grewe, F, & Uy, JAC (2022) Early stages of speciation with gene flow in the Amazilia Hummingbird (Amazilis amazilia) subspecies complex of Western South America. Ecology and Evolution 12: e8895. web
Niziolek, LC, Hornbeck, SE, Scott, C, Feinman, GM, Grewe, F, & Wagner, CR (2022) Reconstructing Asia's Ancient Ivory Trade: PCR and NGS Analysis of Elephant Tusk Sections from the Field Museum's Java Sea Shipwreck Collection. Research and Technical Studies Group Postprints 9: 103–109. pdf
Ametrano, CG, Lumbsch, HT, DiStefano, I, Sangvichien, E, Muggia, L, & Grewe, F (2022) Should we hail the Red King: evolutionary consequences of a mutualistic lifestyle in genomes of lichenized fungi. Ecology and Evolution 12: e8471. web
2021
Grewe, F, Kronforst, MR, Pierce, NE, & Moreau, CS (2021) Museum genomics reveals the Xerces blue butterfly (Glaucopsyche xerces) was a distinct species driven to extinction. Biology Letters 17(7): 20210123. cover, web, press: NYT, PBS, ScienceNews, CNN, Gizmodo, Spektrum.de, and others
Jorna, J, Linde, J, Searle, P, Jackson, A, Nielsen, M-E, Nate, M, Saxton, N, Grewe, F, Herrera-Campos, MdlA, Spjut, R, Wu, H, Ho, B, Leavitt, S, & Lumbsch, T (2021) Species boundaries in the messy middle – testing the hypothesis of micro-endemism in a recently diverged lineage of coastal fog desert lichen fungi. Ecology and Evolution 11: 18615–18632. web
Barcenas-Peña, A, Diaz, R, Grewe, F, Widhelm, T, & Lumbsch, HT (2021) Contributions to the phylogeny of Lepraria (Stereocaulaceae) species from the Southern Hemisphere, including three new species. The Bryologist 124: 494–505. web
McKenzie, SK, Winston, ME, Grewe, F, Vargas Asensio, G, Rodríguez-Hernández, N, Rubin, BER, Murillo-Cruz, C, von Beeren, C, Moreau, CS, Suen, G, Pinto-Tomás, AA, & Kronauer, DJC (2021) The genomic basis of army ant chemosensory adaptations. Molecular Ecology 00: 1–15. web
Ametrano, CG, Sun, Y, DiStefano, I, Huhndorf, S, Lumbsch, HT, & Grewe, F (2021) Draft genome sequence of Niebla homalea (Ramalinaceae) in IMA Genome - F15. IMA Fungus 12: 30. web
Patterson, BD, Chaves, HER, Vilela, JF, Soares, AER, & Grewe, F (2021) On the nomenclature of the American clade of weasels (Carnivora: Mustelidae). Journal of Animal Diversity 3: 1–8. web
Widhelm, TJ, Grewe, F, Goffinet, B, Wedin, M, Goward, T, Coca, LF, Distefano, I, Košuthová, A, & Lumbsch, HT (2021) Phylogenomic reconstruction addressing the Peltigeralean backbone (Lecanoromycetes, Ascomycota). Fungal Diversity 110: 59–73. web
Barcenas-Peña, A, Leavitt, SD, Grewe, F, & Lumbsch, HT (2021) Diversity of Xanthoparmelia (Parmeliaceae) species in Mexican xerophytic scrub vegetation, evidenced by molecular, morphological and chemistry data. Anales del Jardín Botánico de Madrid 78(1): e107. pdf
Lagostina, E, Andreev, M, Dal Grande, F, Grewe, F, Lorenz, A, Lumbsch, HT, Rozzi, R, Ruprecht, U, Sancho, LG, Søchting, U, Scur, M, Wirtz, N, & Printzen, C (2021) Effects of dispersal strategy and migration history on genetic diversity and population structure of Antarctic lichens. Journal of Biogeography 48: 1635–1653. web
Alonso-Garcia, M, Grewe, F, Payette, S, & Villarreal, AJ (2021) Population genomics of a reindeer lichen species from North American lichen woodlands. American Journal of Botany 108: 159–171. cover, web
Widhelm, TJ, Grewe, F, Huang, JP, Ramanauskas, K, Mason-Gamer, R, & Lumbsch, HT (2021) Using RADseq to understand the circum-Antarctic distribution of a lichenized fungus, Pseudocyphellaria glabra. Journal of Biogeography 48: 78–90. pdf
2020
Grewe, F, Ametrano, C, Widhelm, TJ, Leavitt, S, Distefano, I, Polyiam, W, Pizarro, D, Wedin, M, Crespo, A, Divakar, PK, & Lumbsch, HT (2020) Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota). IMA Fungus 11: 27. web
Smith, H, Grande, FD, Muggia, L, Keuler, R, Divakar, PK, Grewe, F, Schmitt, I, Lumbsch, HT, & Leavitt, SD (2020) Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis. Symbiosis 82: 133–147. pdf
Bradshaw, M, Grewe, F, Thomas, A, Harrison, CH, Lindgren, H, Muggia, L, St Clair, LL, Lumbsch, HT, & Leavitt, SD (2020) Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi. BMC Evolutionary Biology 20: 2. web
Keuler, R, Garretson, A, Saunders, T, Erickson, RJ, St Andre, N, Grewe, F, Smith, H, Lumbsch, HT, Huang, JP, St Clair, LL, & Leavitt, SD (2020) Genome-scale data reveal the role of hybridization in lichen-forming fungi. Scientific Reports 10: 1497. web
Pizarro, D, Divakar, PK, Grewe, F, Crespo, A, Dal Grande, F, & Lumbsch, HT (2020) Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi. Genome Biology and Evolution 12: 1858–1868. web
Grewe, F, Distefano, I, Huhndorf, S, Sun, Y, Ametrano, C, Divakar, PK, & Lumbsch, HT (2020) Draft genome sequence of Physcia stellaris (Physciaceae) in IMA Genome - F13. IMA Fungus 11: 19. web
2019
Ametrano, CG, Grewe, F, Crous, PW, Goodwin, SB, Liang, C, Selbmann, L, Lumbsch, HT, Leavitt, SD, & Muggia, L (2019) Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 10: 19. web
Mower, JP, Ma, PF, Grewe, F, Taylor, A, Michael, TP, VanBuren, R, & Qiu, YL (2019) Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat. New Phytologist 222: 1061–1075. web
Voight, JR, Marshall, BA, Judge, J, Halanych, KM, Li, Y, Bernardino, AF, Grewe, F, & Maddox, JD (2019) Life in wood: preliminary phylogeny of deep-sea wood-boring bivalves (Xylophagaidae), with descriptions of three new genera and one new species. Journal of Molluscan Studies 85: 232–243. pdf
Widhelm, TJ, Grewe, F, Huang, JP, Mercado-Diaz, JA, Goffinet, B, Lucking, R, Moncada, B, Mason-Gamer, R, & Lumbsch, HT (2019) Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Scientific Reports 9: 8968. web
2018
Barcenas-Pena, A, Leavitt, SD, Huang, JP, Grewe, F, & Lumbsch, HT (2018) Phylogenetic study and taxonomic revision of the Xanthoparmelia mexicana group, including the description of a new species (Parmeliaceae, Ascomycota). MycoKeys: 13–28. web
Grewe, F, Lagostina, E, Wu, H, Printzen, C, & Lumbsch, HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys: 91–113. web
Leavitt, SD, Kirika, PM, Amo De Paz, G, Huang, J-P, Hur, J-S, Elix, JA, Grewe, F, Divakar, PK, & Lumbsch, HT (2018) Assessing phylogeny and historical biogeography of the largest genus of lichen-forming fungi, Xanthoparmelia (Parmeliaceae, Ascomycota). The Lichenologist 50: 299–312. pdf
Pizarro, D, Divakar, PK, Grewe, F, Leavitt, SD, Huang, J-P, Dal Grande, F, Schmitt, I, Wedin, M, Crespo, A, & Lumbsch, HT (2018) Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi. Fungal Diversity 92: 31–41. pdf
2017
Grewe, F, Huang, JP, Leavitt, SD, & Lumbsch, HT (2017) Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNA. Scientific Reports 7: 9884. web
2016
Grewe, F, Zhu, A, & Mower, JP (2016) Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium. Genome Biology and Evolution 8: 3193–3201. web
Guo, W, Grewe, F, Fan, W, Young, GJ, Knoop, V, Palmer, JD, & Mower, JP (2016) Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution. Molecular Biology and Evolution 33: 1448–1460. web
Knie, N, Grewe, F, Fischer, S, & Knoop, V (2016) Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles. BMC Evolutionary Biology 16: 134. pdf
Knie, N, Grewe, F, & Knoop, V (2016) Monilophyte mitochondrial rps1 genes carry a unique group II intron that likely originated from an ancient paralog in rpl2. RNA 22: 1338–1348. pdf
Leavitt, SD*, Grewe, F*, Widhelm, T, Muggia, L, Wray, B, & Lumbsch, HT (2016) Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches. Scientific Reports 6: 22262. *Co-first authorship. pdf
Lutz, HL, Marra, NJ, Grewe, F, Carlson, JS, Palinauskas, V, Valkiunas, G, & Stanhope, MJ (2016) Laser capture microdissection microscopy and genome sequencing of the avian malaria parasite, Plasmodium relictum. Parasitology Research 115: 4503–4510. pdf
Sultan, LD, Mileshina, D, Grewe, F, Rolle, K, Abudraham, S, Glodowicz, P, Niazi, AK, Keren, I, Shevtsov, S, Klipcan, L, Barciszewski, J, Mower, JP, Dietrich, A, & Ostersetzer-Biran, O (2016) The Reverse Transcriptase/RNA Maturase Protein MatR Is Required for the Splicing of Various Group II Introns in Brassicaceae Mitochondria. Plant Cell 28: 2805–2829. pdf
2015
Guo, W, Grewe, F, & Mower, JP (2015) Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants. PloS One 10: e0117075. pdf
Knie, N, Fischer, S, Grewe, F, Polsakiewicz, M, & Knoop, V (2015) Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns. Molecular Phylogenetics and Evolution 90: 140–149. pdf
Park, S, Grewe, F, Zhu, A, Ruhlman, TA, Sabir, J, Mower, JP, & Jansen, RK (2015) Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. New Phytologist 208: 570–583. pdf
2014
Grewe, F, Edger, PP, Keren, I, Sultan, L, Pires, JC, Ostersetzer-Biran, O, & Mower, JP (2014) Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Mitochondrion 19 Pt B: 135–143. pdf
Guo, W, Grewe, F, Cobo-Clark, A, Fan, W, Duan, Z, Adams, RP, Schwarzbach, AE, & Mower, JP (2014) Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during cupressophyte evolution. Genome Biology and Evolution 6: 580–590. pdf
Jain, K, Krause, K, Grewe, F, Nelson, GF, Weber, AP, Christensen, AC, & Mower, JP (2014) Extreme features of the Galdieria sulphuraria organellar genomes: a consequence of polyextremophily? Genome Biology and Evolution 7: 367–380. pdf
2013
Grewe, F, Guo, W, Gubbels, EA, Hansen, AK, & Mower, JP (2013) Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes. BMC Evolutionary Biology 13: 8. pdf
2011
Grewe, F, Herres, S, Viehover, P, Polsakiewicz, M, Weisshaar, B, & Knoop, V (2011) A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Research 39: 2890–2902. pdf
Hecht, J*, Grewe, F*, & Knoop, V (2011) Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biology and Evolution 3: 344–358. *Co-first authorship. pdf
Knoop, V, Volkmar, U, Hecht, J, & Grewe, F (2011) Mitochondrial Genome Evolution in the Plant Lineage. In: Plant Mitochondria, pp. 3–29. pdf
2010
Lenz, H, Rudinger, M, Volkmar, U, Fischer, S, Herres, S, Grewe, F, & Knoop, V (2010) Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature. Current Genetics 56: 189–201. pdf
2009
Grewe, F, Viehoever, P, Weisshaar, B, & Knoop, V (2009) A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Research 37: 5093–5104. pdf
2005
Groth-Malonek, M, Pruchner, D, Grewe, F, & Knoop, V (2005) Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants. Molecular Biology and Evolution 22: 117–125. pdf