A. Jonathan Shaw

Professor of Biology

Box 90338, 137 Bio Sciences, 130 Science Drive, Durham, NC 27708
Campus Box: 
Box 90338, Durham, NC 27708-0338
(919) 660-7344
My research centers on the evolution and diversity of bryophytes. Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the arthrodontous mosses, studies of hybridization using molecular and morphological markers, and investigations of cryptic speciation within geographically widespread species. My own particular focus (as opposed to those of post-docs and graduate students in the lab) at present is the genus Sphagnum (peatmosses). Ongoing research is grounded in phylogenetic analyses at various levels of biological organization from populations up to genus-wide. We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. I have a special interest in the genetic structure of both rare and widespread species. Morphological and molecular information is being used to explore geographic patterns in phylogenetic diversity within the peatmosses. Of particular interest are biogeographic relationships between boreal, tropical, and Southern Hemisphere taxa, and between New and Old World taxa. Our data base presently includes nucleotide sequences from multiple loci representing some 500-600 accessions of peatmosses. Additional information about this ongoing work can be found here. The bryology laboratory is engaged in ongoing collaborative research projects with the New York Botanical Garden, the University of Connecticut, the Missouri Botanical Garden, and the University of Alberta. Additional information about these projects can be found here. I serve as Curator of the Bryophyte Herbarium, which includes approximately 230,000 collections of mosses, liverworts, and hornworts. The collections represent a central resource for bryological research at Duke, and we are actively integrating molecular investigations with field work and collections- based approaches.


  • Ph.D., University of Michigan at Ann Arbor 1983

  • M.S., University of Alberta (Canada) 1980

  • B.S., Cornell University 1977

Goffinet, B, and Shaw, AJ. Bryophyte biology, second edition. January 1, 2008. Full Text

Shaw, AJ, Schmutz, J, Devos, N, Shu, S, Carrell, AA, and Weston, DJ. "The Sphagnum Genome Project. A New Model for Ecological and Evolutionary Genomics.", 167-187. January 1, 2016. Full Text

Goffinet, B, Buck, WR, and Shaw, AJ. "Morphology, anatomy, and classification of the bryophyta." In Bryophyte Biology, Second Edition, 55-138. January 1, 2008. Full Text

Shaw, AJ. "Bryophyte species and speciation." In Bryophyte Biology, Second Edition, 445-486. January 1, 2008. Full Text

Shaw, AJ, Carter, BE, Aguero, B, da Costa, DP, and Crowl, AA. "Range change evolution of peat mosses (Sphagnum) within and between climate zones." Global Change Biology 25, no. 1 (January 2019): 108-120. Full Text

Laenen, B, Patiño, J, Hagborg, A, Désamoré, A, Wang, J, Shaw, AJ, Goffinet, B, and Vanderpoorten, A. "Evolutionary origin of the latitudinal diversity gradient in liverworts." Molecular Phylogenetics and Evolution 127 (October 2018): 606-612. Full Text

Nelson, JM, Hauser, DA, Hinson, R, and Shaw, AJ. "A novel experimental system using the liverwort Marchantia polymorpha and its fungal endophytes reveals diverse and context-dependent effects." The New Phytologist 218, no. 3 (May 2018): 1217-1232. Full Text

Weston, DJ, Turetsky, MR, Johnson, MG, Granath, G, Lindo, Z, Belyea, LR, Rice, SK, Hanson, DT, Engelhardt, KAM, Schmutz, J, Dorrepaal, E, Euskirchen, ES, Stenøien, HK, Szövényi, P, Jackson, M, Piatkowski, BT, Muchero, W, Norby, RJ, Kostka, JE, Glass, JB, Rydin, H, Limpens, J, Tuittila, E-S, Ullrich, KK, Carrell, A, Benscoter, BW, Chen, J-G, Oke, TA, Nilsson, MB, Ranjan, P, Jacobson, D, Lilleskov, EA, Clymo, RS, and Shaw, AJ. "The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project." The New Phytologist 217, no. 1 (January 2018): 16-25. Full Text

Yousefi, N, Hassel, K, Flatberg, KI, Kemppainen, P, Trucchi, E, Shaw, AJ, Kyrkjeeide, MO, Szövényi, P, and Stenøien, HK. "Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum." American Journal of Botany (July 28, 2017). Full Text

Carter, BE, Larraín, J, Manukjanová, A, Shaw, B, Shaw, AJ, Heinrichs, J, de Lange, P, Suleiman, M, Thouvenot, L, and von Konrat, M. "Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta)." Molecular Phylogenetics and Evolution 107 (February 2017): 16-26. Full Text

Patiño, J, Wang, J, Renner, MAM, Gradstein, SR, Laenen, B, Devos, N, Shaw, AJ, and Vanderpoorten, A. "Range size heritability and diversification patterns in the liverwort genus Radula." Molecular phylogenetics and evolution 106 (January 2017): 73-85. Full Text

Boquete, MT, Fernández, JA, Aboal, JR, and Shaw, AJ. "Significance of the intraspecific morphological variability in biomonitoring studies with mosses: Among-populations and between-sexes approach." Environmental and Experimental Botany 130 (October 1, 2016): 106-112. Full Text

Jonathan Shaw, A, Devos, N, Liu, Y, Cox, CJ, Goffinet, B, Flatberg, KI, and Shaw, B. "Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)." Annals of Botany 118, no. 2 (August 2016): 185-196. Full Text

Johnson, MG, Gardner, EM, Liu, Y, Medina, R, Goffinet, B, Shaw, AJ, Zerega, NJC, and Wickett, NJ. "HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment." Applications in Plant Sciences 4, no. 7 (July 12, 2016). Full Text


Shaw, AJ, Cox, CJ, and Melosik, I. "Diversification of peatmosses: A phylogenetic approach." Symposium on Molecular Systematics of Bryophytes. Missouri Bot Garden, St Louis, MO. September 2003.: MISSOURI BOTANICAL GARDEN, January 1, 2004.


Selected Grants

Collaborative Research:AToL: Assembling the Pleurocarp Tree of Life: Resolving the Rapid Radiation Using Genomics and awarded by National Science Foundation (Principal Investigator). 2013 to 2017

ARTS: Collaborative Research: A Model Systematic Treatment of a Hyper-Diverse Line awarded by National Science Foundation (Co-Principal Investigator). 2012 to 2017

Applying methods for the study of plant microbe interactions awarded by Oak Ridge National Laboratory (Principal Investigator). 2015 to 2016

Digitization TCN: Collaborative Research: North American Lichens and Bryophytes awarded by National Science Foundation (Co-Principal Investigator). 2011 to 2016

REVSYS: Systematics and evolution of the "Pacific Rim Clade" awarded by National Science Foundation (Principal Investigator). 2006 to 2014

PEET: Systematics of the Daltoniaceae (Bryophyta) awarded by National Science Foundation (Principal Investigator). 2005 to 2012

ATOL: Collaborative Research - Assembling the liverwort tree of life awarded by National Science Foundation (Principal Investigator). 2006 to 2011

DISSERTATION RESEARCH: Speciation and hybridization in the moss genus Sphagnum awarded by National Science Foundation (Principal Investigator). 2007 to 2010